plasmid02 · March 20, 2018 13:58
diff --git a/2018-03-20-Staph_genomes.bib b/2018-03-20-Staph_genomes.bib
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 @ARTICLE{Uhlemann2014-jn,
  title    = "Molecular tracing of the emergence, diversification, and
              transmission of S. aureus sequence type 8 in a New York community",
  author   = "Uhlemann, Anne-Catrin and Dordel, Janina and Knox, Justin R and
              Raven, Kathy E and Parkhill, Julian and Holden, Matthew T G and
              Peacock, Sharon J and Lowy, Franklin D",
  abstract = "During the last 2 decades, community-associated
              methicillin-resistant Staphylococcus aureus (CA-MRSA) strains
              have dramatically increased the global burden of S. aureus
              infections. The pandemic sequence type (ST)8/pulsed-field gel
              type USA300 is the dominant CA-MRSA clone in the United States,
              but its evolutionary history and basis for biological success are
              incompletely understood. Here, we use whole-genome sequencing of
              387 ST8 isolates drawn from an epidemiological network of CA-MRSA
              infections and colonizations in northern Manhattan to explore
              short-term evolution and transmission patterns. Phylogenetic
              analysis predicted that USA300 diverged from a most common recent
              ancestor around 1993. We found evidence for multiple
              introductions of USA300 and reconstructed the phylogeographic
              spread of isolates across neighborhoods. Using pair-wise
              single-nucleotide polymorphism distances as a measure of genetic
              relatedness between isolates, we observed that most USA300
              isolates had become endemic in households, indicating their
              critical role as reservoirs for transmission and diversification.
              Using the maximum single-nucleotide polymorphism variability of
              isolates from within households as a threshold, we identified
              several possible transmission networks beyond households. Our
              study also revealed the evolution of a fluoroquinolone-resistant
              subpopulation in the mid-1990s and its subsequent expansion at a
              time of high-frequency outpatient antibiotic use. This
              high-resolution phylogenetic analysis of ST8 has documented the
              genomic changes associated with USA300 evolution and how some of
              its recent evolution has been shaped by antibiotic use. By
              integrating whole-genome sequencing with detailed epidemiological
              analyses, our study provides an important framework for
              delineating the full diversity and spread of USA300 and other
              emerging pathogens in large urban community populations.",
  journal  = "Proc. Natl. Acad. Sci. U. S. A.",
  month    =  apr,
  year     =  2014,
  keywords = "Staphylococcus;evolution;colonization;Staph\_evolutionary\_history;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Boyle-Vavra2015-pc,
  title     = "{USA300} and {USA500} Clonal Lineages of Staphylococcus aureus
               Do Not Produce a Capsular Polysaccharide Due to Conserved
               Mutations in the cap5 Locus",
  author    = "Boyle-Vavra, Susan and Li, Xue and Alam, Md Tauqeer and Read,
               Timothy D and Sieth, Julia and Cywes-Bentley, Colette and
               Dobbins, Ginette and David, Michael Z and Kumar, Neha and Eells,
               Samantha J and Miller, Loren G and Boxrud, David J and Chambers,
               Henry F and Lynfield, Ruth and Lee, Jean C and Daum, Robert S",
  abstract  = "UNLABELLED: The surface capsular polysaccharide (CP) is a
               virulence factor that has been used as an antigen in several
               successful vaccines against bacterial pathogens. A vaccine has
               not yet been licensed against Staphylococcus aureus, although
               two multicomponent vaccines that contain CP antigens are in
               clinical trials. In this study, we evaluated CP production in
               USA300 methicillin-resistant S. aureus (MRSA) isolates that have
               become the predominant community-associated MRSA clones in the
               United States. We found that all 167 USA300 MRSA and 50 USA300
               methicillin-susceptible S. aureus (MSSA) isolates were CP
               negative (CP(-)). Moreover, all 16 USA500 isolates, which have
               been postulated to be the progenitor lineage of USA300, were
               also CP(-). Whole-genome sequence analysis of 146 CP(-) USA300
               MRSA isolates revealed they all carry a cap5 locus with 4
               conserved mutations compared with strain Newman. Genetic
               complementation experiments revealed that three of these
               mutations (in the cap5 promoter, cap5D nucleotide 994, and cap5E
               nucleotide 223) ablated CP production in USA300 and that Cap5E75
               Asp, located in the coenzyme-binding domain, is essential for
               capsule production. All but three USA300 MSSA isolates had the
               same four cap5 mutations found in USA300 MRSA isolates. Most
               isolates with a USA500 pulsotype carried three of these four
               USA300-specific mutations, suggesting the fourth mutation
               occurred in the USA300 lineage. Phylogenetic analysis of the cap
               loci of our USA300 isolates as well as publicly available
               genomes from 41 other sequence types revealed that the
               USA300-specific cap5 mutations arose sequentially in S. aureus
               in a common ancestor of USA300 and USA500 isolates. IMPORTANCE:
               The USA300 MRSA clone emerged as a community-associated pathogen
               in the United States nearly 20 years ago. Since then, it has
               rapidly disseminated and now causes health care-associated
               infections. This study shows that the CP-negative (CP(-))
               phenotype has persisted among USA300 isolates and is a universal
               and characteristic trait of this highly successful MRSA lineage.
               It is important to note that a vaccine consisting solely of CP
               antigens would not likely demonstrate high efficacy in the U.S.
               population, where about half of MRSA isolates comprise USA300.
               Moreover, conversion of a USA300 strain to a CP-positive (CP(+))
               phenotype is unlikely in vivo or in vitro since it would require
               the reversion of 3 mutations. We have also established that
               USA300 MSSA isolates and USA500 isolates are CP(-) and provide
               new insight into the evolution of the USA300 and USA500
               lineages.",
  journal   = "MBio",
  publisher = "American Society for Microbiology",
  volume    =  6,
  number    =  2,
  pages     = "e02585--14",
  month     =  apr,
  year      =  2015,
  keywords  = "Staphylococcus;My
               Publications;My\_Peer\_reviewed;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers"
 }

 @ARTICLE{Alam2015-oc,
  title     = "Transmission and Microevolution of {USA300} {MRSA} in {U.S}.
               Households: Evidence from {Whole-Genome} Sequencing",
  author    = "Alam, Md Tauqeer and Read, Timothy D and Petit, Robert A and
               Boyle-Vavra, Susan and Miller, Loren G and Eells, Samantha J and
               Daum, Robert S and David, Michael Z",
  abstract  = "UNLABELLED: Methicillin-resistant Staphylococcus aureus (MRSA)
               USA300 is a successful S. aureus clone in the United States and
               a common cause of skin and soft tissue infections (SSTIs). We
               performed whole-genome sequencing (WGS) of 146 USA300 MRSA
               isolates from SSTIs and colonization cultures obtained from an
               investigation conducted from 2008 to 2010 in Chicago and Los
               Angeles households that included an index case with an S. aureus
               SSTI. Identifying unique single nucleotide polymorphisms (SNPs)
               and analyzing whole-genome phylogeny, we characterized isolates
               to understand transmission dynamics, genetic relatedness, and
               microevolution of USA300 MRSA within the households. We also
               compared the 146 USA300 MRSA isolates from our study with the
               previously published genome sequences of the USA300 MRSA
               isolates from San Diego (n = 35) and New York City (n = 277). We
               found little genetic variation within the USA300 MRSA household
               isolates from Los Angeles (mean number of SNPs $\pm$ standard
               deviation, 17.6 $\pm$ 35; $\pi$ nucleotide diversity, 3.1
               $\times$ 10(-5)) or from Chicago (mean number of SNPs $\pm$
               standard deviation, 12 $\pm$ 19; $\pi$ nucleotide diversity, 3.1
               $\times$ 10(-5)). The isolates within a household clustered into
               closely related monophyletic groups, suggesting the introduction
               into and transmission within each household of a single common
               USA300 ancestral strain. From a Bayesian evolutionary
               reconstruction, we inferred that USA300 persisted within
               households for 2.33 to 8.35 years prior to sampling. We also
               noted that fluoroquinolone-resistant USA300 clones emerged
               around 1995 and were more widespread in Los Angeles and New York
               City than in Chicago. Our findings strongly suggest that unique
               USA300 MRSA isolates are transmitted within households that
               contain an individual with an SSTI. Decolonization of household
               members may be a critical component of prevention programs to
               control USA300 MRSA spread in the United States. IMPORTANCE:
               USA300, a virulent and easily transmissible strain of
               methicillin-resistant Staphylococcus aureus (MRSA), is the
               predominant community-associated MRSA clone in the United
               States. It most commonly causes skin infections but also causes
               necrotizing pneumonia and endocarditis. Strategies to limit the
               spread of MRSA in the community can only be effective if we
               understand the most common sources of transmission and the
               microevolutionary processes that provide a fitness advantage to
               MRSA. We performed a whole-genome sequence comparison of 146
               USA300 MRSA isolates from Chicago and Los Angeles. We show that
               households represent a frequent site of transmission and a
               long-term reservoir of USA300 strains; individuals within
               households transmit the same USA300 strain among themselves. Our
               study also reveals that a large proportion of the USA300
               isolates sequenced are resistant to fluoroquinolone antibiotics.
               The significance of this study is that if households serve as
               long-term reservoirs of USA300, household MRSA eradication
               programs may result in a uniquely effective control method.",
  journal   = "MBio",
  publisher = "American Society for Microbiology",
  volume    =  6,
  number    =  2,
  pages     = "e00054--15",
  month     =  mar,
  year      =  2015,
  keywords  = "Staphylococcus;My Publications;bacterial comparative
               genomics;antibiotcs-evolution-fitness;My\_Peer\_reviewed;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Glaser2016-qq,
  title    = "Demography and Intercontinental Spread of the {USA300}
              {Community-Acquired} {Methicillin-Resistant} Staphylococcus
              aureus Lineage",
  author   = "Glaser, Philippe and Martins-Sim{\~o}es, Patr{\'\i}cia and
              Villain, Adrien and Barbier, Maxime and Tristan, Anne and
              Bouchier, Christiane and Ma, Laurence and Bes, Michele and
              Laurent, Frederic and Guillemot, Didier and Wirth, Thierry and
              Vandenesch, Fran{\c c}ois",
  abstract = "Community-acquired methicillin-resistant Staphylococcus aureus
              (CA-MRSA) was recognized worldwide during the 1990s; in less than
              a decade, several genetically distinct CA-MRSA lineages carrying
              Panton-Valentine leukocidin genes have emerged on every
              continent. Most notably, in the United States, the sequence type
              18-IV (ST8-IV) clone known as USA300 has become highly prevalent,
              outcompeting methicillin-susceptible S. aureus (MSSA) and other
              MRSA strains in both community and hospital settings. CA-MRSA
              bacteria are much less prevalent in Europe, where the European
              ST80-IV European CA-MRSA clone, USA300 CA-MRSA strains, and other
              lineages, such as ST22-IV, coexist. The question that arises is
              whether the USA300 CA-MRSA present in Europe (i) was imported
              once or on very few occasions, followed by a broad geographic
              spread, anticipating an increased prevalence in the future, or
              (ii) derived from multiple importations with limited spreading
              success. In the present study, we applied whole-genome sequencing
              to a collection of French USA300 CA-MRSA strains responsible for
              sporadic cases and micro-outbreaks over the past decade and
              United States ST8 MSSA and MRSA isolates. Genome-wide
              phylogenetic analysis demonstrated that the population structure
              of the French isolates is the product of multiple introductions
              dating back to the onset of the USA300 CA-MRSA clone in North
              America. Coalescent-based demography of the USA300 lineage shows
              that a strong expansion occurred during the 1990s concomitant
              with the acquisition of the arginine catabolic mobile element and
              antibiotic resistance, followed by a sharp decline initiated
              around 2008, reminiscent of the rise-and-fall pattern previously
              observed in the ST80 lineage. A future expansion of the USA300
              lineage in Europe is therefore very unlikely.IMPORTANCE To trace
              the origin, evolution, and dissemination pattern of the USA300
              CA-MRSA clone in France, we sequenced a collection of strains of
              this lineage from cases reported in France in the last decade and
              compared them with 431 ST8 strains from the United States. We
              determined that the French CA-MRSA USA300 sporadic and
              micro-outbreak isolates resulted from multiple independent
              introductions of the USA300 North American lineage. At a global
              level, in the transition from an MSSA lineage to a successful
              CA-MRSA clone, it first became resistant to multiple antibiotics
              and acquired the arginine catabolic mobile element and
              subsequently acquired resistance to fluoroquinolones, and these
              two steps were associated with a dramatic demographic expansion.
              This expansion was followed by the current stabilization and
              expected decline of this lineage. These findings highlight the
              significance of horizontal gene acquisitions and point mutations
              in the success of such disseminated clones and illustrate their
              cyclic and sporadic life cycle.",
  journal  = "MBio",
  volume   =  7,
  number   =  1,
  month    =  mar,
  year     =  2016,
  keywords = "
              Staphylococcus;evolution;demography;Staph\_evolutionary\_history;bacterial
              comparative
              genomics;Staph\_evolutionary\_history/USA300\_evolution;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Read-lab-shared;Papers\_for\_Michelle;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers"
 }

 @ARTICLE{Toleman2016-qd,
  title    = "Systematic surveillance detects multiple silent introductions and
              household transmission of methicillin-resistant Staphylococcus
              aureus {USA300} in the east of England",
  author   = "Toleman, Michelle S and Reuter, Sandra and Coll, Francesc and
              Harrison, Ewan M and Blane, Beth and Brown, Nicholas M and
              T{\"o}r{\"o}k, M Est{\'e}e and Parkhill, Julian and Peacock,
              Sharon J",
  abstract = "Background. The spread of USA300 methicillin-resistant
              Staphylococcus aureus (MRSA) across the United States (US)
              resulted in an epidemic of infections. In Europe, only sporadic
              cases or small clusters of USA300 infections are described and
              its prevalence in England is unknown. We conducted prospective
              surveillance for USA300 in the east of England.Methods. We
              undertook a 12-month prospective observational cohort study of
              all individuals with MRSA isolated from community and hospital
              samples submitted to a microbiology laboratory. At least one MRSA
              isolate from each individual was whole-genome sequenced. USA300
              was identified based on sequence analysis, and phylogenetic
              comparisons were made between these and USA300 genomes from the
              US.Results. Between April 2012-April 2013, we sequenced 2,283
              MRSA isolates (carriage screens and clinical samples) from 1,465
              individuals. USA300 was isolated from 24 (1.6\%) cases. Ten cases
              (42\%) had skin and soft tissue infection and two cases had
              invasive disease. Phylogenetic analyses identified multiple
              introductions and household transmission of USA300.Conclusions.
              Use of a diagnostic laboratory as a sentinel for surveillance has
              identified repeated introductions of USA300 into the east of
              England in 2012-2013, with evidence for limited transmission. Our
              results show how systematic surveillance could provide an
              early-warning of strain emergence and dissemination.",
  journal  = "J. Infect. Dis.",
  month    =  apr,
  year     =  2016,
  keywords = "Staphylococcus;bacterial comparative
              genomics;Staph\_evolutionary\_history;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Ge2017-du,
  title    = "{MRSA} and multidrug-resistant Staphylococcus aureus in {U.S}.
              retail meats, 2010-2011",
  author   = "Ge, Beilei and Mukherjee, Sampa and Hsu, Chih-Hao and Davis,
              Johnnie A and Tran, Thu Thuy T and Yang, Qianru and Abbott, Jason
              W and Ayers, Sherry L and Young, Shenia R and Crarey, Emily T and
              Womack, Niketta A and Zhao, Shaohua and McDermott, Patrick F",
  abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) has been
              detected in retail meats, although large-scale studies are
              scarce. We conducted a one-year survey in 2010-2011 within the
              framework of the National Antimicrobial Resistance Monitoring
              System. Among 3520 retail meats collected from eight U.S. states,
              982 (27.9\%) contained S. aureus and 66 (1.9\%) were positive for
              MRSA. Approximately 10.4\% (107/1032) of S. aureus isolates,
              including 37.2\% (29/78) of MRSA, were multidrug-resistant
              (MDRSA). Turkey had the highest MRSA prevalence (3.5\%), followed
              by pork (1.9\%), beef (1.7\%), and chicken (0.3\%). Whole-genome
              sequencing was performed for all 66 non-redundant MRSA. Among
              five multilocus sequence types identified, ST8 (72.7\%) and ST5
              (22.7\%) were most common and livestock-associated MRSA ST398 was
              assigned to one pork isolate. Eleven spa types were represented,
              predominately t008 (43.9\%) and t2031 (22.7\%). All four types of
              meats harbored t008, whereas t2031 was recovered from turkey
              only. The majority of MRSA (84.8\%) possessed SCCmec IV and
              62.1\% harbored Panton-Valentine leukocidin. Pulsed-field gel
              electrophoresis showed that all ST8 MRSA belonged to the
              predominant human epidemic clone USA300, and others included
              USA100 and USA200. We conclude that a diverse MRSA population was
              present in U.S. retail meats, albeit at low prevalence.",
  journal  = "Food Microbiol.",
  volume   =  62,
  pages    = "289--297",
  month    =  apr,
  year     =  2017,
  keywords = "LA-MRSA; MDRSA; MRSA; Retail meat; ST398;
              USA300;Staphylococcus;colonization;Staph\_evolutionary\_history;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Popovich2017-mo,
  title    = "Genomic and Epidemiological Evidence for Community Origins of
              {Hospital-Onset} {Methicillin-Resistant} Staphylococcus aureus
              Bloodstream Infections",
  author   = "Popovich, Kyle J and Snitkin, Evan S and Hota, Bala and Green,
              Stefan J and Pirani, Ali and Aroutcheva, Alla and Weinstein,
              Robert A",
  abstract = "Background.: We examined whether disparities existed in
              hospital-onset (HO) Staphylococcus aureus bloodstream infections
              (BSIs) and used whole-genome sequencing (WGS) to identify factors
              associated with USA300 transmission networks. Methods.: We
              evaluated HO methicillin-susceptible S. aureus (MSSA) and HO
              methicillin-resistant S. aureus (MRSA) BSIs for 2009-2013 at 2
              hospitals and used an adjusted incidence for modeling. WGS and
              phylogenetic analyses were performed on a sample of USA300 BSI
              isolates. Epidemiologic data were analyzed in the context of
              phylogenetic reconstructions. Results.: On multivariate analysis,
              male sex, African-American race, and non-Hispanic white
              race/ethnicity were significantly associated with HO-MRSA BSIs
              whereas Hispanic ethnicity was negatively associated (rate ratio,
              0.41; P = .002). Intermixing of community-onset and HO-USA300
              strains on the phylogenetic tree indicates that these strains
              derive from a common pool. African-American race was the only
              factor associated with genomic clustering of isolates.
              Conclusions.: In a multicenter assessment of HO-S. aureus BSIs,
              African-American race was significantly associated with HO-MRSA
              but not MSSA BSIs. There appears to be a nexus of USA300
              community and hospital transmission networks, with a community
              factor being the primary driver. Our data suggest that HO-USA300
              BSIs likely are due to colonizing strains acquired in the
              community before hospitalization. Therefore, prevention efforts
              may need to extend to the community for maximal benefit.",
  journal  = "J. Infect. Dis.",
  month    =  may,
  year     =  2017,
  keywords = "MRSA; Whole genome sequencing; bacteremia.;
              disparities;Staphylococcus;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Planet2016-jd,
  title       = "Global Spread of the {Community-Associated}
                 {Methicillin-Resistant} Staphylococcus aureus {USA300} Latin
                 American Variant",
  author      = "Planet, Paul J and Diaz, Lorena and Rios, Rafael and Arias,
                 Cesar A",
  journal     = "J. Infect. Dis.",
  volume      =  214,
  number      =  10,
  pages       = "1609--1610",
  month       =  nov,
  year        =  2016,
  keywords    = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN",
  language    = "en",
  original_id = "379c0306-8718-0c37-9696-1b028a15d914"
 }

 @ARTICLE{Popovich2016-nk,
  title    = "Genomic Epidemiology of {USA300} {Methicillin-Resistant}
              Staphylococcus aureus in an Urban Community",
  author   = "Popovich, Kyle J and Snitkin, Evan and Green, Stefan J and
              Aroutcheva, Alla and Hayden, Mary K and Hota, Bala and Weinstein,
              Robert A",
  abstract = "BACKGROUND: In a community, it is unknown what factors account
              for transmission of methicillin-resistant Staphylococcus aureus
              (MRSA). We integrated whole genome sequencing (WGS) and
              epidemiologic data to identify factors associated with MRSA
              transmission networks in an urban community. METHODS: WGS was
              performed on colonizing USA300 MRSA isolates from 74 individuals
              within 72 hours of admission to a public hospital in Chicago, IL.
              Single nucleotide variants (SNVs) were used to reconstruct the
              phylogeny of sequenced isolates, and epidemiologic data was
              overlaid to identify factors associated with transmission
              networks. RESULTS: The maximum within-patient SNV difference for
              an individual with multisite colonization was 41 SNVs, with no
              systematic divergence among body sites. We observed a minimum of
              7 SNVs and maximum of 153 SNVs between isolates from different
              individuals. We identified 4 pairs of individuals whose isolates
              were within 40 SNVs of each other. Putting our isolates in the
              context of previously sequenced USA300 isolates from other
              communities, we identified a 13-member group and two 4-member
              groups that represent samples from putative local transmission
              networks. Individuals in these groups were more likely to be
              African American, to be human immunodeficiency virus-infected, to
              reside in high detainee release areas, and to be current users of
              illicit drugs. CONCLUSIONS: Using WGS, we observed potential
              transmission networks in an urban community and that certain
              epidemiologic factors were associated with inclusion in these
              networks. Future work with contact tracing and advanced molecular
              diagnostics may allow for identification of MRSA ``epicenters''
              in the community where interventions can be targeted.",
  journal  = "Clin. Infect. Dis.",
  volume   =  62,
  number   =  1,
  pages    = "37--44",
  month    =  jan,
  year     =  2016,
  keywords = "MRSA; whole genome
              sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Connolly2017-su,
  title    = "The identification of Staphylococcus aureus factors required for
              pathogenicity and growth in human blood",
  author   = "Connolly, John and Boldock, Emma and Prince, Lynne R and Renshaw,
              Stephen A and Whyte, Moira K and Foster, Simon J",
  abstract = "Staphylococcus aureus is a human commensal but also has
              devastating potential as an opportunist pathogen. S. aureus
              bacteraemia is often associated with an adverse outcome. To
              identify potential targets for novel control approaches we have
              identified S. aureus components that are required for growth on
              human blood. An ordered transposon mutant library was screened,
              identifying 9 genes involved specifically in haemolysis or growth
              on human blood agar compared to the parental strain. Three genes
              (purA, purB and pabA) were subsequently found to be required for
              pathogenesis in the zebrafish embryo infection model. The pabA
              growth defect was specific to the red blood cell component of
              human blood, showing no growth difference compared to the
              parental strain on human serum, human plasma, sheep or horse
              blood. PabA is required in the tetrahydrofolate (THF)
              biosynthesis pathway. The pabA growth defect was found to be due
              to a combination of loss of THF-dependent dTMP production by the
              enzyme ThyA and an increased demand for pyrimidines in human
              blood. Our work highlights pabA and the pyrimidine salvage
              pathway as potential targets for novel therapeutics and suggests
              a previously undefined role for a human blood factor in the
              activity of sulphonamide antibiotics.",
  journal  = "Infect. Immun.",
  month    =  aug,
  year     =  2017,
  keywords = "Staphylococcus;bacerial\_genetics;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Read-lab-shared",
  language = "en"
 }

 @ARTICLE{Von_Dach2016-wg,
  title    = "Comparative Genomics of {Community-Associated}
              {Methicillin-Resistant} Staphylococcus aureus Shows the Emergence
              of Clone {ST8-USA300} in Geneva, Switzerland",
  author   = "Von Dach, Elodie and Diene, Seydina M and Fankhauser, Carolina
              and Schrenzel, Jacques and Harbarth, Stephan and Fran{\c c}ois,
              Patrice",
  abstract = "BACKGROUND: Previous investigations of community-associated
              methicillin-resistant Staphylococcus aureus(CA-MRSA) isolates
              have revealed a wide diversity of genetic backgrounds, with only
              sporadic occurrence of ST8-USA300, in Geneva, Switzerland. We
              conducted a molecular epidemiologic analysis to identify the
              origin of a sudden increase of ST8 PVL-positive isolates in
              Geneva during 2013. METHODS: On the basis of prospective CA-MRSA
              surveillance, we collected colonizing and infecting ST8-USA300
              isolates and compared them to non-ST8 CA-MRSA isolates.
              Whole-genome sequencing (WGS) was performed for each isolate of
              this collection, and discriminating molecular features were
              linked to patient data. RESULTS: In 2013, 22 isolates with the
              ST8-USA300 profile were identified among 46 cases of CA-MRSA. WGS
              revealed 2 groups of strains that differed by the type of the
              SCCmec IV element encoded and whether they harbored an arginine
              catabolism mobile element (ACME) locus. ACME-negative strains
              were mainly isolated from patients traveling in or originating
              from South America. Single-nucleotide polymorphism positions in
              isolate groups were used to infer their common ancestor,
              determine their geographical origin, and trace their relatedness.
              CONCLUSIONS: WGS allowed the identification of transmission
              events and revealed that the increased prevalence of USA300
              CA-MRSA isolates resulted from multiple importation events from
              the Americas but not from local clonal expansion of a successful
              clone.",
  journal  = "J. Infect. Dis.",
  volume   =  213,
  number   =  9,
  pages    = "1370--1379",
  month    =  may,
  year     =  2016,
  keywords = "USA300; comparative genomics; epidemiological survey; genome
              evolution; high throughput sequencing; importation event;
              methicillin-resistant Staphylococcus
              aureus;Staphylococcus;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN",
  language = "en"
 }

 % The entry below contains non-ASCII chars that could not be converted
 % to a LaTeX equivalent.
 @ARTICLE{Jamrozy2016-vu,
  title     = "Pan-genomic perspective on the evolution of the Staphylococcus
               aureus {USA300} epidemic",
  author    = "Jamrozy, Dorota M and Harris, Simon R and Mohamed, Naglaa and
               Peacock, Sharon J and Tan, Charles Y and Parkhill, Julian and
               Anderson, Annaliesa S and Holden, Matthew T G",
  abstract  = "Staphylococcus aureus USA300 represents the dominant
               community-associated methicillin-resistant S. aureus lineage in
               the USA, where it is a major cause of skin and soft tissue
               infections. Previous comparative genomic studies have described
               the population structure and evolution of USA300 based on
               geographically restricted isolate collections. Here, we
               investigated the USA300 population by sequencing genomes of a
               geographically distributed panel of 191 clinical S. aureus
               isolates belonging to clonal complex 8 (CC8), derived from the
               Tigecycline Evaluation and Surveillance Trial program. Isolates
               were collected at 12 healthcare centres across nine USA states
               in 2004, 2009 or 2010. Reconstruction of evolutionary
               relationships revealed that CC8 was dominated by USA300 isolates
               (154/191, 81 \%), which were heterogeneous and demonstrated
               limited phylogeographic clustering. Analysis of the USA300 core
               genomes revealed an increase in median pairwise SNP distance
               from 62 to 98 between 2004 and 2010, with a stable pattern of
               above average dN/dS ratios. The phylogeny of the USA300
               population indicated that early diversification events led to
               the formation of nested clades, which arose through cumulative
               acquisition of predominantly non-synonymous SNPs in various
               coding sequences. The accessory genome of USA300 was largely
               homogenous and consisted of elements previously associated with
               this lineage. We observed an emergence of SCCmec negative and
               ACME negative USA300 isolates amongst more recent samples, and
               an increase in the prevalence of ϕSa5 prophage. Together, the
               analysed S. aureus USA300 collection revealed an evolving
               pan-genome through increased core genome heterogeneity and
               temporal variation in the frequency of certain accessory
               elements.",
  journal   = "Microb Genom",
  publisher = "Microbiology Society",
  volume    =  2,
  number    =  5,
  pages     = "e000058",
  month     =  may,
  year      =  2016,
  keywords  = "Evolution; MRSA;
               USA300;Staphylococcus;pangenome;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers",
  language  = "en"
 }

 % The entry below contains non-ASCII chars that could not be converted
 % to a LaTeX equivalent.
 @ARTICLE{Straus2017-ku,
  title    = "Origin, evolution, and global transmission of community-acquired
              Staphylococcus aureus {ST8}",
  author   = "Strau{\ss}, Lena and Stegger, Marc and Akpaka, Patrick Eberechi
              and Alabi, Abraham and Breurec, Sebastien and Coombs, Geoffrey
              and Egyir, Beverly and Larsen, Anders Rhod and Laurent, Frederic
              and Monecke, Stefan and Peters, Georg and Skov, Robert and
              Strommenger, Birgit and Vandenesch, Fran{\c c}ois and Schaumburg,
              Frieder and Mellmann, Alexander",
  abstract = "USA300 is a pandemic clonal lineage of hypervirulent,
              community-acquired, methicillin-resistant Staphylococcus aureus
              (CA-MRSA) with specific molecular characteristics. Despite its
              high clinical relevance, the evolutionary origin of USA300
              remained unclear. We used comparative genomics of 224 temporal
              and spatial diverse S. aureus isolates of multilocus sequence
              type (ST) 8 to reconstruct the molecular evolution and global
              dissemination of ST8, including USA300. Analyses of core SNP
              diversity and accessory genome variations showed that the
              ancestor of all ST8 S. aureus most likely emerged in Central
              Europe in the mid-19th century. From here, ST8 was exported to
              North America in the early 20th century and progressively
              acquired the USA300 characteristics Panton-Valentine leukocidin
              (PVL), SCCmec IVa, the arginine catabolic mobile element (ACME),
              and a specific mutation in capsular polysaccharide gene cap5E
              Although the PVL-encoding phage ϕSa2USA was introduced into the
              ST8 background only once, various SCCmec types were introduced to
              ST8 at different times and places. Starting from North America,
              USA300 spread globally, including Africa. African USA300 isolates
              have aberrant spa-types (t112, t121) and form a monophyletic
              group within the clade of North American USA300. Large parts of
              ST8 methicillin-susceptible S. aureus (MSSA) isolated in Africa
              represent a symplesiomorphic group of ST8 (i.e., a group
              representing the characteristics of the ancestor), which are
              rarely found in other world regions. Isolates previously
              discussed as USA300 ancestors, including USA500 and a
              ``historic'' CA-MRSA from Western Australia, were shown to be
              only distantly related to recent USA300 clones.",
  journal  = "Proc. Natl. Acad. Sci. U. S. A.",
  month    =  nov,
  year     =  2017,
  keywords = "Africa; CA-MRSA; USA300; comparative genomics; molecular
              evolution;Staphylococcus;Staphylococcus\_aureus\_genome\_papers/USA300\_genome\_PRJN;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Spoor2013-nc,
  title    = "Livestock Origin for a Human Pandemic Clone of
              {Community-Associated} {Methicillin-Resistant} Staphylococcus
              aureus",
  author   = "Spoor, L E and Mcadam, P R and Weinert, L A and Rambaut, A and
              Hasman, H and Aarestrup, F M and Kearns, A M and Larsen, A R and
              Skov, R L and Fitzgerald, J R",
  journal  = "MBio",
  volume   =  4,
  number   =  4,
  pages    = "e00356--13--e00356--13",
  year     =  2013,
  keywords = "Staphylococcus;imported\_from\_papers\_14Nov2013;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
 }

 @ARTICLE{Kos2012-xa,
  title    = "Comparative Genomics of {Vancomycin-Resistant} Staphylococcus
              aureus Strains and Their Positions within the Clade Most Commonly
              Associated with {Methicillin-Resistant} S. aureus
              {Hospital-Acquired} Infection in the United States",
  author   = "Kos, V N and Desjardins, C A and Griggs, A and Cerqueira, G and
              Van Tonder, A and Holden, M T G and Godfrey, P and Palmer, K L
              and Bodi, K and Mongodin, E F and Wortman, J and Feldgarden, M
              and Lawley, T and Gill, S R and Haas, B J and Birren, B and
              Gilmore, M S",
  abstract = "ABSTRACT Staphylococcus aureus is a human commensal bacterium and
              a prominent cause of infections globally. The high incidence of
              S. aureus infections is compounded by the ability of the microbe
              to readily acquire resistance to antibiotics. In the United
              States, methicillin-resistant S. aureus (MRSA) is a leading cause
              of morbidity and mortality by a single infectious agent.
              Therapeutic options for severe MRSA infections are limited to a
              few antibiotics to which the organism is typically susceptible,
              including vancomycin. Acquisition of high-level vancomycin
              resistance by MRSA is a major concern, but to date, there have
              been only 12 vancomycin-resistant S. aureus (VRSA) isolates
              reported in the United States and all belong to a phylogenetic
              lineage known as clonal complex 5. To gain enhanced understanding
              of the genetic characteristics conducive to the acquisition of
              vancomycin resistance by S. aureus, V. N. Kos et al. performed
              whole-genome sequencing of all 12 VRSA isolates and compared the
              DNA sequences to the genomes of other S. aureus strains. The
              findings provide new information about the evolutionary history
              of VRSA and identify genetic features that may bear on the
              relationship between S. aureus clonal complex 5 strains and the
              acquisition of vancomycin resistance genes from enterococci.",
  journal  = "MBio",
  volume   =  3,
  number   =  3,
  pages    = "e00112--12--e00112--12",
  year     =  2012,
  keywords = "
              antibiotics;Staphylococcus;imported\_from\_papers\_14Nov2013;bacterial
              comparative genomics;Teaching antibiotic resistance
              genomics;R-M;Staph\_evolutionary\_history;antibiotcs-evolution-fitness;MRSA-VRSA-gene\_transfer;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Lowder2009-jk,
  title    = "Recent human-to-poultry host jump, adaptation, and pandemic
              spread of Staphylococcus aureus",
  author   = "Lowder, V, Bethan and Guinane, Caitriona M and Ben Zakour, Nouri
              L and Weinert, Lucy A and Conway-Morris, Andrew and Cartwright,
              Robyn A and Simpson, A John and Rambaut, Andrew and N{\"u}bel,
              Ulrich and Fitzgerald, J Ross",
  abstract = "The impact of globalization on the emergence and spread of
              pathogens is an important veterinary and public health issue.
              Staphylococcus aureus is a notorious human pathogen associated
              with serious nosocomial and community-acquired infections. In
              addition, S. aureus is a major cause of animal diseases including
              skeletal infections of poultry, which are a large economic burden
              on the global broiler chicken industry. Here, we provide evidence
              that the majority of S. aureus isolates from broiler chickens are
              the descendants of a single human-to-poultry host jump that
              occurred approximately 38 years ago (range, 30 to 63 years ago)
              by a subtype of the worldwide human ST5 clonal lineage unique to
              Poland. In contrast to human subtypes of the ST5 radiation, which
              demonstrate strong geographic clustering, the poultry ST5 clade
              was distributed in different continents, consistent with wide
              dissemination via the global poultry industry distribution
              network. The poultry ST5 clade has undergone genetic
              diversification from its human progenitor strain by acquisition
              of novel mobile genetic elements from an avian-specific accessory
              gene pool, and by the inactivation of several proteins important
              for human disease pathogenesis. These genetic events have
              resulted in enhanced resistance to killing by chicken
              heterophils, reflecting avian host-adaptive evolution. Taken
              together, we have determined the evolutionary history of a major
              new animal pathogen that has undergone rapid avian host
              adaptation and intercontinental dissemination. These data provide
              a new paradigm for the impact of human activities on the
              emergence of animal pathogens.",
  journal  = "Proc. Natl. Acad. Sci. U. S. A.",
  volume   =  106,
  number   =  46,
  pages    = "19545--19550",
  year     =  2009,
  keywords = "Staphylococcus;imported\_from\_papers\_14Nov2013;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
 }

 @ARTICLE{Harris2010-uv,
  title    = "Evolution of {MRSA} During Hospital Transmission and
              Intercontinental Spread",
  author   = "Harris, S R and Feil, E J and Holden, M T G and Quail, M A and
              Nickerson, E K and Chantratita, N and Gardete, S and Tavares, A
              and Day, N and Lindsay, J A and Edgeworth, J D and de Lencastre,
              H and Parkhill, J and Peacock, S J and Bentley, S D",
  abstract = "Current methods for differentiating isolates of predominant
              lineages of pathogenic bacteria often do not provide sufficient
              resolution to define precise relationships. Here, we describe a
              high-throughput genomics approach that provides a high-resolution
              view of the epidemiology and microevolution of a dominant strain
              of methicillin-resistant Staphylococcus aureus (MRSA). This
              approach reveals the global geographic structure within the
              lineage, its intercontinental transmission through four decades,
              and the potential to trace person-to-person transmission within a
              hospital environment. The ability to interrogate and resolve
              bacterial populations is applicable to a range of infectious
              diseases, as well as microbial ecology.",
  journal  = "Science",
  volume   =  327,
  number   =  5964,
  pages    = "469--474",
  year     =  2010,
  keywords = "Staphylococcus;imported\_from\_papers\_14Nov2013;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Howden2010-ek,
  title    = "Complete genome sequence of Staphylococcus aureus strain
              {JKD6008}, an {ST239} clone of methicillin-resistant
              Staphylococcus aureus with intermediate-level vancomycin
              resistance",
  author   = "Howden, Benjamin P and Seemann, Torsten and Harrison, Paul F and
              McEvoy, Chris R and Stanton, Jo-Ann L and Rand, Christy J and
              Mason, Chris W and Jensen, Slade O and Firth, Neville and Davies,
              John K and Johnson, Paul D R and Stinear, Timothy P",
  abstract = "We report here the complete 2.92-Mb genome sequence of a clinical
              isolate of methicillin-resistant Staphylococcus aureus subsp.
              aureus that demonstrates intermediate-level vancomycin
              resistance. The strain, named JKD6008, belongs to multilocus
              sequence type 239 and was isolated from the bloodstream of a
              patient in New Zealand in 2003.",
  journal  = "J. Bacteriol.",
  volume   =  192,
  number   =  21,
  pages    = "5848--5849",
  year     =  2010,
  keywords = "Staphylococcus;imported\_from\_papers\_14Nov2013;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Gao2010-fv,
  title     = "Two novel point mutations in clinical Staphylococcus aureus
               reduce linezolid susceptibility and switch on the stringent
               response to promote persistent infection",
  author    = "Gao, Wei and Chua, Kyra and Davies, John K and Newton, Hayley J
               and Seemann, Torsten and Harrison, Paul F and Holmes, Natasha E
               and Rhee, Hyun-Woo and Hong, Jong-In and Hartland, Elizabeth L
               and Stinear, Timothy P and Howden, Benjamin P",
  abstract  = "Staphylococcus aureus frequently invades the human bloodstream,
               leading to life threatening bacteremia and often secondary foci
               of infection. Failure of antibiotic therapy to eradicate
               infection is frequently described; in some cases associated with
               altered S. aureus antimicrobial resistance or the small colony
               variant (SCV) phenotype. Newer antimicrobials, such as
               linezolid, remain the last available therapy for some patients
               with multi-resistant S. aureus infections. Using comparative and
               functional genomics we investigated the molecular determinants
               of resistance and SCV formation in sequential S. aureus isolates
               from a patient who had a persistent and recurrent S. aureus
               infection, after failed therapy with multiple antimicrobials,
               including linezolid. Two point mutations in key staphylococcal
               genes dramatically affected clinical behaviour of the bacterium,
               altering virulence and antimicrobial resistance. Most
               strikingly, a single nucleotide substitution in relA (SACOL1689)
               reduced RelA hydrolase activity and caused accumulation of the
               intracellular signalling molecule guanosine 3',
               5'-bis(diphosphate) (ppGpp) and permanent activation of the
               stringent response, which has not previously been reported in S.
               aureus. Using the clinical isolate and a defined mutant with an
               identical relA mutation, we demonstrate for the first time the
               impact of an active stringent response in S. aureus, which was
               associated with reduced growth, and attenuated virulence in the
               Galleria mellonella model. In addition, a mutation in rlmN
               (SACOL1230), encoding a ribosomal methyltransferase that
               methylates 23S rRNA at position A2503, caused a reduction in
               linezolid susceptibility. These results reinforce the exquisite
               adaptability of S. aureus and show how subtle molecular changes
               cause major alterations in bacterial behaviour, as well as
               highlighting potential weaknesses of current antibiotic
               treatment regimens.",
  journal   = "PLoS Pathog.",
  publisher = "Public Library of Science",
  volume    =  6,
  number    =  6,
  pages     = "e1000944",
  year      =  2010,
  keywords  = "Staphylococcus;imported\_from\_papers\_14Nov2013;bacterial
               comparative genomics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Young2012-vu,
  title    = "Evolutionary dynamics of Staphylococcus aureus during progression
              from carriage to disease",
  author   = "Young, Bernadette C and Golubchik, Tanya and Batty, Elizabeth M
              and Fung, Rowena and Larner-Svensson, Hanna and Votintseva,
              Antonina A and Miller, Ruth R and Godwin, Heather and Knox, Kyle
              and Everitt, Richard G and Iqbal, Zamin and Rimmer, Andrew J and
              Cule, Madeleine and Ip, Camilla L C and Didelot, Xavier and
              Harding, Rosalind M and Donnelly, Peter and Peto, Tim E and
              Crook, Derrick W and Bowden, Rory and Wilson, Daniel J",
  abstract = "Whole-genome sequencing offers new insights into the evolution of
              bacterial pathogens and the etiology of bacterial disease.
              Staphylococcus aureus is a major cause of bacteria-associated
              mortality and invasive disease and is carried asymptomatically by
              27\% of adults. Eighty percent of bacteremias match the carried
              strain. However, the role of evolutionary change in the pathogen
              during the progression from carriage to disease is incompletely
              understood. Here we use high-throughput genome sequencing to
              discover the genetic changes that accompany the transition from
              nasal carriage to fatal bloodstream infection in an individual
              colonized with methicillin-sensitive S. aureus. We found a
              single, cohesive population exhibiting a repertoire of 30
              single-nucleotide polymorphisms and four insertion/deletion
              variants. Mutations accumulated at a steady rate over a 13-mo
              period, except for a cluster of mutations preceding the
              transition to disease. Although bloodstream bacteria differed by
              just eight mutations from the original nasally carried bacteria,
              half of those mutations caused truncation of proteins, including
              a premature stop codon in an AraC-family transcriptional
              regulator that has been implicated in pathogenicity. Comparison
              with evolution in two asymptomatic carriers supported the
              conclusion that clusters of protein-truncating mutations are
              highly unusual. Our results demonstrate that bacterial diversity
              in vivo is limited but nonetheless detectable by whole-genome
              sequencing, enabling the study of evolutionary dynamics within
              the host. Regulatory or structural changes that occur during
              carriage may be functionally important for pathogenesis;
              therefore identifying those changes is a crucial step in
              understanding the biological causes of invasive bacterial
              disease.",
  journal  = "Proceedings of the National Academy of Sciences",
  volume   =  109,
  number   =  12,
  pages    = "4550--4555",
  year     =  2012,
  keywords = "Staphylococcus;colonization;imported\_from\_papers\_14Nov2013;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Kser2012-yi,
  title    = "Rapid whole-genome sequencing for investigation of a neonatal
              {MRSA} outbreak",
  author   = "K{\"o}ser, Claudio U and Holden, Matthew T G and Ellington,
              Matthew J and Cartwright, Edward J P and Brown, Nicholas M and
              Ogilvy-Stuart, Amanda L and Hsu, Li Yang and Chewapreecha, Claire
              and Croucher, Nicholas J and Harris, Simon R and Sanders, Mandy
              and Enright, Mark C and Dougan, Gordon and Bentley, Stephen D and
              Parkhill, Julian and Fraser, Louise J and Betley, Jason R and
              Schulz-Trieglaff, Ole B and Smith, Geoffrey P and Peacock, Sharon
              J",
  abstract = "BACKGROUND:Isolates of methicillin-resistant Staphylococcus
              aureus (MRSA) belonging to a single lineage are often
              indistinguishable by means of current typing techniques.
              Whole-genome sequencing may provide improved resolution to define
              transmission pathways and characterize outbreaks.METHODS:We
              investigated a putative MRSA outbreak in a neonatal intensive
              care unit. By using rapid high-throughput sequencing technology
              with a clinically relevant turnaround time, we retrospectively
              sequenced the DNA from seven isolates associated with the
              outbreak and another seven MRSA isolates associated with carriage
              of MRSA or bacteremia in the same hospital.RESULTS:We constructed
              a phylogenetic tree by comparing single-nucleotide polymorphisms
              (SNPs) in the core genome to a reference genome (an epidemic MRSA
              clone, EMRSA-15 [sequence type 22]). This revealed a distinct
              cluster of outbreak isolates and clear separation between these
              and the nonoutbreak isolates. A previously missed transmission
              event was detected between two patients with bacteremia who were
              not part of the outbreak. We created an artificial ``resistome''
              of antibiotic-resistance genes and demonstrated concordance
              between it and the results of phenotypic susceptibility testing;
              we also created a ``toxome'' consisting of toxin genes. One
              outbreak isolate had a hypermutator phenotype with a higher
              number of SNPs than the other outbreak isolates, highlighting the
              difficulty of imposing a simple threshold for the number of SNPs
              between isolates to decide whether they are part of a recent
              transmission chain.CONCLUSIONS:Whole-genome sequencing can
              provide clinically relevant data within a time frame that can
              influence patient care. The need for automated data
              interpretation and the provision of clinically meaningful reports
              represent hurdles to clinical implementation. (Funded by the U.K.
              Clinical Research Collaboration Translational Infection Research
              Initiative and others.).",
  journal  = "N. Engl. J. Med.",
  volume   =  366,
  number   =  24,
  pages    = "2267--2275",
  year     =  2012,
  keywords = "Staphylococcus;imported\_from\_papers\_14Nov2013;Teaching
              antibiotic resistance
              genomics;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Kant2015-wt,
  title    = "Genome Sequences of Four Staphylococcus aureus Strains Isolated
              from Bovine Mastitis",
  author   = "Kant, Ravi and Taponen, Suvi and Koort, Joanna and Paulin, Lars
              and {\AA}vall-J{\"a}{\"a}skel{\"a}inen, Silja and Palva, Airi",
  abstract = "Staphylococcus aureus is a major causative agent of mastitis in
              dairy cows. The pathogenicity of S. aureus may vary; it is able
              to cause severe clinical mastitis, but most often it is
              associated with chronic subclinical mastitis. Here, we present
              the genome assemblies of four S. aureus strains from bovine
              mastitis.",
  journal  = "Genome Announc.",
  volume   =  3,
  number   =  2,
  month    =  apr,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Findley2014-rn,
  title    = "The skin microbiome: a focus on pathogens and their association
              with skin disease",
  author   = "Findley, Keisha and Grice, Elizabeth A",
  journal  = "PLoS Pathog.",
  volume   =  10,
  number   =  10,
  pages    = "e1004436",
  month    =  oct,
  year     =  2014,
  keywords = "microbiome;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Jia2015-ri,
  title    = "Characterization and complete genome sequence analysis of
              Staphylococcus aureus bacteriophage {JS01}",
  author   = "Jia, Hongying and Dong, Wenyang and Yuan, Lvfeng and Ma, Jiale
              and Bai, Qinqin and Pan, Zihao and Lu, Chengping and Yao, Huochun",
  abstract = "Staphylococcus aureus is a primary pathogen that causes bovine
              mastitis resulting in serious economic losses and herd management
              problems in dairy cows. A novel bacteriophage, JS01, specifically
              infecting bovine S. aureus, was isolated from milk of
              mastitis-affected cattle. TEM observation showed that it belonged
              to the family Siphovirus. The JS01 strain demonstrated a broad
              host range. The prediction result of PHACTS suggested that the
              JS01 strain was temperate phage. The JS01 genome is 43,458 bp
              long, with a GC content of 33.32\% and no tRNAs. Annotation and
              functional analysis of the predicted ORFs revealed six functional
              groups: structure and morphology, DNA replication and regulation,
              packaging, lysogeny, lysis, and pathogenicity. Comparative
              analysis between JS01, S. aureus MSSA476, and S. aureus prophage
              PVL was also performed. The characterization and genomic analysis
              of JS01 provide a better understanding of S. aureus-targeting
              bacteriophages and useful information for the development of
              phage-based biocontrol agents against S. aureus.",
  journal  = "Virus Genes",
  volume   =  50,
  number   =  2,
  pages    = "345--348",
  month    =  apr,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Zhang2014-eo,
  title    = "Complete Genome Sequence of Staphylococcus aureus {XN108}, an
              {ST239-MRSA-SCCmec} {III} Strain with Intermediate Vancomycin
              Resistance Isolated in Mainland China",
  author   = "Zhang, Xia and Xu, Xiaomeng and Yuan, Wenchang and Hu, Qiwen and
              Shang, Weilong and Hu, Xiaomei and Tong, Yigang and Rao, Xiancai",
  abstract = "ST239-MRSA-SCCmec III (ST239, sequence type 239; MRSA,
              methicillin-resistant Staphylococcus aureus; SCCmec III,
              staphylococcal cassette chromosome mec type III) is the most
              predominant clone of hospital-acquired methicillin-resistant S.
              aureus in mainland China. We report here the complete genome
              sequence of XN108, the first vancomycin-intermediate S. aureus
              strain isolated from a steam-burned patient with a wound
              infection.",
  journal  = "Genome Announc.",
  volume   =  2,
  number   =  4,
  month    =  jul,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Suhaili2014-nb,
  title    = "Draft Genome Sequence of {Methicillin-Resistant} Staphylococcus
              aureus {KT/Y21}, a Sequence Type 772 ({ST772}) Strain Isolated
              from a Pediatric Blood Sample in Terengganu, Malaysia",
  author   = "Suhaili, Zarizal and Lean, Soo-Sum and Yahya, Azifah and Mohd
              Desa, Mohd Nasir and Ali, Abdul Manaf and Yeo, Chew Chieng",
  abstract = "Here, we report the draft genome sequence of a
              methicillin-resistant Staphylococcus aureus (MRSA) strain,
              KT/Y21, isolated from a blood sample of a pediatric patient. This
              strain belongs to sequence type 772 (ST772), harbors the
              staphylococcal cassette chromosome mec element (SCCmec) type V,
              and is positive for the Panton-Valentine leukocidin (PVL)
              pathogenic determinant.",
  journal  = "Genome Announc.",
  volume   =  2,
  number   =  2,
  month    =  apr,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Swift2014-si,
  title    = "Complete Genome Sequence of Staphylococcus aureus Phage {GRCS}",
  author   = "Swift, Steven M and Nelson, Daniel C",
  abstract = "The Staphylococcus aureus phage GRCS was isolated from a sewage
              treatment facility in India and has shown potential for phage
              therapy in a mouse model of bacteremia. Here, we report the
              complete genome sequence of this bacteriophage.",
  journal  = "Genome Announc.",
  volume   =  2,
  number   =  2,
  month    =  apr,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Hernandez2014-ft,
  title    = "Genome Sequences of Sequence Type 45 ({ST45}) Persistent
              {Methicillin-Resistant} Staphylococcus aureus ({MRSA}) Bacteremia
              Strain 300-169 and {ST45} Resolving {MRSA} Bacteremia Strain
              301-188",
  author   = "Hernandez, David and Seidl, Kati and Corvaglia, Anna-Rita and
              Bayer, Arnold S and Xiong, Yan Q and Fran{\c c}ois, Patrice",
  abstract = "Persistent methicillin-resistant Staphylococcus aureus (MRSA)
              bacteremia (positive blood cultures after $\geq$7 days)
              represents a challenging subset of invasive MRSA infections. The
              comparison of genome sequences of persistent (300-169) and
              resolving (301-188) MRSA bacteremia isolates with similar genetic
              background (sequence type 45 [ST45]) will help us to better
              understand underlying mechanisms of persistent MRSA bacteremia.",
  journal  = "Genome Announc.",
  volume   =  2,
  number   =  2,
  month    =  mar,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Velusamy2014-ja,
  title    = "Draft Genome Sequences of Staphylococcus aureus {AMRF1} ({ST22})
              and {AMRF2} ({ST672)}, Ocular {Methicillin-Resistant} Isolates",
  author   = "Velusamy, Nithya and Prakash, Logambiga and Sivakumar, Neelamegam
              and Antony, Aju and Prajna, Lalitha and Mohankumar, Vidyarani and
              Devarajan, Bharanidharan",
  abstract = "Sequence type 22 (ST22) and ST672 are the two major emerging
              clones of community-acquired methicillin-resistant Staphylococcus
              aureus in India. ST672 strains were found to cause severe ocular
              infections. We report the draft genome sequences of two emerging
              strains of methicillin-resistant S. aureus, AMRF1 (ST22) and
              AMRF2 (ST672), isolated from patients with ocular infections.",
  journal  = "Genome Announc.",
  volume   =  2,
  number   =  2,
  month    =  mar,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Gill2014-ui,
  title    = "Revised Genome Sequence of Staphylococcus aureus Bacteriophage
              {K}",
  author   = "Gill, Jason J",
  abstract = "Bacteriophage K is a member of the virulent Twort-like group of
              myophages infecting Staphylococcus aureus. The revised sequence
              presented here includes 12,436 bp of additional sequence not
              present in the previously available phage K genome (GenBank
              accession no. NC\_005880) and updated annotations, and has been
              reopened at the predicted terminal repeat boundary.",
  journal  = "Genome Announc.",
  volume   =  2,
  number   =  1,
  month    =  jan,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Wang2014-mb,
  title    = "Genome Sequence of Staphylococcus aureus Strain {LCT-SA67}, a
              Space Flight Strain with Altered Carbon Source Utilization
              Properties",
  author   = "Wang, Junfeng and Li, Yinhu and Guo, Jun and Zhang, Xuelin and
              Guo, Yinghua and Chang, De and Li, Tianzhi and Xu, Guogang and
              Dai, Wenkui and Liu, Changting",
  abstract = "An increasing number of studies have confirmed that space flight
              environments can have a significant effect on a variety of
              microbial properties. To explore the effect of these environments
              on Staphylococcus aureus, we present the draft genome sequence of
              an S. aureus strain, named LCT-SA67, which was isolated after
              space flight.",
  journal  = "Genome Announc.",
  volume   =  2,
  number   =  1,
  month    =  feb,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Jia2013-jj,
  title    = "Complete Genome Sequence of Staphylococcus aureus Siphovirus
              Phage {JS01}",
  author   = "Jia, Hongying and Bai, Qinqin and Yang, Yongchun and Yao, Huochun",
  abstract = "Staphylococcus aureus is the most prevalent and economically
              significant pathogen causing bovine mastitis. We isolated and
              characterized one staphylophage from the milk of
              mastitis-affected cattle and sequenced its genome. Transmission
              electron microscopy (TEM) observation shows that it belongs to
              the family Siphovirus. We announce here its complete genome
              sequence and report major findings from the genomic analysis.",
  journal  = "Genome Announc.",
  volume   =  1,
  number   =  6,
  month    =  nov,
  year     =  2013,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Sabirova2014-ac,
  title    = "Complete Genome Sequences of Two Prolific {Biofilm-Forming}
              Staphylococcus aureus Isolates Belonging to {USA300} and
              {EMRSA-15} Clonal Lineages",
  author   = "Sabirova, J S and Xavier, B B and Hernalsteens, J-P and De Greve,
              H and Ieven, M and Goossens, H and Malhotra-Kumar, S",
  abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) causes serious
              infections that are even more difficult to treat when associated
              with a biofilm phenotype that facilitates evasion of the host
              immune system and antibiotics. As a first step toward
              understanding the mechanisms underlying biofilm formation, we
              sequenced the genomes of two prolific biofilm-forming strains
              belonging to the two most important globally disseminated clonal
              lineages, USA300 and EMRSA-15.",
  journal  = "Genome Announc.",
  volume   =  2,
  number   =  3,
  month    =  jun,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Murali2014-ap,
  title    = "Genome Sequences of Four Clinical Staphylococcus aureus Strains
              with Diverse Drug Resistance Profiles Isolated from Diabetic Foot
              Ulcers",
  author   = "Murali, Thokur Sreepathy and Paul, Bobby and Parikh, Hersh and
              Singh, Rana Pratap and Kavitha, Shettigar and Bhat, Manoj K and
              Satyamoorthy, Kapaettu",
  abstract = "Staphylococcus aureus is a major pathogen associated with
              diabetic foot ulcer infections. To gain insight into their
              pathogenicity and virulence potential, we report draft genome
              sequences of four strains of Staphylococcus aureus, isolated from
              diabetic foot ulcers, showing profiles with various degrees of
              resistance to common antibiotics.",
  journal  = "Genome Announc.",
  volume   =  2,
  number   =  2,
  month    =  mar,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Kim2014-bx,
  title    = "Genome sequence of type strain of Staphylococcus aureus subsp.
              aureus",
  author   = "Kim, Bong-Soo and Yi, Hana and Chun, Jongsik and Cha, Chang-Jun",
  abstract = "BACKGROUND: Staphylococcus aureus is a pathogen that causes food
              poisoning and community-associated infection with antibiotic
              resistance. This species is an indigenous intestinal microbe
              found in infants and not found in adult intestine. The relatively
              small genome size and rapid evolution of antibiotic resistance
              genes in the species have been drawing an increasing attention in
              public health. To extend our understanding of the species and use
              the genome data for comparative genomic studies, we sequenced the
              type strain of S. aureus subsp. aureus DSM 20231T. RESULTS:
              Seventeen contigs were generated using hybrid assembly of
              sequences derived from the Roche 454 and Illumina systems. The
              length of the genome sequence was 2,902,619 bases with a G + C
              content of 32.8\%. Among the 2,550 annotated CDSs, 44 CDSs were
              annotated to antibiotic resistance genes and 13 CDSs were related
              to methicillin resistance. It is interesting to note that this
              strain was first isolated in 1884 before methicillin was
              generally used on patients. CONCLUSIONS: The present study
              analyzed the genome sequence of S. aureus subsp. aureus type
              strain as the reference sequence for comparative genomic analyses
              of clinical isolates. Methicillin resistance genes found in the
              genome indicate the presence of antibiotic resistance mechanism
              prior to the usage of antibiotics. Further comparative genomic
              studies of methicillin-resistant strains based on this reference
              genome would help to understand the evolution of resistance
              mechanism and dissemination of resistance genes.",
  journal  = "Gut Pathog.",
  volume   =  6,
  number   =  1,
  pages    = "6",
  month    =  mar,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Tobes2013-xp,
  title    = "Noncontiguous Finished Genome Sequence of Staphylococcus aureus
              {KLT6}, a Staphylococcal Enterotoxin {B-Positive} Strain Involved
              in a Food Poisoning Outbreak in Switzerland",
  author   = "Tobes, Raquel and Manrique, Marina and Brozynska, Marta and
              Stephan, Roger and Pareja, Eduardo and Johler, Sophia",
  abstract = "We present the first complete genome sequence of a Staphylococcus
              aureus strain assigned to clonal complex 12. The strain was
              isolated in a food poisoning outbreak due to contaminated potato
              salad in Switzerland in 2009, and it produces staphylococcal
              enterotoxin B.",
  journal  = "Genome Announc.",
  volume   =  1,
  number   =  3,
  month    =  may,
  year     =  2013,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Stegger2013-hj,
  title    = "Genome Sequence of Staphylococcus aureus Strain {CA-347}, a
              {USA600} {Methicillin-Resistant} Isolate",
  author   = "Stegger, Marc and Driebe, Elizabeth M and Roe, Chandler and
              Lemmer, Darrin and Bowers, Jolene R and Engelthaler, David M and
              Keim, Paul and Andersen, Paal S",
  abstract = "The Staphylococcus aureus clonal lineage CC45 is a predominant
              colonizer of healthy individuals in northern Europe and
              constitutes a highly basal cluster of the S. aureus population.
              Here, we report the complete genome sequence of S. aureus strain
              CA-347 (NRS648), a representative of the methicillin-resistant
              USA600 clone predominantly found in the United States.",
  journal  = "Genome Announc.",
  volume   =  1,
  number   =  4,
  month    =  jul,
  year     =  2013,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Chen2013-df,
  title     = "Complete genome sequence of Staphylococcus aureus Z172, a
               vancomycin-intermediate and daptomycin-nonsusceptible
               methicillin-resistant strain isolated in Taiwan",
  author    = "Chen, Feng-Jui and Lauderdale, Tsai-Ling and Wang, Lih-Shinn and
               Huang, I-Wen",
  abstract  = "ABSTRACT We report the complete genome sequence of Z172, a
               representative strain of sequence type 239-staphylococcal
               cassette chromosome mec type III (ST239-SCCmec type III)
               hospital-associated methicillin-resistant Staphylococcus aureus
               in Taiwan. Strain Z172 ...",
  journal   = "Genome Announc.",
  publisher = "Am Soc Microbiol",
  volume    =  1,
  number    =  6,
  pages     = "e01011--13",
  year      =  2013,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{McDonald2013-xz,
  title    = "Draft Genome Sequence of {Methicillin-Susceptible} Staphylococcus
              aureus Strain {06BA18369}, a Pathogen Associated with Skin and
              Soft Tissue Infections in Northern Saskatchewan, Canada",
  author   = "McDonald, Ryan R and Golding, George R and Irvine, James and
              Graham, Morag R and Tyler, Shaun and Mulvey, Michael R and
              Levett, Paul N",
  abstract = "Here, we announce the draft sequence of a representative
              methicillin-susceptible Staphylococcus aureus (MSSA) isolate
              (06BA18369) whose strain type (spa type t311) was commonly
              isolated from skin and soft tissue coinfections with
              Streptococcus pyogenes. This strain sequence provides insight
              into a highly successful community-associated MSSA strain type.",
  journal  = "Genome Announc.",
  volume   =  1,
  number   =  3,
  month    =  jun,
  year     =  2013,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Corvaglia2013-gt,
  title    = "{Whole-Genome} Sequences of Two Staphylococcus aureus {ST398}
              Strains of Human Origin, {S94} and {S100}",
  author   = "Corvaglia, Anna-Rita and Fran{\c c}ois, Patrice and Bertrand,
              Xavier and Quentin, Roland and Hernandez, David and van der
              Mee-Marquet, Nathalie",
  abstract = "Sequence type 398 (ST398) Staphylococcus aureus was originally
              associated with animal infection. We announce the complete genome
              sequences of two ST398 methicillin-susceptible S. aureus strains
              of human origin, S94 and S100. The genome sequences assist in the
              characterization of interesting ST398 features related to host
              specificities.",
  journal  = "Genome Announc.",
  volume   =  1,
  number   =  5,
  month    =  aug,
  year     =  2013,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Fraunholz2013-le,
  title    = "Complete Genome Sequence of Staphylococcus aureus 6850, a Highly
              Cytotoxic and Clinically Virulent {Methicillin-Sensitive} Strain
              with Distant Relatedness to Prototype Strains",
  author   = "Fraunholz, Martin and Bernhardt, J{\"o}rg and Schuldes, J{\"o}rg
              and Daniel, Rolf and Hecker, Michael and Sinha, Bhanu",
  abstract = "Staphylococcus aureus is a frequent human commensal bacterium and
              pathogen. Here we report the complete genome sequence of strain
              6850 (spa type t185; sequence type 50 [ST50]), a highly cytotoxic
              and clinically virulent methicillin-sensitive strain from a
              patient with complicated S. aureus bacteremia associated with
              osteomyelitis and septic arthritis.",
  journal  = "Genome Announc.",
  volume   =  1,
  number   =  5,
  month    =  sep,
  year     =  2013,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Harro2013-ua,
  title    = "Draft Genome Sequence of the {Methicillin-Resistant}
              Staphylococcus aureus Isolate {MRSA-M2}",
  author   = "Harro, Janette M and Daugherty, Sean and Bruno, Vincent M and
              Jabra-Rizk, Mary Ann and Rasko, David A and Shirtliff, Mark E",
  abstract = "We report the draft genome sequence of a methicillin-resistant
              strain of Staphylococcus aureus, designated MRSA-M2. This
              clinical isolate was obtained from an osteomyelitis patient
              undergoing treatment at the University of Texas Medical Branch
              (Galveston, TX). This strain is an ST30, spa type T019, agr III
              strain and has been utilized as a model S. aureus strain in a
              number of proteomic, transcriptomic, and animal model studies.",
  journal  = "Genome Announc.",
  volume   =  1,
  number   =  1,
  month    =  jan,
  year     =  2013,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Hernandez2014-ul,
  title    = "De novo finished 2.8 Mbp Staphylococcus aureus genome assembly
              from 100 bp short and long range paired-end reads",
  author   = "Hernandez, David and Tewhey, Ryan and Veyrieras, Jean-Baptiste
              and Farinelli, Laurent and {\O}ster{\aa}s, Magne and Fran{\c
              c}ois, Patrice and Schrenzel, Jacques",
  abstract = "MOTIVATION: Paired-end sequencing allows circumventing the
              shortness of the reads produced by second generation sequencers
              and is essential for de novo assembly of genomes. However,
              obtaining a finished genome from short reads is still an open
              challenge. We present an algorithm that exploits the pairing
              information issued from inserts of potentially any length. The
              method determines paths through an overlaps graph by using a
              constrained search tree. We also present a method that
              automatically determines suited overlaps cutoffs according to the
              contextual coverage, reducing thus the need for manual
              parameterization. Finally, we introduce an interactive mode that
              allows querying an assembly at targeted regions. RESULTS: We
              assess our methods by assembling two Staphylococcus aureus
              strains that were sequenced on the Illumina platform. Using 100
              bp paired-end reads and minimal manual curation, we produce a
              finished genome sequence for the previously undescribed isolate
              SGH-10-168. AVAILABILITY AND IMPLEMENTATION: The presented
              algorithms are implemented in the standalone Edena software,
              freely available under the General Public License (GPLv3) at
              www.genomic.ch/edena.php.",
  journal  = "Bioinformatics",
  volume   =  30,
  number   =  1,
  pages    = "40--49",
  month    =  jan,
  year     =  2014,
  keywords = "Staphylococcus;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Golubchik2013-cy,
  title     = "Within-host evolution of Staphylococcus aureus during
               asymptomatic carriage",
  author    = "Golubchik, Tanya and Batty, Elizabeth M and Miller, Ruth R and
               Farr, Helen and Young, Bernadette C and Larner-Svensson, Hanna
               and Fung, Rowena and Godwin, Heather and Knox, Kyle and
               Votintseva, Antonina and Everitt, Richard G and Street, Teresa
               and Cule, Madeleine and Ip, Camilla L C and Didelot, Xavier and
               Peto, Timothy E A and Harding, Rosalind M and Wilson, Daniel J
               and Crook, Derrick W and Bowden, Rory",
  abstract  = "BACKGROUND: Staphylococcus aureus is a major cause of healthcare
               associated mortality, but like many important bacterial
               pathogens, it is a common constituent of the normal human body
               flora. Around a third of healthy adults are carriers. Recent
               evidence suggests that evolution of S. aureus during nasal
               carriage may be associated with progression to invasive disease.
               However, a more detailed understanding of within-host evolution
               under natural conditions is required to appreciate the
               evolutionary and mechanistic reasons why commensal bacteria such
               as S. aureus cause disease. Therefore we examined in detail the
               evolutionary dynamics of normal, asymptomatic carriage.
               Sequencing a total of 131 genomes across 13 singly colonized
               hosts using the Illumina platform, we investigated diversity,
               selection, population dynamics and transmission during the
               short-term evolution of S. aureus. PRINCIPAL FINDINGS: We
               characterized the processes by which the raw material for
               evolution is generated: micro-mutation (point mutation and small
               insertions/deletions), macro-mutation (large
               insertions/deletions) and the loss or acquisition of mobile
               elements (plasmids and bacteriophages). Through an analysis of
               synonymous, non-synonymous and intergenic mutations we
               discovered a fitness landscape dominated by purifying selection,
               with rare examples of adaptive change in genes encoding
               surface-anchored proteins and an enterotoxin. We found evidence
               for dramatic, hundred-fold fluctuations in the size of the
               within-host population over time, which we related to the cycle
               of colonization and clearance. Using a newly-developed
               population genetics approach to detect recent transmission among
               hosts, we revealed evidence for recent transmission between some
               of our subjects, including a husband and wife both carrying
               populations of methicillin-resistant S. aureus (MRSA).
               SIGNIFICANCE: This investigation begins to paint a picture of
               the within-host evolution of an important bacterial pathogen
               during its prevailing natural state, asymptomatic carriage.
               These results also have wider significance as a benchmark for
               future systematic studies of evolution during invasive S. aureus
               disease.",
  journal   = "PLoS One",
  publisher = "Public Library of Science",
  volume    =  8,
  number    =  5,
  pages     = "e61319",
  month     =  may,
  year      =  2013,
  keywords  = "evolution;colonization;Staphylococcus;within-host-evolution;Staph\_evolutionary\_history/USA300\_evolution;Staph\_evolutionary\_history;imported\_from\_papers\_14Nov2013;Staph\_evolutionary\_history/Staph\_population\_dynamics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Suzuki2012-cj,
  title     = "Comparative genomic analysis of the genus Staphylococcus
               including Staphylococcus aureus and its newly described sister
               species Staphylococcus simiae",
  author    = "Suzuki, Haruo and Lef{\'e}bure, Tristan and Bitar, Paulina
               Pavinski and Stanhope, Michael J",
  abstract  = "BACKGROUND:Staphylococcus belongs to the Gram-positive low G + C
               content group of the Firmicutes division of bacteria.
               Staphylococcus aureus is an important human and veterinary
               pathogen that causes a broad spectrum of diseases, and has
               developed important multidrug resistant forms such as
               methicillin-resistant S. aureus (MRSA). Staphylococcus simiae
               was isolated from South American squirrel monkeys in 2000, and
               is a coagulase-negative bacterium, closely related, and possibly
               the sister group, to S. aureus. Comparative genomic analyses of
               closely related bacteria with different phenotypes can provide
               information relevant to understanding adaptation to host
               environment and mechanisms of pathogenicity.RESULTS:We
               determined a Roche/454 draft genome sequence for S. simiae and
               included it in comparative genomic analyses with 11 other
               Staphylococcus species including S. aureus. A genome based
               phylogeny of the genus confirms that S. simiae is the sister
               group to S. aureus and indicates that the most basal
               Staphylococcus lineage is Staphylococcus pseudintermedius,
               followed by Staphylococcus carnosus. Given the primary niche of
               these two latter taxa, compared to the other species in the
               genus, this phylogeny suggests that human adaptation evolved
               after the split of S. carnosus. The two coagulase-positive
               species (S. aureus and S. pseudintermedius) are not
               phylogenetically closest but share many virulence factors
               exclusively, suggesting that these genes were acquired by
               horizontal transfer. Enrichment in genes related to mobile
               elements such as prophage in S. aureus relative to S. simiae
               suggests that pathogenesis in the S. aureus group has developed
               by gene gain through horizontal transfer, after the split of S.
               aureus and S. simiae from their common
               ancestor.CONCLUSIONS:Comparative genomic analyses across 12
               Staphylococcus species provide hypotheses about lineages in
               which human adaptation has taken place and contributions of
               horizontal transfer in pathogenesis.",
  journal   = "BMC Genomics",
  publisher = "BioMed Central Ltd",
  volume    =  13,
  pages     = "38",
  year      =  2012,
  keywords  = "Staphylococcus;imported\_from\_papers\_14Nov2013;bacterial
               comparative genomics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Everitt2014-tp,
  title    = "Mobile elements drive recombination hotspots in the core genome
              of Staphylococcus aureus",
  author   = "Everitt, Richard G and Didelot, Xavier and Batty, Elizabeth M and
              Miller, Ruth R and Knox, Kyle and Young, Bernadette C and Bowden,
              Rory and Auton, Adam and Votintseva, Antonina and
              Larner-Svensson, Hanna and Charlesworth, Jane and Golubchik,
              Tanya and Ip, Camilla L C and Godwin, Heather and Fung, Rowena
              and Peto, Tim E A and Walker, A Sarah and Crook, Derrick W and
              Wilson, Daniel J",
  abstract = "Horizontal gene transfer is an important driver of bacterial
              evolution, but genetic exchange in the core genome of clonal
              species, including the major pathogen Staphylococcus aureus, is
              incompletely understood. Here we reveal widespread homologous
              recombination in S. aureus at the species level, in contrast to
              its near-complete absence between closely related strains. We
              discover a patchwork of hotspots and coldspots at fine scales
              falling against a backdrop of broad-scale trends in rate
              variation. Over megabases, homoplasy rates fluctuate 1.9-fold,
              peaking towards the origin-of-replication. Over kilobases, we
              find core recombination hotspots of up to 2.5-fold enrichment
              situated near fault lines in the genome associated with mobile
              elements. The strongest hotspots include regions flanking
              conjugative transposon ICE6013, the staphylococcal cassette
              chromosome (SCC) and genomic island $\nu$Sa$\alpha$. Mobile
              element-driven core genome transfer represents an opportunity for
              adaptation and challenges our understanding of the recombination
              landscape in predominantly clonal pathogens, with important
              implications for genotype-phenotype mapping.",
  journal  = "Nat. Commun.",
  volume   =  5,
  pages    = "3956",
  month    =  may,
  year     =  2014,
  keywords = "
              Staphylococcus;evolution;teaching-tutorial;recombination;bacterial
              comparative
              genomics;Staph\_evolutionary\_history;Staph\_evolutionary\_history/Teaching\_Prokaryotic\_evolution;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Holt2011-bo,
  title    = "A Very {Early-Branching} Staphylococcus aureus Lineage Lacking
              the Carotenoid Pigment Staphyloxanthin",
  author   = "Holt, D C and Holden, M T G and Tong, S Y C and Castillo-Ramirez,
              S and Clarke, L and Quail, M A and Currie, B J and Parkhill, J
              and Bentley, S D and Feil, E J and Giffard, P M",
  journal  = "Genome Biol. Evol.",
  volume   =  3,
  number   =  0,
  pages    = "881--895",
  year     =  2011,
  keywords = "Staphylococcus;imported\_from\_papers\_14Nov2013;Staph\_evolutionary\_history;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Koch2014-bi,
  title    = "Evolution of Resistance to a {Last-Resort} Antibiotic in
              Staphylococcus aureus via Bacterial Competition",
  author   = "Koch, Gudrun and Yepes, Ana and F{\"o}rstner, Konrad U and
              Wermser, Charlotte and Stengel, Stephanie T and Modamio, Jennifer
              and Ohlsen, Knut and Foster, Kevin R and Lopez, Daniel",
  abstract = "Antibiotic resistance is a key medical concern, with antibiotic
              use likely being an important cause. However, here we describe an
              alternative route to clinically relevant antibiotic resistance
              that occurs solely due to competitive interactions among
              bacterial cells. We consistently observe that isolates of
              Methicillin-resistant Staphylococcus aureus diversify
              spontaneously into two distinct, sequentially arising strains.
              The first evolved strain outgrows the parent strain via secretion
              of surfactants and a toxic bacteriocin. The second is resistant
              to the bacteriocin. Importantly, this second strain is also
              resistant to intermediate levels of vancomycin. This so-called
              VISA (vancomycin-intermediate S. aureus) phenotype is seen in
              many hard-to-treat clinical isolates. This strain diversification
              also occurs during in vivo infection in a mouse model, which is
              consistent with the fact that both coevolved phenotypes resemble
              strains commonly found in clinic. Our study shows how competition
              between coevolving bacterial strains can generate antibiotic
              resistance and recapitulate key clinical phenotypes.",
  journal  = "Cell",
  volume   =  158,
  number   =  5,
  pages    = "1060--1071",
  month    =  aug,
  year     =  2014,
  keywords = "
              antibiotics;Staphylococcus;Staph\_evolutionary\_history;bacterial
              comparative
              genomics;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Benson2014-jp,
  title    = "Evolution of hypervirulence by a {MRSA} clone through acquisition
              of a transposable element",
  author   = "Benson, Meredith A and Ohneck, Elizabeth A and Ryan, Chanelle and
              Alonzo, 3rd, Francis and Smith, Hannah and Narechania, Apurva and
              Kolokotronis, Sergios-Orestis and Satola, Sarah W and Uhlemann,
              Anne-Catrin and Sebra, Robert and Deikus, Gintaras and Shopsin,
              Bo and Planet, Paul J and Torres, Victor J",
  abstract = "Staphylococcus aureus has evolved as a pathogen that causes a
              range of diseases in humans. There are two dominant modes of
              evolution thought to explain most of the virulence differences
              between strains. First, virulence genes may be acquired from
              other organisms. Second, mutations may cause changes in the
              regulation and expression of genes. Here we describe an
              evolutionary event in which transposition of an IS element has a
              direct impact on virulence gene regulation resulting in
              hypervirulence. Whole-genome analysis of a methicillin-resistant
              S. aureus (MRSA) strain USA500 revealed acquisition of a
              transposable element (IS256) that is absent from close relatives
              of this strain. Of the multiple copies of IS256 found in the
              USA500 genome, one was inserted in the promoter sequence of
              repressor of toxins (Rot), a master transcriptional regulator
              responsible for the expression of virulence factors in S. aureus.
              We show that insertion into the rot promoter by IS256 results in
              the derepression of cytotoxin expression and increased virulence.
              Taken together, this work provides new insight into evolutionary
              strategies by which S. aureus is able to modify its virulence
              properties and demonstrates a novel mechanism by which horizontal
              gene transfer directly impacts virulence through altering toxin
              regulation.",
  journal  = "Mol. Microbiol.",
  volume   =  93,
  number   =  4,
  pages    = "664--681",
  month    =  aug,
  year     =  2014,
  keywords = "Staphylococcus;toxicity;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers"
 }

 @ARTICLE{Chua2014-sh,
  title    = "Hyperexpression of alpha-hemolysin explains enhanced virulence of
              sequence type 93 community-associated methicillin-resistant
              Staphylococcus aureus",
  author   = "Chua, Kyra and Monk, Ian and Lin, Ya-Hsun and Seemann, Torsten
              and Tuck, Kellie and Porter, Jessica and Stepnell, Justin and
              Coombs, Geoffrey and Davies, John and Stinear, Timothy and
              Howden, Benjamin",
  abstract = "BACKGROUND:The community-associated methicillin-resistant S.
              aureus (CA-MRSA) ST93 clone is becoming dominant in Australia and
              is clinically highly virulent. In addition, sepsis and skin
              infection models demonstrate that ST93 CA-MRSA is the most
              virulent global clone of S. aureus tested to date. While the
              determinants of virulence have been studied in other clones of
              CA-MRSA, the basis for hypervirulence in ST93 CA-MRSA has not
              been defined.RESULTS:Here, using a geographically and temporally
              dispersed collection of ST93 isolates we demonstrate that the
              ST93 population hyperexpresses key CA-MRSA exotoxins, in
              particular alpha-hemolysin, in comparison to other global clones.
              Gene deletion and complementation studies, and virulence
              comparisons in a murine skin infection model, showed
              unequivocally that increased expression of alpha-hemolysin is the
              key staphylococcal virulence determinant for this clone. Genome
              sequencing and comparative genomics of strains with divergent
              exotoxin profiles demonstrated that, like other S. aureus clones,
              the quorum sensing agr system is the master regulator of toxin
              expression and virulence in ST93 CA-MRSA. However, we also
              identified a previously uncharacterized AraC/XylS family
              regulator (AryK) that potentiates toxin expression and virulence
              in S. aureus.CONCLUSIONS:These data demonstrate that
              hyperexpression of alpha-hemolysin mediates enhanced virulence in
              ST93 CA-MRSA, and additional control of exotoxin production, in
              particular alpha-hemolysin, mediated by regulatory systems other
              than agr have the potential to fine-tune virulence in CA-MRSA.",
  journal  = "BMC Microbiol.",
  volume   =  14,
  number   =  1,
  pages    = "31",
  year     =  2014,
  keywords = "Staphylococcus;toxicity;antibiotics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Long2014-hn,
  title    = "Absence of {Patient-to-Patient} Intrahospital Transmission of
              Staphylococcus aureus as Determined by {Whole-Genome} Sequencing",
  author   = "Long, S Wesley and Beres, Stephen B and Olsen, Randall J and
              Musser, James M",
  abstract = "Nosocomial transmission of pathogens is a major health care
              challenge. The increasing spread of antibiotic-resistant strains
              represents an ongoing threat to public health. Previous
              Staphylococcus aureus transmission studies have focused on
              transmission of S. aureus between asymptomatic carriers or used
              low-resolution typing methods such as multilocus sequence typing
              (MLST) or spa typing. To identify patient-to-patient
              intrahospital transmission using high-resolution genetic
              analysis, we sequenced the genomes of a consecutive set of 398 S.
              aureus isolates from sterile-site infections. The S. aureus
              strains were collected from four hospitals in the Houston
              Methodist Hospital System over a 6-month period. Importantly, we
              discovered no evidence of transmission of S. aureus between
              patients with sterile-site infections. The lack of intrahospital
              transmission may reflect a fundamental difference between
              day-to-day transmission events in the hospital setting and the
              more frequently studied outbreak scenarios.IMPORTANCE Previous
              studies have suggested that nosocomial transmission of S. aureus
              is common. Our data revealed an unexpected lack of evidence for
              intrahospital transmission of S. aureus between patients with
              invasive infections. This finding has important implications for
              hospital infection control and public health efforts. In
              addition, our data demonstrate that highly related pools of S.
              aureus strains exist in the community which may complicate
              outbreak investigations.",
  journal  = "MBio",
  volume   =  5,
  number   =  5,
  month    =  oct,
  year     =  2014,
  keywords = "Staphylococcus;bacterial comparative
              genomics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Parker2014-bc,
  title    = "Genome Sequence of Bacterial Interference Strain Staphylococcus
              aureus {502A}",
  author   = "Parker, Dane and Narechania, Apurva and Sebra, Robert and Deikus,
              Gintaras and Larussa, Samuel and Ryan, Chanelle and Smith, Hannah
              and Prince, Alice and Mathema, Barun and Ratner, Adam J and
              Kreiswirth, Barry and Planet, Paul J",
  abstract = "Staphylococcus aureus 502A was a strain used in bacterial
              interference programs during the 1960s and early 1970s. Infants
              were deliberately colonized with 502A with the goal of preventing
              colonization with more invasive strains. We present the completed
              genome sequence of this organism.",
  journal  = "Genome Announc.",
  volume   =  2,
  number   =  2,
  month    =  apr,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Gordon2014-jf,
  title    = "Prediction of Staphylococcus aureus antimicrobial resistance by
              whole-genome sequencing",
  author   = "Gordon, N C and Price, J R and Cole, K and Everitt, R and Morgan,
              M and Finney, J and Kearns, A M and Pichon, B and Young, B and
              Wilson, D J and Llewelyn, M J and Paul, J and Peto, T E A and
              Crook, D W and Walker, A S and Golubchik, T",
  abstract = "Whole-genome sequencing (WGS) could potentially provide a single
              platform for extracting all the information required to predict
              an organism's phenotype. However, its ability to provide accurate
              predictions has not yet been demonstrated in large independent
              studies of specific organisms. In this study, we aimed to develop
              a genotypic prediction method for antimicrobial susceptibilities.
              The whole genomes of 501 unrelated Staphylococcus aureus isolates
              were sequenced, and the assembled genomes were interrogated using
              BLASTn for a panel of known resistance determinants (chromosomal
              mutations and genes carried on plasmids). Results were compared
              with phenotypic susceptibility testing for 12 commonly used
              antimicrobial agents (penicillin, methicillin, erythromycin,
              clindamycin, tetracycline, ciprofloxacin, vancomycin,
              trimethoprim, gentamicin, fusidic acid, rifampin, and mupirocin)
              performed by the routine clinical laboratory. We investigated
              discrepancies by repeat susceptibility testing and manual
              inspection of the sequences and used this information to optimize
              the resistance determinant panel and BLASTn algorithm. We then
              tested performance of the optimized tool in an independent
              validation set of 491 unrelated isolates, with phenotypic results
              obtained in duplicate by automated broth dilution (BD Phoenix)
              and disc diffusion. In the validation set, the overall
              sensitivity and specificity of the genomic prediction method were
              0.97 (95\% confidence interval [95\% CI], 0.95 to 0.98) and 0.99
              (95\% CI, 0.99 to 1), respectively, compared to standard
              susceptibility testing methods. The very major error rate was
              0.5\%, and the major error rate was 0.7\%. WGS was as sensitive
              and specific as routine antimicrobial susceptibility testing
              methods. WGS is a promising alternative to culture methods for
              resistance prediction in S. aureus and ultimately other major
              bacterial pathogens.",
  journal  = "J. Clin. Microbiol.",
  volume   =  52,
  number   =  4,
  pages    = "1182--1191",
  month    =  apr,
  year     =  2014,
  keywords = "antibiotics;Staphylococcus;Teaching antibiotic resistance
              genomics;Read-lab-shared;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers;GWAS-bacteria"
 }

 @ARTICLE{Dean2014-fn,
  title    = "Identification of point mutations in clinical Staphylococcus
              aureus strains that produce small-colony variants auxotrophic for
              menadione",
  author   = "Dean, Melissa A and Olsen, Randall J and Long, S Wesley and
              Rosato, Adriana E and Musser, James M",
  abstract = "Staphylococcus aureus small-colony variants (SCVs) are implicated
              in chronic and relapsing infections that are difficult to
              diagnose and treat. Despite many years of study, the underlying
              molecular mechanisms and virulence effect of the small-colony
              phenotype remain incompletely understood. We sequenced the
              genomes of five S. aureus SCV strains recovered from human
              patients and discovered previously unidentified nonsynonymous
              point mutations in three genes encoding proteins in the menadione
              biosynthesis pathway. Analysis of genetic revertants and
              complementation with wild-type alleles confirmed that these
              mutations caused the SCV phenotype and decreased virulence for
              mice.",
  journal  = "Infect. Immun.",
  volume   =  82,
  number   =  4,
  pages    = "1600--1605",
  month    =  apr,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{McCarthy2014-np,
  title    = "Extensive horizontal gene transfer during Staphylococcus aureus
              co-colonization in vivo",
  author   = "McCarthy, Alex J and Loeffler, Anette and Witney, Adam A and
              Gould, Katherine A and Lloyd, David H and Lindsay, Jodi A",
  abstract = "Staphylococcus aureus is a commensal and major pathogen of humans
              and animals. Comparative genomics of S. aureus populations
              suggests that colonization of different host species is
              associated with carriage of mobile genetic elements (MGE),
              particularly bacteriophages and plasmids capable of encoding
              virulence, resistance, and immune evasion pathways.
              Antimicrobial-resistant S. aureus of livestock are a potential
              zoonotic threat to human health if they adapt to colonize humans
              efficiently. We utilized the technique of experimental evolution
              and co-colonized gnotobiotic piglets with both human- and
              pig-associated variants of the lineage clonal complex 398, and
              investigated growth and genetic changes over 16 days using whole
              genome sequencing. The human isolate survived co-colonization on
              piglets more efficiently than in vitro. During co-colonization,
              transfer of MGE from the pig to the human isolate was detected
              within 4 h. Extensive and repeated transfer of two bacteriophages
              and three plasmids resulted in colonization with isolates
              carrying a wide variety of mobilomes. Whole genome sequencing of
              progeny bacteria revealed no acquisition of core genome
              polymorphisms, highlighting the importance of MGE. Staphylococcus
              aureus bacteriophage recombination and integration into novel
              sites was detected experimentally for the first time. During
              colonization, clones coexisted and diversified rather than a
              single variant dominating. Unexpectedly, each piglet carried
              unique populations of bacterial variants, suggesting limited
              transmission of bacteria between piglets once colonized. Our data
              show that horizontal gene transfer occurs at very high frequency
              in vivo and significantly higher than that detectable in vitro.",
  journal  = "Genome Biol. Evol.",
  volume   =  6,
  number   =  10,
  pages    = "2697--2708",
  month    =  oct,
  year     =  2014,
  keywords = "bacteriophage; experimental evolution; host adaptation; plasmid;
              population
              dynamics;Staphylococcus;colonization;recombination;Staph\_evolutionary\_history/Staph\_population\_dynamics;Staph\_evolutionary\_history/staph
              microbial interactions;bacterial comparative
              genomics;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
 }

 @ARTICLE{Kobayashi2012-he,
  title    = "Genomic analysis of the emergence of vancomycin-resistant
              Staphylococcus aureus",
  author   = "Kobayashi, Scott D and Musser, James M and DeLeo, Frank R",
  abstract = "Staphylococcus aureus is a human commensal bacterium and a
              prominent cause of infections globally. The high incidence of S.
              aureus infections is compounded by the ability of the microbe to
              readily acquire resistance to antibiotics. In the United States,
              methicillin-resistant S. aureus (MRSA) is a leading cause of
              morbidity and mortality by a single infectious agent. Therapeutic
              options for severe MRSA infections are limited to a few
              antibiotics to which the organism is typically susceptible,
              including vancomycin. Acquisition of high-level vancomycin
              resistance by MRSA is a major concern, but to date, there have
              been only 12 vancomycin-resistant S. aureus (VRSA) isolates
              reported in the United States and all belong to a phylogenetic
              lineage known as clonal complex 5. To gain enhanced understanding
              of the genetic characteristics conducive to the acquisition of
              vancomycin resistance by S. aureus, V. N. Kos et al. performed
              whole-genome sequencing of all 12 VRSA isolates and compared the
              DNA sequences to the genomes of other S. aureus strains. The
              findings provide new information about the evolutionary history
              of VRSA and identify genetic features that may bear on the
              relationship between S. aureus clonal complex 5 strains and the
              acquisition of vancomycin resistance genes from enterococci.",
  journal  = "MBio",
  volume   =  3,
  number   =  4,
  month    =  jun,
  year     =  2012,
  keywords = "Staphylococcus;antibiotcs-evolution-fitness;MRSA-VRSA-gene\_transfer;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Holden2013-bu,
  title    = "A genomic portrait of the emergence, evolution, and global spread
              of a methicillin-resistant Staphylococcus aureus pandemic",
  author   = "Holden, Matthew T G and Hsu, Li Yang and Kurt, Kevin and Weinert,
              Lucy A and Mather, Alison E and Harris, Simon R and Strommenger,
              Birgit and Layer, Franziska and Witte, Wolfgang and de Lencastre,
              Herminia and Skov, Robert and Westh, Henrik and Zemlickov{\'a},
              Helena and Coombs, Geoffrey and Kearns, Angela M and Hill, Robert
              L R and Edgeworth, Jonathan and Gould, Ian and Gant, Vanya and
              Cooke, Jonathan and Edwards, Giles F and McAdam, Paul R and
              Templeton, Kate E and McCann, Angela and Zhou, Zhemin and
              Castillo-Ram{\'\i}rez, Santiago and Feil, Edward J and Hudson,
              Lyndsey O and Enright, Mark C and Balloux, Francois and Aanensen,
              David M and Spratt, Brian G and Fitzgerald, J Ross and Parkhill,
              Julian and Achtman, Mark and Bentley, Stephen D and N{\"u}bel,
              Ulrich",
  abstract = "The widespread use of antibiotics in association with
              high-density clinical care has driven the emergence of
              drug-resistant bacteria that are adapted to thrive in
              hospitalized patients. Of particular concern are globally
              disseminated methicillin-resistant Staphylococcus aureus (MRSA)
              clones that cause outbreaks and epidemics associated with health
              care. The most rapidly spreading and tenacious
              health-care-associated clone in Europe currently is EMRSA-15,
              which was first detected in the UK in the early 1990s and
              subsequently spread throughout Europe and beyond. Using
              phylogenomic methods to analyze the genome sequences for 193 S.
              aureus isolates, we were able to show that the current pandemic
              population of EMRSA-15 descends from a health-care-associated
              MRSA epidemic that spread throughout England in the 1980s, which
              had itself previously emerged from a primarily
              community-associated methicillin-sensitive population. The
              emergence of fluoroquinolone resistance in this EMRSA-15 subclone
              in the English Midlands during the mid-1980s appears to have
              played a key role in triggering pandemic spread, and occurred
              shortly after the first clinical trials of this drug.
              Genome-based coalescence analysis estimated that the population
              of this subclone over the last 20 yr has grown four times faster
              than its progenitor. Using comparative genomic analysis we
              identified the molecular genetic basis of 99.8\% of the
              antimicrobial resistance phenotypes of the isolates, highlighting
              the potential of pathogen genome sequencing as a diagnostic tool.
              We document the genetic changes associated with adaptation to the
              hospital environment and with increasing drug resistance over
              time, and how MRSA evolution likely has been influenced by
              country-specific drug use regimens.",
  journal  = "Genome Res.",
  volume   =  23,
  number   =  4,
  pages    = "653--664",
  year     =  2013,
  keywords = "
              Staphylococcus;antibiotics;imported\_from\_papers\_14Nov2013;Staph\_evolutionary\_history;bacterial
              comparative
              genomics;antibiotcs-evolution-fitness;MRSA-VRSA-gene\_transfer;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Baba2002-mu,
  title    = "Genome and virulence determinants of high virulence
              community-acquired {MRSA}",
  author   = "Baba, Tadashi and Takeuchi, Fumihiko and Kuroda, Makoto and
              Yuzawa, Harumi and Aoki, Ken-Ichi and Oguchi, Akio and Nagai,
              Yoshimi and Iwama, Natsuko and Asano, Kazuyuki and Naimi, Timothy
              and Kuroda, Hiroko and Cui, Longzhu and Yamamoto, Kenji and
              Hiramatsu, Keiichi",
  abstract = "BACKGROUND: A new type of meticillin-resistant Staphylococcus
              aureus (MRSA), designated community-acquired MRSA, is becoming
              increasingly noticeable in the community, some strains of which
              cause fatal infections in otherwise healthy individuals. By
              contrast with hospital-acquired MRSA, community-acquired MRSA is
              more susceptible to non b-lactam antibiotics. We investigated the
              high virulence potential of certain strains of this bacterium.
              METHODS: We ascertained the whole genome sequence of MW2, a
              strain of community-acquired MRSA, by shotgun cloning and
              sequencing. MW2 caused fatal septicaemia and septic arthritis in
              a 16-month-old girl in North Dakota, USA, in 1998. The genome of
              this strain was compared with those of hospital-acquired MRSA
              strains, including N315 and Mu50. FINDINGS: Meticillin resistance
              gene (mecA) in MW2 was carried by a novel allelic form (type IVa)
              of staphylococcal cassette chromosome mec (SCCmec), by contrast
              with type II in N315 and Mu50. Type IVa SCCmec did not carry any
              of the multiple antibiotic resistance genes reported in type II
              SCCmec. By contrast, 19 additional virulence genes were recorded
              in the MW2 genome. All but two of these virulence genes were
              noted in four of the seven genomic islands of MW2.
              INTERPRETATION: MW2 carried a range of virulence and resistance
              genes that was distinct from those displayed on the chromosomes
              of extant S aureus strains. Most genes were carried by specific
              allelic forms of genomic islands in the MW2 chromosome. The
              combination of allelic forms of genomic islands is the genetic
              basis that determines the pathogenicity of medically important
              phenotypes of S aureus, including those of community-acquired
              MRSA strains.",
  journal  = "Lancet",
  volume   =  359,
  number   =  9320,
  pages    = "1819--1827",
  month    =  may,
  year     =  2002,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Rossi2014-hc,
  title    = "Transferable vancomycin resistance in a community-associated
              {MRSA} lineage",
  author   = "Rossi, Fl{\'a}via and Diaz, Lorena and Wollam, Aye and Panesso,
              Diana and Zhou, Yanjiao and Rincon, Sandra and Narechania, Apurva
              and Xing, Galen and Di Gioia, Thais S R and Doi, Andr{\'e} and
              Tran, Truc T and Reyes, Jinnethe and Munita, Jose M and Carvajal,
              Lina P and Hernandez-Roldan, Alejandra and Brand{\~a}o, Denise
              and van der Heijden, Inneke Marie and Murray, Barbara E and
              Planet, Paul J and Weinstock, George M and Arias, Cesar A",
  abstract = "We report the case of a patient from Brazil with a bloodstream
              infection caused by a strain of methicillin-resistant
              Staphylococcus aureus (MRSA) that was susceptible to vancomycin
              (designated BR-VSSA) but that acquired the vanA gene cluster
              during antibiotic therapy and became resistant to vancomycin
              (designated BR-VRSA). Both strains belong to the sequence type
              (ST) 8 community-associated genetic lineage that carries the
              staphylococcal chromosomal cassette mec (SCCmec) type IVa and the
              S. aureus protein A gene (spa) type t292 and are phylogenetically
              related to MRSA lineage USA300. A conjugative plasmid of 55,706
              bp (pBRZ01) carrying the vanA cluster was identified and readily
              transferred to other staphylococci. The pBRZ01 plasmid harbors
              DNA sequences that are typical of the plasmid-associated
              replication genes rep24 or rep21 described in
              community-associated MRSA strains from Australia (pWBG745). The
              presence and dissemination of community-associated MRSA
              containing vanA could become a serious public health concern.",
  journal  = "N. Engl. J. Med.",
  volume   =  370,
  number   =  16,
  pages    = "1524--1531",
  month    =  apr,
  year     =  2014,
  keywords = "Staphylococcus;antibiotics;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Gill2005-zg,
  title    = "Insights on evolution of virulence and resistance from the
              complete genome analysis of an early methicillin-resistant
              Staphylococcus aureus strain and a biofilm-producing
              methicillin-resistant Staphylococcus epidermidis strain",
  author   = "Gill, Steven R and Fouts, Derrick E and Archer, Gordon L and
              Mongodin, Emmanuel F and Deboy, Robert T and Ravel, Jacques and
              Paulsen, Ian T and Kolonay, James F and Brinkac, Lauren and
              Beanan, Mauren and Dodson, Robert J and Daugherty, Sean C and
              Madupu, Ramana and Angiuoli, Samuel V and Durkin, A Scott and
              Haft, Daniel H and Vamathevan, Jessica and Khouri, Hoda and
              Utterback, Terry and Lee, Chris and Dimitrov, George and Jiang,
              Lingxia and Qin, Haiying and Weidman, Jan and Tran, Kevin and
              Kang, Kathy and Hance, Ioana R and Nelson, Karen E and Fraser,
              Claire M",
  abstract = "Staphylococcus aureus is an opportunistic pathogen and the major
              causative agent of numerous hospital- and community-acquired
              infections. Staphylococcus epidermidis has emerged as a causative
              agent of infections often associated with implanted medical
              devices. We have sequenced the approximately 2.8-Mb genome of S.
              aureus COL, an early methicillin-resistant isolate, and the
              approximately 2.6-Mb genome of S. epidermidis RP62a, a
              methicillin-resistant biofilm isolate. Comparative analysis of
              these and other staphylococcal genomes was used to explore the
              evolution of virulence and resistance between these two species.
              The S. aureus and S. epidermidis genomes are syntenic throughout
              their lengths and share a core set of 1,681 open reading frames.
              Genome islands in nonsyntenic regions are the primary source of
              variations in pathogenicity and resistance. Gene transfer between
              staphylococci and low-GC-content gram-positive bacteria appears
              to have shaped their virulence and resistance profiles.
              Integrated plasmids in S. epidermidis carry genes encoding
              resistance to cadmium and species-specific LPXTG surface
              proteins. A novel genome island encodes multiple phenol-soluble
              modulins, a potential S. epidermidis virulence factor. S.
              epidermidis contains the cap operon, encoding the polyglutamate
              capsule, a major virulence factor in Bacillus anthracis.
              Additional phenotypic differences are likely the result of single
              nucleotide polymorphisms, which are most numerous in cell
              envelope proteins. Overall differences in pathogenicity can be
              attributed to genome islands in S. aureus which encode
              enterotoxins, exotoxins, leukocidins, and leukotoxins not found
              in S. epidermidis.",
  journal  = "J. Bacteriol.",
  volume   =  187,
  number   =  7,
  pages    = "2426--2438",
  month    =  apr,
  year     =  2005,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Diep2006-mj,
  title    = "Complete genome sequence of {USA300}, an epidemic clone of
              community-acquired meticillin-resistant Staphylococcus aureus",
  author   = "Diep, Binh An and Gill, Steven R and Chang, Richard F and Phan,
              Tiffany Haivan and Chen, Jason H and Davidson, Matthew G and Lin,
              Felice and Lin, Jessica and Carleton, Heather A and Mongodin,
              Emmanuel F and Sensabaugh, George F and Perdreau-Remington,
              Fran{\c c}oise",
  abstract = "BACKGROUND: USA300, a clone of meticillin-resistant
              Staphylococcus aureus, is a major source of community-acquired
              infections in the USA, Canada, and Europe. Our aim was to
              sequence its genome and compare it with those of other strains of
              S aureus to try to identify genes responsible for its distinctive
              epidemiological and virulence properties. METHODS: We ascertained
              the genome sequence of FPR3757, a multidrug resistant USA300
              strain, by random shotgun sequencing, then compared it with the
              sequences of ten other staphylococcal strains. FINDINGS: Compared
              with closely related S aureus, we noted that almost all of the
              unique genes in USA300 clustered in novel allotypes of mobile
              genetic elements. Some of the unique genes are involved in
              pathogenesis, including Panton-Valentine leucocidin and molecular
              variants of enterotoxin Q and K. The most striking feature of the
              USA300 genome is the horizontal acquisition of a novel mobile
              genetic element that encodes an arginine deiminase pathway and an
              oligopeptide permease system that could contribute to growth and
              survival of USA300. We did not detect this element, termed
              arginine catabolic mobile element (ACME), in other S aureus
              strains. We noted a high prevalence of ACME in S epidermidis,
              suggesting not only that ACME transfers into USA300 from S
              epidermidis, but also that this element confers a selective
              advantage to this ubiquitous commensal of the human skin.
              INTERPRETATION: USA300 has acquired mobile genetic elements that
              encode resistance and virulence determinants that could enhance
              fitness and pathogenicity.",
  journal  = "Lancet",
  volume   =  367,
  number   =  9512,
  pages    = "731--739",
  month    =  mar,
  year     =  2006,
  keywords = "Staphylococcus;bacterial comparative
              genomics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Viana2015-wo,
  title     = "A single natural nucleotide mutation alters bacterial pathogen
               host tropism",
  author    = "Viana, David and Comos, Mar{\'\i}a and McAdam, Paul R and Ward,
               Melissa J and Selva, Laura and Guinane, Caitriona M and
               Gonz{\'a}lez-Mu{\~n}oz, Beatriz M and Tristan, Anne and Foster,
               Simon J and Ross Fitzgerald, J and Penad{\'e}s, Jos{\'e} R",
  abstract  = "Jose Penades and colleagues examine host adaptation and
               specificity for Staphylococcus aureus with analysis of the
               whole-genome sequences of strains isolated from humans or
               rabbits. They find that a rabbit-specific clone evolved through
               a human-to-rabbit host jump, enabled by a single mutation in
               dltB.",
  journal   = "Nat. Genet.",
  publisher = "Nature Publishing Group",
  month     =  feb,
  year      =  2015,
  keywords  = "Staphylococcus;colonization;bacerial\_genetics;bacterial
               comparative
               genomics;Staph\_evolutionary\_history;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;GWAS-bacteria;Staph\_evolution\_toxins;Staph-animal-human"
 }

 @ARTICLE{Ward2014-bz,
  title    = "{Time-Scaled} Evolutionary Analysis of the Transmission and
              Antibiotic Resistance Dynamics of Staphylococcus aureus Clonal
              Complex 398",
  author   = "Ward, M J and Gibbons, C L and McAdam, P R and van Bunnik, B A D
              and Girvan, E K and Edwards, G F and Fitzgerald, J R and
              Woolhouse, M E J",
  abstract = "Staphylococcus aureus clonal complex 398 (CC398) is associated
              with disease in humans and livestock, and its origins and
              transmission have generated considerable interest. We performed a
              time-scaled phylogenetic analysis of CC398, including sequenced
              isolates from the United Kingdom (Scotland), along with publicly
              available genomes. Using state-of-the-art methods for mapping
              traits onto phylogenies, we quantified transitions between host
              species to identify sink and source populations for CC398 and
              employed a novel approach to investigate the gain and loss of
              antibiotic resistance in CC398 over time. We identified distinct
              human- and livestock-associated CC398 clades and observed
              multiple transmissions of CC398 from livestock to humans and
              between countries, lending quantitative support to previous
              reports. Of note, we identified a subclade within the
              livestock-associated clade comprised of isolates from hospital
              environments and newborn babies, suggesting that
              livestock-associated CC398 is capable of onward transmission in
              hospitals. In addition, our analysis revealed significant
              differences in the dynamics of resistance to methicillin and
              tetracycline related to contrasting historical patterns of
              antibiotic usage between the livestock industry and human
              medicine. We also identified significant differences in patterns
              of gain and loss of different tetracycline resistance
              determinants, which we ascribe to epistatic interactions between
              the resistance genes and/or differences in the modes of
              inheritance of the resistance determinants.",
  journal  = "Appl. Environ. Microbiol.",
  volume   =  80,
  number   =  23,
  pages    = "7275--7282",
  month    =  dec,
  year     =  2014,
  keywords = "
              antibiotics;Staphylococcus;Staph\_evolutionary\_history;bacterial
              comparative
              genomics;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
 }

 @ARTICLE{Stinear2014-ay,
  title    = "Adaptive Change Inferred from Genomic Population Analysis of the
              {ST93} Epidemic Clone of {Community-Associated} Methicillin
              Resistant Staphylococcus aureus",
  author   = "Stinear, Timothy P. and Holt, Kathryn E. and Chua, Kyra and
              Stepnell, Justin and Tuck, Kellie L. and Coombs, Geoffrey and
              Harrison, Paul Francis and Seemann, Torsten and Howden, Benjamin
              P.",
  abstract = "Community associated methicillin resistant Staphylococcus aureus
              (CA-MRSA) has emerged as a major public health problem around the
              world. In Australia, ST93-IV[2B] is the dominant CA-MRSA clone
              and displays significantly greater virulence than other S.
              aureus. Here we have examined the evolution of ST93 via genomic
              analysis of 12 MSSA and 44 MRSA ST93 isolates, collected from
              around Australia over a 17-year period. Comparative analysis
              revealed a core genome of 2.6 Mb, sharing greater than 99.7\%
              nucleotide identity. The accessory genome was 0.45 Mb and
              comprised additional mobile DNA elements, harboring resistance to
              erythromycin, trimethoprim and tetracycline. Phylogenetic
              inference revealed a molecular clock and suggested that a single
              clone of methicillin susceptible, Panton-Valentine leukocidin
              (PVL) positive, ST93 S. aureus likely spread from North Western
              Australia in the early 1970s, acquiring methicillin resistance at
              least twice in the mid 1990s. We also explored associations
              between genotype and important MRSA phenotypes including
              oxacillin MIC and production of exotoxins ($\alpha$-hemolysin,
              $\delta$-hemolysin, PSM$\alpha$3, and PVL). High-level expression
              of $\alpha$-hemolysin is a signature feature of ST93 and reduced
              expression in eight isolates was readily explained by mutations
              in the agr locus. However, subtle but significant decreases in
              $\delta$-hemolysin were also noted over time that coincided with
              decreasing oxacillin resistance and were independent of agr
              mutations. The evolution of ST93 S. aureus is thus associated
              with a reduction in both exotoxin expression and oxacillin MIC,
              suggesting MRSA ST93 isolates are under pressure for adaptive
              change.",
  journal  = "Genome Biol. Evol.",
  month    =  jan,
  year     =  2014,
  keywords = "
              Staphylococcus;antibiotics;oxacillin;Staph\_evolutionary\_history;bacterial
              comparative
              genomics;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Paterson2015-nr,
  title    = "Capturing the cloud of diversity reveals complexity and
              heterogeneity of {MRSA} carriage, infection and transmission",
  author   = "Paterson, Gavin K and Harrison, Ewan M and Murray, Gemma G R and
              Welch, John J and Warland, James H and Holden, Matthew T G and
              Morgan, Fiona J E and Ba, Xiaoliang and Koop, Gerrit and Harris,
              Simon R and Maskell, Duncan J and Peacock, Sharon J and Herrtage,
              Michael E and Parkhill, Julian and Holmes, Mark A",
  abstract = "Genome sequencing is revolutionizing clinical microbiology and
              our understanding of infectious diseases. Previous studies have
              largely relied on the sequencing of a single isolate from each
              individual. However, it is not clear what degree of bacterial
              diversity exists within, and is transmitted between individuals.
              Understanding this 'cloud of diversity' is key to accurate
              identification of transmission pathways. Here, we report the deep
              sequencing of methicillin-resistant Staphylococcus aureus among
              staff and animal patients involved in a transmission network at a
              veterinary hospital. We demonstrate considerable within-host
              diversity and that within-host diversity may rise and fall over
              time. Isolates from invasive disease contained multiple mutations
              in the same genes, including inactivation of a global regulator
              of virulence and changes in phage copy number. This study
              highlights the need for sequencing of multiple isolates from
              individuals to gain an accurate picture of transmission networks
              and to further understand the basis of pathogenesis.",
  journal  = "Nat. Commun.",
  volume   =  6,
  pages    = "6560",
  year     =  2015,
  keywords = "Staphylococcus;colonization;evolution;phage;bacterial comparative
              genomics;Staph\_evolutionary\_history/staph microbial
              interactions;Staph\_evolutionary\_history;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
 }

 @ARTICLE{Moon2015-ue,
  title    = "Phage-mediated horizontal transfer of a Staphylococcus aureus
              virulence-associated genomic island",
  author   = "Moon, Bo Youn and Park, Joo Youn and Hwang, Sun Yung and
              Robinson, D Ashley and Thomas, Jonathan C and Fitzgerald, J Ross
              and Park, Yong Ho and Seo, Keun Seok",
  abstract = "Staphylococcus aureus is a major pathogen of humans and animals.
              The capacity of S. aureus to adapt to different host species and
              tissue types is strongly influenced by the acquisition of mobile
              genetic elements encoding determinants involved in niche
              adaptation. The genomic islands $\nu$Sa$\alpha$ and
              $\nu$Sa$\beta$ are found in almost all S. aureus strains and are
              characterized by extensive variation in virulence gene content.
              However the basis for the diversity and the mechanism underlying
              mobilization of the genomic islands between strains are
              unexplained. Here, we demonstrated that the genomic island,
              $\nu$Sa$\beta$, encoding an array of virulence factors including
              staphylococcal superantigens, proteases, and leukotoxins, in
              addition to bacteriocins, was transferrable in vitro to human and
              animal strains of multiple S. aureus clones via a resident
              prophage. The transfer of the $\nu$Sa$\beta$ appears to have been
              accomplished by multiple conversions of transducing phage
              particles carrying overlapping segments of the $\nu$Sa$\beta$.
              Our findings solve a long-standing mystery regarding the
              diversification and spread of the genomic island $\nu$Sa$\beta$,
              highlighting the central role of bacteriophages in the pathogenic
              evolution of S. aureus.",
  journal  = "Sci. Rep.",
  volume   =  5,
  pages    = "9784",
  month    =  apr,
  year     =  2015,
  keywords = "Staphylococcus;plasmid;phage;Staph\_evolutionary\_history;Read-lab-shared;MRSA-VRSA-gene\_transfer;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Hsu2015-dp,
  title    = "Evolutionary dynamics of methicillin-resistant Staphylococcus
              aureus within a healthcare system",
  author   = "Hsu, Li-Yang and Harris, Simon R and Chlebowicz, Monika A and
              Lindsay, Jodi A and Koh, Tse-Hsien and Krishnan, Prabha and Tan,
              Thean-Yen and Hon, Pei-Yun and Grubb, Warren B and Bentley,
              Stephen D and Parkhill, Julian and Peacock, Sharon J and Holden,
              Matthew Tg",
  abstract = "BACKGROUND: In the past decade, several countries have seen
              gradual replacement of endemic multi-resistant
              healthcare-associated methicillin-resistant Staphylococcus aureus
              (MRSA) with clones that are more susceptible to antibiotic
              treatment. One example is Singapore, where MRSA ST239, the
              dominant clone since molecular profiling of MRSA began in the
              mid-1980s, has been replaced by ST22 isolates belonging to
              EMRSA-15, a recently emerged pandemic lineage originating from
              Europe. RESULTS: We investigated the population structure of MRSA
              in Singaporean hospitals spanning three decades, using whole
              genome sequencing. Applying Bayesian phylogenetic methods we
              report that prior to the introduction of ST22, the ST239 MRSA
              population in Singapore originated from multiple introductions
              from the surrounding region; it was frequently transferred within
              the healthcare system resulting in a heterogeneous hospital
              population. Following the introduction of ST22 around the
              beginning of the millennium, this clone spread rapidly through
              Singaporean hospitals, supplanting the endemic ST239 population.
              Coalescent analysis revealed that although the genetic diversity
              of ST239 initially decreased as ST22 became more dominant, from
              2007 onwards the genetic diversity of ST239 began to increase
              once more, which was not associated with the emergence of a
              sub-clone of ST239. Comparative genomic analysis of the accessory
              genome of the extant ST239 population identified that the
              Arginine Catabolic Mobile Element arose multiple times, thereby
              introducing genes associated with enhanced skin colonization into
              this population. CONCLUSIONS: Our results clearly demonstrate
              that, alongside clinical practice and antibiotic usage,
              competition between clones also has an important role in driving
              the evolution of nosocomial pathogen populations.",
  journal  = "Genome Biol.",
  volume   =  16,
  number   =  1,
  pages    = "81",
  month    =  apr,
  year     =  2015,
  keywords = "Staphylococcus;evolution;bacterial comparative
              genomics;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Hau2017-mi,
  title    = "Draft Genome Sequences of 50 {Methicillin-Resistant}
              Staphylococcus aureus Sequence Type 5 Isolates Obtained from a
              {U.S}. Hospital",
  author   = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and
              Nicholson, Tracy L",
  abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) can be a
              commensal or pathogen in humans. Pathogenicity and disease are
              related to the acquisition of mobile genetic elements encoding
              virulence and antimicrobial resistance genes. Here, we report
              draft genome sequences for 50 clinical MRSA isolates from humans
              with MRSA-related disease.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  44,
  month    =  nov,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Guinane2010-pb,
  title    = "Evolutionary genomics of Staphylococcus aureus reveals insights
              into the origin and molecular basis of ruminant host adaptation",
  author   = "Guinane, Caitriona M and Ben Zakour, Nouri L and Tormo-Mas, Maria
              A and Weinert, Lucy A and Lowder, Bethan V and Cartwright, Robyn
              A and Smyth, Davida S and Smyth, Cyril J and Lindsay, Jodi A and
              Gould, Katherine A and Witney, Adam and Hinds, Jason and
              Bollback, Jonathan P and Rambaut, Andrew and Penad{\'e}s,
              Jos{\'e} R and Fitzgerald, J Ross",
  abstract = "Phenotypic biotyping has traditionally been used to differentiate
              bacteria occupying distinct ecological niches such as host
              species. For example, the capacity of Staphylococcus aureus from
              sheep to coagulate ruminant plasma, reported over 60 years ago,
              led to the description of small ruminant and bovine S. aureus
              ecovars. The great majority of small ruminant isolates are
              represented by a single, widespread clonal complex (CC133) of S.
              aureus, but its evolutionary origin and the molecular basis for
              its host tropism remain unknown. Here, we provide evidence that
              the CC133 clone evolved as the result of a human to ruminant host
              jump followed by adaptive genome diversification. Comparative
              whole-genome sequencing revealed molecular evidence for host
              adaptation including gene decay and diversification of proteins
              involved in host-pathogen interactions. Importantly, several
              novel mobile genetic elements encoding virulence proteins with
              attenuated or enhanced activity in ruminants were widely
              distributed in CC133 isolates, suggesting a key role in its
              host-specific interactions. To investigate this further, we
              examined the activity of a novel staphylococcal pathogenicity
              island (SaPIov2) found in the great majority of CC133 isolates
              which encodes a variant of the chromosomally encoded von
              Willebrand-binding protein (vWbp(Sov2)), previously demonstrated
              to have coagulase activity for human plasma. Remarkably, we
              discovered that SaPIov2 confers the ability to coagulate ruminant
              plasma suggesting an important role in ruminant disease
              pathogenesis and revealing the origin of a defining phenotype of
              the classical S. aureus biotyping scheme. Taken together, these
              data provide broad new insights into the origin and molecular
              basis of S. aureus ruminant host specificity.",
  journal  = "Genome Biol. Evol.",
  volume   =  2,
  pages    = "454--466",
  month    =  jul,
  year     =  2010,
  keywords = "Staphylococcus;colonization;host-pathogen;bacterial comparative
              genomics;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
 }

 @ARTICLE{Kuroda2001-wn,
  title    = "Whole genome sequencing of meticillin-resistant Staphylococcus
              aureus",
  author   = "Kuroda, M and Ohta, T and Uchiyama, I and Baba, T and Yuzawa, H
              and Kobayashi, I and Cui, L and Oguchi, A and Aoki, K and Nagai,
              Y and Lian, J and Ito, T and Kanamori, M and Matsumaru, H and
              Maruyama, A and Murakami, H and Hosoyama, A and Mizutani-Ui, Y
              and Takahashi, N K and Sawano, T and Inoue, R and Kaito, C and
              Sekimizu, K and Hirakawa, H and Kuhara, S and Goto, S and
              Yabuzaki, J and Kanehisa, M and Yamashita, A and Oshima, K and
              Furuya, K and Yoshino, C and Shiba, T and Hattori, M and
              Ogasawara, N and Hayashi, H and Hiramatsu, K",
  abstract = "BACKGROUND: Staphylococcus aureus is one of the major causes of
              community-acquired and hospital-acquired infections. It produces
              numerous toxins including superantigens that cause unique disease
              entities such as toxic-shock syndrome and staphylococcal scarlet
              fever, and has acquired resistance to practically all
              antibiotics. Whole genome analysis is a necessary step towards
              future development of countermeasures against this organism.
              METHODS: Whole genome sequences of two related S aureus strains
              (N315 and Mu50) were determined by shot-gun random sequencing.
              N315 is a meticillin-resistant S aureus (MRSA) strain isolated in
              1982, and Mu50 is an MRSA strain with vancomycin resistance
              isolated in 1997. The open reading frames were identified by use
              of GAMBLER and GLIMMER programs, and annotation of each was done
              with a BLAST homology search, motif analysis, and protein
              localisation prediction. FINDINGS: The Staphylococcus genome was
              composed of a complex mixture of genes, many of which seem to
              have been acquired by lateral gene transfer. Most of the
              antibiotic resistance genes were carried either by plasmids or by
              mobile genetic elements including a unique resistance island.
              Three classes of new pathogenicity islands were identified in the
              genome: a toxic-shock-syndrome toxin island family, exotoxin
              islands, and enterotoxin islands. In the latter two pathogenicity
              islands, clusters of exotoxin and enterotoxin genes were found
              closely linked with other gene clusters encoding putative
              pathogenic factors. The analysis also identified 70 candidates
              for new virulence factors. INTERPRETATION: The remarkable ability
              of S aureus to acquire useful genes from various organisms was
              revealed through the observation of genome complexity and
              evidence of lateral gene transfer. Repeated duplication of genes
              encoding superantigens explains why S aureus is capable of
              infecting humans of diverse genetic backgrounds, eliciting severe
              immune reactions. Investigation of many newly identified gene
              products, including the 70 putative virulence factors, will
              greatly improve our understanding of the biology of staphylococci
              and the processes of infectious diseases caused by S aureus.",
  journal  = "Lancet",
  volume   =  357,
  number   =  9264,
  pages    = "1225--1240",
  month    =  apr,
  year     =  2001,
  keywords = "antibiotics;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Roach2015-ns,
  title    = "A Year of Infection in the Intensive Care Unit: Prospective Whole
              Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic
              Transmissions and Novel Microbiota",
  author   = "Roach, David J and Burton, Joshua N and Lee, Choli and
              Stackhouse, Bethany and Butler-Wu, Susan M and Cookson, Brad T
              and Shendure, Jay and Salipante, Stephen J",
  abstract = "Bacterial whole genome sequencing holds promise as a disruptive
              technology in clinical microbiology, but it has not yet been
              applied systematically or comprehensively within a clinical
              context. Here, over the course of one year, we performed
              prospective collection and whole genome sequencing of nearly all
              bacterial isolates obtained from a tertiary care hospital's
              intensive care units (ICUs). This unbiased collection of 1,229
              bacterial genomes from 391 patients enables detailed exploration
              of several features of clinical pathogens. A sizable fraction of
              isolates identified as clinically relevant corresponded to
              previously undescribed species: 12\% of isolates assigned a
              species-level classification by conventional methods actually
              qualified as distinct, novel genomospecies on the basis of
              genomic similarity. Pan-genome analysis of the most frequently
              encountered pathogens in the collection revealed substantial
              variation in pan-genome size (1,420 to 20,432 genes) and the rate
              of gene discovery (1 to 152 genes per isolate sequenced).
              Surprisingly, although potential nosocomial transmission of
              actively surveilled pathogens was rare, 8.7\% of isolates
              belonged to genomically related clonal lineages that were present
              among multiple patients, usually with overlapping hospital
              admissions, and were associated with clinically significant
              infection in 62\% of patients from which they were recovered.
              Multi-patient clonal lineages were particularly evident in the
              neonatal care unit, where seven separate Staphylococcus
              epidermidis clonal lineages were identified, including one
              lineage associated with bacteremia in 5/9 neonates. Our study
              highlights key differences in the information made available by
              conventional microbiological practices versus whole genome
              sequencing, and motivates the further integration of microbial
              genome sequencing into routine clinical care.",
  journal  = "PLoS Genet.",
  volume   =  11,
  number   =  7,
  pages    = "e1005413",
  month    =  jul,
  year     =  2015,
  keywords = "Staphylococcus;pangenome;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Burd2014-nc,
  title     = "Development of oxacillin resistance in a patient with recurrent
               Staphylococcus aureus bacteremia",
  author    = "Burd, Eileen M and Alam, Mohammad Tauqeer and Passalacqua, Karla
               D and Kalokhe, Ameeta S and Eaton, Molly E and Satola, Sarah W
               and Kraft, Colleen S and Read, Timothy D",
  abstract  = "Whole-genome sequencing was used to compare longitudinal
               isolates of Staphylococcus aureus that developed resistance to
               oxacillin (MIC up to 16 $\mu$g/ml). The mecA gene was absent. A
               novel 5-bp TATCC frameshift insertion in a gene encoding an ABC
               transporter similar to that of the teichoic acid translocation
               ATP-binding protein TagH and a 3-bp GCT nonframeshift insertion
               in the pdhA pyruvate dehydrogenase gene were detected in the
               oxacillin-resistant isolates.",
  journal   = "J. Clin. Microbiol.",
  publisher = "American Society for Microbiology",
  volume    =  52,
  number    =  8,
  pages     = "3114--3117",
  month     =  aug,
  year      =  2014,
  keywords  = "oxacillin;antibiotics;Staphylococcus;My
               Publications;My\_Peer\_reviewed;Staphylococcus\_aureus\_genome\_papers"
 }

 % The entry below contains non-ASCII chars that could not be converted
 % to a LaTeX equivalent.
 @ARTICLE{Alam2014-fv,
  title     = "Dissecting vancomycin-intermediate resistance in Staphylococcus
               aureus using genome-wide association",
  author    = "Alam, Md Tauqeer and Petit, 3rd, Robert A and Crispelll, 3rd,
               Emily K and Thornton, Timothy A and Conneely, Karen N and Jiang,
               Yunxuan and Satola, Sarah W and Read, Timothy D",
  abstract  = "Vancomycin-intermediate Staphylococcus aureus (VISA) is
               currently defined as having minimal inhibitory concentration
               (MIC) of 4-8 µg/ml. VISA evolves through changes in multiple
               genetic loci with at least 16 candidate genes identified in
               clinical and in vitro-selected VISA strains. We report a
               whole-genome comparative analysis of 49 vancomycin-sensitive S.
               aureus and 26 VISA strains. Resistance to vancomycin was
               determined by broth microdilution, Etest, and population
               analysis profile-area under the curve (PAP-AUC). Genome-wide
               association studies (GWAS) of 55,977 single-nucleotide
               polymorphisms identified in one or more strains found one highly
               significant association (P = 8.78 E-08) between a nonsynonymous
               mutation at codon 481 (H481) of the rpoB gene and increased
               vancomycin MIC. Additionally, we used a database of public S.
               aureus genome sequences to identify rare mutations in candidate
               genes associated with VISA. On the basis of these data, we
               proposed a preliminary model called ECM+RMCG for the VISA
               phenotype as a benchmark for future efforts. The model predicted
               VISA based on the presence of a rare mutation in a set of
               candidate genes (walKR, vraSR, graSR, and agrA) and/or three
               previously experimentally verified mutations (including the rpoB
               H481 locus) with an accuracy of 81\% and a sensitivity of 73\%.
               Further, the level of resistance measured by both Etest and
               PAP-AUC regressed positively with the number of mutations
               present in a strain. This study demonstrated 1) the power of
               GWAS for identifying common genetic variants associated with
               antibiotic resistance in bacteria and 2) that rare mutations in
               candidate gene, identified using large genomic data sets, can
               also be associated with resistance phenotypes.",
  journal   = "Genome Biol. Evol.",
  publisher = "Oxford University Press",
  volume    =  6,
  number    =  5,
  pages     = "1174--1185",
  month     =  apr,
  year      =  2014,
  keywords  = "bacteria; genomics; phylogeny; whole-genome
               sequencing;Staphylococcus;confirmed\_SA-resistance-mutation;My
               Publications;antibiotcs-evolution-fitness;My\_Peer\_reviewed;Staphylococcus\_aureus\_genome\_papers;GWAS-bacteria"
 }

 @ARTICLE{Laabei2014-tg,
  title     = "Predicting the virulence of {MRSA} from its genome sequence",
  author    = "Laabei, Maisem and Recker, Mario and Rudkin, Justine K and
               Aldeljawi, Mona and Gulay, Zeynep and Sloan, Tim J and Williams,
               Paul and Endres, Jennifer L and Bayles, Kenneth W and Fey, Paul
               D and Yajjala, Vijaya Kumar and Widhelm, Todd and Hawkins, Erica
               and Lewis, Katie and Parfett, Sara and Scowen, Lucy and Peacock,
               Sharon J and Holden, Matthew and Wilson, Daniel and Read,
               Timothy D and van den Elsen, Jean and Priest, Nicholas K and
               Feil, Edward J and Hurst, Laurence D and Josefsson, Elisabet and
               Massey, Ruth C",
  abstract  = "Microbial virulence is a complex and often multifactorial
               phenotype, intricately linked to a pathogen's evolutionary
               trajectory. Toxicity, the ability to destroy host cell
               membranes, and adhesion, the ability to adhere to human tissues,
               are the major virulence factors of many bacterial pathogens,
               including Staphylococcus aureus. Here, we assayed the toxicity
               and adhesiveness of 90 MRSA (methicillin resistant S. aureus)
               isolates and found that while there was remarkably little
               variation in adhesion, toxicity varied by over an order of
               magnitude between isolates, suggesting different evolutionary
               selection pressures acting on these two traits. We performed a
               genome-wide association study (GWAS) and identified a large
               number of loci, as well as a putative network of epistatically
               interacting loci, that significantly associated with toxicity.
               Despite this apparent complexity in toxicity regulation, a
               predictive model based on a set of significant single nucleotide
               polymorphisms (SNPs) and insertion and deletions events (indels)
               showed a high degree of accuracy in predicting an isolate's
               toxicity solely from the genetic signature at these sites. Our
               results thus highlight the potential of using sequence data to
               determine clinically relevant parameters and have further
               implications for understanding the microbial virulence of this
               opportunistic pathogen.",
  journal   = "Genome Res.",
  publisher = "Cold Spring Harbor Lab",
  volume    =  24,
  number    =  5,
  pages     = "839--849",
  month     =  may,
  year      =  2014,
  keywords  = "bacerial\_genetics;Staphylococcus;toxicity;My
               Publications;My\_Peer\_reviewed;Read-lab-shared;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers;GWAS-bacteria;Staph\_evolution\_toxins"
 }

 @ARTICLE{Passalacqua2012-yq,
  title     = "A mutation in the {PP2C} phosphatase gene in a Staphylococcus
               aureus {USA300} clinical isolate with reduced susceptibility to
               vancomycin and daptomycin",
  author    = "Passalacqua, Karla D and Satola, Sarah W and Crispell, Emily K
               and Read, Timothy D",
  journal   = "Antimicrob. Agents Chemother.",
  publisher = "American Society for Microbiology",
  volume    =  56,
  number    =  10,
  pages     = "5212--5223",
  year      =  2012,
  keywords  = "Staphylococcus;My
               Publications;imported\_from\_papers\_14Nov2013;My\_Peer\_reviewed;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Nubel2010-gs,
  title    = "A timescale for evolution, population expansion, and spatial
              spread of an emerging clone of methicillin-resistant
              Staphylococcus aureus",
  author   = "N{\"u}bel, Ulrich and Dordel, Janina and Kurt, Kevin and
              Strommenger, Birgit and Westh, Henrik and Shukla, Sanjay K and
              Zemlickov{\'a}, Helena and Leblois, Rapha{\"e}l and Wirth,
              Thierry and Jombart, Thibaut and Balloux, Fran{\c c}ois and
              Witte, Wolfgang",
  abstract = "Due to the lack of fossil evidence, the timescales of bacterial
              evolution are largely unknown. The speed with which genetic
              change accumulates in populations of pathogenic bacteria,
              however, is a key parameter that is crucial for understanding the
              emergence of traits such as increased virulence or antibiotic
              resistance, together with the forces driving pathogen spread.
              Methicillin-resistant Staphylococcus aureus (MRSA) is a common
              cause of hospital-acquired infections. We have investigated an
              MRSA strain (ST225) that is highly prevalent in hospitals in
              Central Europe. By using mutation discovery at 269 genetic loci
              (118,804 basepairs) within an international isolate collection,
              we ascertained extremely low diversity among European ST225
              isolates, indicating that a recent population bottleneck had
              preceded the expansion of this clone. In contrast, US isolates
              were more divergent, suggesting they represent the ancestral
              population. While diversity was low, however, our results
              demonstrate that the short-term evolutionary rate in this natural
              population of MRSA resulted in the accumulation of measurable DNA
              sequence variation within two decades, which we could exploit to
              reconstruct its recent demographic history and the spatiotemporal
              dynamics of spread. By applying Bayesian coalescent methods on
              DNA sequences serially sampled through time, we estimated that
              ST225 had diverged since approximately 1990 (1987 to 1994), and
              that expansion of the European clade began in 1995 (1991 to
              1999), several years before the new clone was recognized.
              Demographic analysis based on DNA sequence variation indicated a
              sharp increase of bacterial population size from 2001 to 2004,
              which is concordant with the reported prevalence of this strain
              in several European countries. A detailed ancestry-based
              reconstruction of the spatiotemporal dispersal dynamics suggested
              a pattern of frequent transmission of the ST225 clone among
              hospitals within Central Europe. In addition, comparative
              genomics indicated complex bacteriophage dynamics.",
  journal  = "PLoS Pathog.",
  volume   =  6,
  number   =  4,
  pages    = "e1000855",
  month    =  apr,
  year     =  2010,
  keywords = "Staphylococcus;evolution;bacterial comparative
              genomics;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Harris2013-mf,
  title     = "Whole-genome sequencing for analysis of an outbreak of
               meticillin-resistant Staphylococcus aureus: a descriptive study",
  author    = "Harris, Simon R and Cartwright, Edward J P and T{\"o}r{\"o}k, M
               Est{\'e}e and Holden, Matthew T G and Brown, Nicholas M and
               Ogilvy-Stuart, Amanda L and Ellington, Matthew J and Quail,
               Michael A and Bentley, Stephen D and Parkhill, Julian and
               Peacock, Sharon J",
  abstract  = "BACKGROUND: The emergence of meticillin-resistant Staphylococcus
               aureus (MRSA) that can persist in the community and replace
               existing hospital-adapted lineages of MRSA means that it is
               necessary to understand transmission dynamics in terms of
               hospitals and the community as one entity. We assessed the use
               of whole-genome sequencing to enhance detection of MRSA
               transmission between these settings. METHODS: We studied a
               putative MRSA outbreak on a special care baby unit (SCBU) at a
               National Health Service Foundation Trust in Cambridge, UK. We
               used whole-genome sequencing to validate and expand findings
               from an infection-control team who assessed the outbreak through
               conventional analysis of epidemiological data and antibiogram
               profiles. We sequenced isolates from all colonised patients in
               the SCBU, and sequenced MRSA isolates from patients in the
               hospital or community with the same antibiotic susceptibility
               profile as the outbreak strain. FINDINGS: The hospital
               infection-control team identified 12 infants colonised with MRSA
               in a 6 month period in 2011, who were suspected of being linked,
               but a persistent outbreak could not be confirmed with
               conventional methods. With whole-genome sequencing, we
               identified 26 related cases of MRSA carriage, and showed
               transmission occurred within the SCBU, between mothers on a
               postnatal ward, and in the community. The outbreak MRSA type was
               a new sequence type (ST) 2371, which is closely related to ST22,
               but contains genes encoding Panton-Valentine leucocidin.
               Whole-genome sequencing data were used to propose and confirm
               that MRSA carriage by a staff member had allowed the outbreak to
               persist during periods without known infection on the SCBU and
               after a deep clean. INTERPRETATION: Whole-genome sequencing
               holds great promise for rapid, accurate, and comprehensive
               identification of bacterial transmission pathways in hospital
               and community settings, with concomitant reductions in
               infections, morbidity, and costs. FUNDING: UK Clinical Research
               Collaboration Translational Infection Research Initiative,
               Wellcome Trust, Health Protection Agency, and the National
               Institute for Health Research Cambridge Biomedical Research
               Centre.",
  journal   = "Lancet Infect. Dis.",
  publisher = "Elsevier",
  volume    =  13,
  number    =  2,
  pages     = "130--136",
  month     =  feb,
  year      =  2013,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Stegger2012-hy,
  title     = "Genome sequence of Staphylococcus aureus strain 11819-97, an
               {ST80-IV} European community-acquired methicillin-resistant
               isolate",
  author    = "Stegger, Marc and Price, Lance B and Larsen, Anders R and
               Gillece, John D and Waters, Andrew E and Skov, Robert and
               Andersen, Paal S",
  abstract  = "The European methicillin-resistant Staphylococcus aureus (MRSA)
               clone ST80-IV has historically dominated community-associated
               infections in major parts of Europe and is a lineage strongly
               linked to skin and soft tissue infections. Here, we report the
               genome sequence of an ST80-IV representative, 11819-97, isolated
               from a skin infection in Denmark in 1997.",
  journal   = "J. Bacteriol.",
  publisher = "Am Soc Microbiol",
  volume    =  194,
  number    =  6,
  pages     = "1625--1626",
  month     =  mar,
  year      =  2012,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Treangen2014-oh,
  title     = "Complete Genome Sequence of the Quality Control Strain
               Staphylococcus aureus subsp. aureus {ATCC} 25923",
  author    = "Treangen, Todd J and Maybank, Rosslyn A and Enke, Sana and
               Friss, Mary Beth and Diviak, Lynn F and Karaolis, David K R and
               Koren, Sergey and Ondov, Brian and Phillippy, Adam M and
               Bergman, Nicholas H and Rosovitz, M J",
  abstract  = "Staphylococcus aureus subsp. aureus ATCC 25923 is commonly used
               as a control strain for susceptibility testing to antibiotics
               and as a quality control strain for commercial products. We
               present the completed genome sequence for the strain, consisting
               of the chromosome and a 27.5-kb plasmid.",
  journal   = "Genome Announc.",
  publisher = "Am Soc Microbiol",
  volume    =  2,
  number    =  6,
  month     =  nov,
  year      =  2014,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Price2014-jt,
  title     = "Whole-genome sequencing shows that patient-to-patient
               transmission rarely accounts for acquisition of Staphylococcus
               aureus in an intensive care unit",
  author    = "Price, James R and Golubchik, Tanya and Cole, Kevin and Wilson,
               Daniel J and Crook, Derrick W and Thwaites, Guy E and Bowden,
               Rory and Walker, A Sarah and Peto, Timothy E A and Paul, John
               and Llewelyn, Martin J",
  abstract  = "BACKGROUND: Strategies to prevent Staphylococcus aureus
               infection in hospitals focus on patient-to-patient transmission.
               We used whole-genome sequencing to investigate the role of
               colonized patients as the source of new S. aureus acquisitions,
               and the reliability of identifying patient-to-patient
               transmission using the conventional approach of spa typing and
               overlapping patient stay. METHODS: Over 14 months, all
               unselected patients admitted to an adult intensive care unit
               (ICU) were serially screened for S. aureus. All available
               isolates (n = 275) were spa typed and underwent whole-genome
               sequencing to investigate their relatedness at high resolution.
               RESULTS: Staphylococcus aureus was carried by 185 of 1109
               patients sampled within 24 hours of ICU admission (16.7\%); 59
               (5.3\%) patients carried methicillin-resistant S. aureus (MRSA).
               Forty-four S. aureus (22 MRSA) acquisitions while on ICU were
               detected. Isolates were available for genetic analysis from 37
               acquisitions. Whole-genome sequencing indicated that 7 of these
               37 (18.9\%) were transmissions from other colonized patients.
               Conventional methods (spa typing combined with overlapping
               patient stay) falsely identified 3 patient-to-patient
               transmissions (all MRSA) and failed to detect 2 acquisitions and
               4 transmissions (2 MRSA). CONCLUSIONS: Only a minority of S.
               aureus acquisitions can be explained by patient-to-patient
               transmission. Whole-genome sequencing provides the resolution to
               disprove transmission events indicated by conventional methods
               and also to reveal otherwise unsuspected transmission events.
               Whole-genome sequencing should replace conventional methods for
               detection of nosocomial S. aureus transmission.",
  journal   = "Clin. Infect. Dis.",
  publisher = "cid.oxfordjournals.org",
  volume    =  58,
  number    =  5,
  pages     = "609--618",
  month     =  mar,
  year      =  2014,
  keywords  = "Staphylococcus aureus transmission; adult; intensive care unit;
               spa typing; whole-genome
               sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Sass2012-jk,
  title     = "Genome sequence of Staphylococcus aureus {VC40}, a
               vancomycin-and daptomycin-resistant strain, to study the
               genetics of development of resistance to currently applied
               last-resort antibiotics",
  author    = "Sass, Peter and Berscheid, Anne and Jansen, Andrea and
               Oedenkoven, Marion and Szekat, Christiane and Strittmatter, Axel
               and Gottschalk, Gerhard and Bierbaum, Gabriele",
  abstract  = "ABSTRACT The increasing emergence of multidrug-resistant
               Staphylococcus aureus is a problem of global importance. Here,
               we report the genome of S. aureus VC40, which is resistant to
               the last-resort antibiotics vancomycin and daptomycin. Its
               genome sequence ...",
  journal   = "J. Bacteriol.",
  publisher = "Am Soc Microbiol",
  volume    =  194,
  number    =  8,
  pages     = "2107--2108",
  year      =  2012,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Ip2014-mq,
  title     = "Draft Genome Sequence of {Methicillin-Resistant} Staphylococcus
               aureus {CUHK\_188} ({ST188)}, a Health {Care-Associated}
               Bacteremic Isolate from Hong Kong",
  author    = "Ip, Margaret and Wang, Zheng and Lam, Wai Yip and Zhou, Haokui
               and Tsui, Stephen",
  abstract  = "We report the draft genome sequence of a methicillin-resistant
               Staphylococcus aureus strain designated CUHK\_188, isolated from
               a bacteremic patient undergoing treatment at a university
               teaching hospital in Hong Kong. This strain belongs to sequence
               type 188 (ST188), with spa type t189 and staphylococcal cassette
               chromosome mec type V.",
  journal   = "Genome Announc.",
  publisher = "Am Soc Microbiol",
  volume    =  2,
  number    =  2,
  month     =  apr,
  year      =  2014,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Huang2012-zq,
  title     = "Complete genome sequence of Staphylococcus aureus M013, a
               pvl-positive, {ST59-SCCmec} type {V} strain isolated in Taiwan",
  author    = "Huang, Tzu-Wen and Chen, Feng-Jui and Miu, Wei-Chieh and Liao,
               Tsai-Lien and Lin, Ann-Chi and Huang, I-Wen and Wu, Keh-Ming and
               Tsai, Shih-Feng and Chen, Ying-Tsong and Lauderdale, Tsai-Ling
               Yang",
  abstract  = "We report the complete genome sequence of M013, a representative
               strain of a pvl-positive, sequence type 59-staphylococcal
               cassette chromosome mec type V (ST59-SCCmec type V)
               community-associated methicillin-resistant Staphylococcus aureus
               (CA-MRSA) clone in Taiwan. Comparison of M013 with the genomes
               of two CA-MRSA strains in the United States revealed major
               differences in the regions covering several genomic islands and
               prophages.",
  journal   = "J. Bacteriol.",
  publisher = "Am Soc Microbiol",
  volume    =  194,
  number    =  5,
  pages     = "1256--1257",
  month     =  mar,
  year      =  2012,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Bouchard2012-ud,
  title     = "Genome sequence of Staphylococcus aureus Newbould 305, a strain
               associated with mild bovine mastitis",
  author    = "Bouchard, Damien and Peton, Vincent and Almeida, Sintia and Le
               Mar{\'e}chal, Caroline and Miyoshi, Anderson and Azevedo, Vasco
               and Berkova, Nadia and Rault, Lucie and Fran{\c c}ois, Patrice
               and Schrenzel, Jacques and Even, Sergine and Hernandez, David
               and Le Loir, Yves",
  abstract  = "Staphylococcus aureus is a major etiological agent of mastitis
               in ruminants. We report here the genome sequence of bovine
               strain Newbould 305, isolated in the 1950s in a case of bovine
               mastitis and now used as a model strain able to reproducibly
               induce chronic mastitis in cows.",
  journal   = "J. Bacteriol.",
  publisher = "Am Soc Microbiol",
  volume    =  194,
  number    =  22,
  pages     = "6292--6293",
  month     =  nov,
  year      =  2012,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Schijffelen2013-dh,
  title     = "Whole genome analysis of epidemiologically closely related
               Staphylococcus aureus isolates",
  author    = "Schijffelen, Maarten and Konstantinov, Sergey R and Lina,
               G{\'e}rard and Spiliopoulou, Iris and van Duijkeren, Engeline
               and Brouwer, Ellen C and Fluit, Ad C",
  abstract  = "The change of the bacteria from colonizers to pathogens is
               accompanied by a drastic change in expression profiles. These
               changes may be due to environmental signals or to mutational
               changes. We therefore compared the whole genome sequences of
               four sets of S. aureus isolates. Three sets were from the same
               patients. The isolates of each pair (S1800/S1805, S2396/S2395,
               S2398/S2397, an isolate from colonization and an isolate from
               infection, respectively) were obtained within <30 days of each
               other and the isolate from infection caused skin infections. The
               isolates were then compared for differences in gene content and
               SNPs. In addition, a set of isolates from a colonized pig and a
               farmer from the same farm at the same time (S0462 and S0460)
               were analyzed. The isolates pair S1800/S1805 showed a difference
               in a prophage, but these are easily lost or acquired. However,
               S1805 contained an integrative conjugative element not present
               in S1800. In addition, 92 SNPs were present in a variety of
               genes and the isolates S1800 and S1805 were not considered a
               pair. Between S2395/S2396 two SNPs were present: one was in an
               intergenic region and one was a synonymous mutation in a
               putative membrane protein. Between S2397/S2398 only one
               synonymous mutation in a putative lipoprotein was found. The two
               farm isolates were very similar and showed 12 SNPs in genes that
               belong to a number of different functional categories. However,
               we cannot pinpoint any gene that explains the change from
               carrier status to infection. The data indicate that differences
               between the isolate from infection and the colonizing isolate
               for S2395/S2396 and S2397/S2398 exist as well as between
               isolates from different hosts, but S1800/S1805 are not clonal.",
  journal   = "PLoS One",
  publisher = "dx.plos.org",
  volume    =  8,
  number    =  10,
  pages     = "e78340",
  month     =  oct,
  year      =  2013,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Thomas2012-gq,
  title     = "Draft genome sequences of Staphylococcus aureus sequence type 34
               ({ST34}) and {ST42} hybrids",
  author    = "Thomas, Jonathan C and Godfrey, Paul A and Feldgarden, Michael
               and Robinson, D Ashley",
  abstract  = "Staphylococcus aureus is a major cause of
               antimicrobial-resistant infections of humans. Hybrids of S.
               aureus, which originate from large-scale chromosomal
               recombinations between parents of distinct genetic backgrounds,
               are of interest from clinical and evolutionary perspectives. We
               present draft genome sequences of two S. aureus hybrids of
               sequence type 34 (ST34) and ST42.",
  journal   = "J. Bacteriol.",
  publisher = "Am Soc Microbiol",
  volume    =  194,
  number    =  10,
  pages     = "2740--2741",
  month     =  may,
  year      =  2012,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Larner-Svensson2013-jf,
  title     = "Complete Genome Sequence of Staphylococcus aureus Strain M1, a
               Unique {t024-ST8-IVa} Danish {Methicillin-Resistant} S. aureus
               Clone",
  author    = "Larner-Svensson, Hanna and Worning, Peder and Bartels, Mette D
               and Hestbjerg Hansen, Lars and Boye, Kit and Westh, Henrik",
  abstract  = "We report the genome sequence, in five contigs, of a
               methicillin-resistant Staphylococcus aureus isolate designated
               M1. This clinical isolate was from the index patient of a
               methicillin-resistant Staphylococcus aureus (MRSA) outbreak in
               Copenhagen, Denmark, that started in 2003. This strain is
               sequence type 8 (ST8), spa type t024, and staphylococcal
               cassette chromosome mec element (SCCmec) type IVa.",
  journal   = "Genome Announc.",
  publisher = "Am Soc Microbiol",
  volume    =  1,
  number    =  3,
  month     =  jun,
  year      =  2013,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Prabhakara2013-hi,
  title     = "Genome sequencing unveils a novel sea enterotoxin-carrying {PVL}
               phage in Staphylococcus aureus {ST772} from India",
  author    = "Prabhakara, Sushma and Khedkar, Supriya and Shambat, Srikanth
               Mairpady and Srinivasan, Rajalakshmi and Basu, Atanu and
               Norrby-Teglund, Anna and Seshasayee, Aswin Sai Narain and
               Arakere, Gayathri",
  abstract  = "Staphylococcus aureus is a major human pathogen, first
               recognized as a leading cause of hospital-acquired infections.
               Community-associated S. aureus (CA-SA) pose a greater threat due
               to increase in severity of infection and disease among children
               and healthy adults. CA-SA strains in India are genetically
               diverse, among which is the sequence type (ST) 772, which has
               now spread to Australia, Europe and Japan. Towards understanding
               the genetic characteristics of ST772, we obtained draft genome
               sequences of five relevant clinical isolates and studied the
               properties of their PVL-carrying prophages, whose presence is a
               defining hallmark of CA-SA. We show that this is a novel
               prophage, which carries the structural genes of the hlb-carrying
               prophage and includes the sea enterotoxin. This architecture
               probably emerged early within the ST772 lineage, at least in
               India. The sea gene, unique to ST772 PVL, despite having
               promoter sequence characteristics typical of low expression,
               appears to be highly expressed during early phase of growth in
               laboratory conditions. We speculate that this might be a
               consequence of its novel sequence context. The crippled nature
               of the hlb-converting prophage in ST772 suggests that widespread
               mobility of the sea enterotoxin might be a selective force
               behind its 'transfer' to the PVL prophage. Wild type ST772
               strains induced strong proliferative responses as well as high
               cytotoxic activity against neutrophils, likely mediated by
               superantigen SEA and the PVL toxin respectively. Both
               proliferation and cytotoxicity were markedly reduced in a cured
               ST772 strain indicating the impact of the phage on virulence.
               The presence of SEA alongside the genes for the immune
               system-modulating PVL toxin may contribute to the success and
               virulence of ST772.",
  journal   = "PLoS One",
  publisher = "dx.plos.org",
  volume    =  8,
  number    =  3,
  pages     = "e60013",
  month     =  mar,
  year      =  2013,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Biswas2015-xv,
  title     = "Draft Genome Sequences of Five Clinical {Methicillin-Resistant}
               Staphylococcus aureus Isolates and a {Methicillin-Resistant}
               Staphylococcus epidermidis Isolate",
  author    = "Biswas, Rajesh Kumar and Kock, Marleen M and Adelowotan, Toyin
               and Strasheim, Wilhelmina and Mahomed, Tanweer Goolam and
               Salawu, Adeola and Ehlers, Marthie M",
  abstract  = "We report the complete draft genome sequences of five
               individually isolated strains of methicillin-resistant
               Staphylococcus aureus (MRSA) and a Staphylococcus epidermidis
               strain. These clinically important isolates have staphylococcal
               cassette chromosome mec type A, while Panton-Valentine
               leukocidin (PVL) toxin coding genes were present in MRSA
               isolates only.",
  journal   = "Genome Announc.",
  publisher = "Am Soc Microbiol",
  volume    =  3,
  number    =  4,
  month     =  jul,
  year      =  2015,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Sassi2014-nj,
  title     = "Draft Genome Sequence of Staphylococcus aureus subsp. aureus
               Strain {HG003}, an {NCTC8325} Derivative",
  author    = "Sassi, Mohamed and Felden, Brice and Augagneur, Yoann",
  abstract  = "We report the draft genome sequence of a Staphylococcus aureus
               NCTC8325 derivative, strain HG003. HG003 contains functional
               global regulators rsbU and tcaR and is therefore considered as a
               reference for studies of regulation and virulence. The genome is
               composed of 2,797,898 bp and will be essential for subsequent
               RNAseq analysis.",
  journal   = "Genome Announc.",
  publisher = "Am Soc Microbiol",
  volume    =  2,
  number    =  4,
  month     =  aug,
  year      =  2014,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Daligault2014-kl,
  title     = "Genome Assembly of {Methicillin-Resistant} Quality Control
               Strain Staphylococcus aureus {CDC73-57501} ({ATCC} 29247)",
  author    = "Daligault, H E and Davenport, K W and Minogue, T D and
               Bishop-Lilly, K A and Broomall, S M and Bruce, D C and Chain, P
               S and Coyne, S R and Freitas, T and Frey, K G and Gibbons, H S
               and Jaissle, J and Lo, C-C and Meincke, L and Munk, A C and
               Redden, C L and Rosenzweig, C N and Johnson, S L",
  abstract  = "Staphylococcus aureus is a major cause of bacterial infections
               in the United States, with high percentages of serious
               infections resistant to a variety of $\beta$-lactam antibiotics.
               Here, we present the scaffolded genome assembly into 16 contigs
               of S. aureus CDC73-57501 (ATCC 29247), a methicillin-resistant
               quality control strain.",
  journal   = "Genome Announc.",
  publisher = "Am Soc Microbiol",
  volume    =  2,
  number    =  5,
  month     =  oct,
  year      =  2014,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Stevens2015-lt,
  title     = "Complete and Assembled Genome Sequence of Staphylococcus aureus
               {RKI4}, a {Food-Poisoning} Strain Exhibiting a Novel S. aureus
               Pathogenicity Island Carrying seb",
  author    = "Stevens, Marc J A and Stephan, Roger and Johler, Sophia",
  abstract  = "The genome of Staphylococcus aureus RKI4, a strain isolated from
               feces of a patient in a case of staphylococcal food poisoning,
               was sequenced using combined Illumina and single-molecule
               real-time sequencing. Hierarchical assembly of the genome
               resulted in a 2,725,654-bp chromosome and a 17,905-bp mobile
               genetic element.",
  journal   = "Genome Announc.",
  publisher = "Am Soc Microbiol",
  volume    =  3,
  number    =  4,
  month     =  jul,
  year      =  2015,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Harrison2013-vq,
  title     = "Whole genome sequencing identifies zoonotic transmission of
               {MRSA} isolates with the novel mecA homologue mecC",
  author    = "Harrison, Ewan M and Paterson, Gavin K and Holden, Matthew T G
               and Larsen, Jesper and Stegger, Marc and Larsen, Anders Rhod and
               Petersen, Andreas and Skov, Robert L and Christensen, Judit
               Marta and Bak Zeuthen, Anne and Heltberg, Ole and Harris, Simon
               R and Zadoks, Ruth N and Parkhill, Julian and Peacock, Sharon J
               and Holmes, Mark A",
  abstract  = "Several methicillin-resistant Staphylococcus aureus (MRSA)
               lineages that carry a novel mecA homologue (mecC) have recently
               been described in livestock and humans. In Denmark, two
               independent human cases of mecC-MRSA infection have been linked
               to a livestock reservoir. We investigated the molecular
               epidemiology of the associated MRSA isolates using whole genome
               sequencing (WGS). Single nucleotide polymorphisms (SNP) were
               defined and compared to a reference genome to place the isolates
               into a phylogenetic context. Phylogenetic analysis revealed two
               distinct farm-specific clusters comprising isolates from the
               human case and their own livestock, whereas human and animal
               isolates from the same farm only differed by a small number of
               SNPs, which supports the likelihood of zoonotic transmission.
               Further analyses identified a number of genes and mutations that
               may be associated with host interaction and virulence. This
               study demonstrates that mecC-MRSA ST130 isolates are capable of
               transmission between animals and humans, and underscores the
               potential of WGS in epidemiological investigations and source
               tracking of bacterial infections.",
  journal   = "EMBO Mol. Med.",
  publisher = "embomolmed.embopress.org",
  volume    =  5,
  number    =  4,
  pages     = "509--515",
  month     =  apr,
  year      =  2013,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
 }

 @ARTICLE{Nair2011-sm,
  title     = "Whole-genome sequencing of Staphylococcus aureus strain
               {RN4220}, a key laboratory strain used in virulence research,
               identifies mutations that affect not only virulence factors but
               also the fitness of the strain",
  author    = "Nair, Dhanalakshmi and Memmi, Guido and Hernandez, David and
               Bard, Jonathan and Beaume, Marie and Gill, Steven and Francois,
               Patrice and Cheung, Ambrose L",
  abstract  = "ABSTRACT Staphylococcus aureus RN4220, a cloning intermediate,
               is sometimes used in virulence, resistance, and metabolic
               studies. Using whole- genome sequencing, we showed that RN4220
               differs from NCTC8325 and contains a number of genetic
               polymorphisms ...",
  journal   = "J. Bacteriol.",
  publisher = "Am Soc Microbiol",
  volume    =  193,
  number    =  9,
  pages     = "2332--2335",
  year      =  2011,
  keywords  = "Staphylococcus;imported\_from\_papers\_14Nov2013;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Li2011-rd,
  title     = "Complete genome sequence of Staphylococcus aureus T0131, an
               {ST239-MRSA-SCCmec} type {III} clone isolated in China",
  author    = "Li, Yang and Cao, Boyang and Zhang, Yongfu and Zhou, Jiali and
               Yang, Bin and Wang, Lei",
  abstract  = "We report here the complete genome sequence of Staphylococcus
               aureus T0131, which is a multiresistant clinical isolate
               recovered in China and the first sequenced epidemic
               ST239-MRSA-SCCmec type III strain obtained in Asia. Comparison
               with two published genomes of ST239 reveals the polymorphism
               among strains of this type from different continents.",
  journal   = "J. Bacteriol.",
  publisher = "Am Soc Microbiol",
  volume    =  193,
  number    =  13,
  pages     = "3411--3412",
  month     =  jul,
  year      =  2011,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Chen2014-tq,
  title     = "Reduced susceptibility to vancomycin in isogenic Staphylococcus
               aureus strains of sequence type 59: tracking evolution and
               identifying mutations by whole-genome sequencing",
  author    = "Chen, Chih-Jung and Lin, Mei-Hui and Shu, Jwu-Ching and Lu,
               Jang-Jih",
  abstract  = "Objectives Vancomycin-intermediate Staphylococcus aureus (VISA)
               and heterogeneous VISA (hVISA) phenotypes are increasingly
               reported in methicillin-resistant S. aureus (MRSA) strains of
               distinct genetic backgrounds. This study tracked genetic
               evolution during the ...",
  journal   = "J. Antimicrob. Chemother.",
  publisher = "Br Soc Antimicrob Chemo",
  volume    =  69,
  number    =  2,
  pages     = "349--354",
  year      =  2014,
  keywords  = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Van_Der_Mee-Marquet2013-sr,
  title     = "Whole-genome sequence of the ancestral animal-borne {ST398}
               Staphylococcus aureus strain {S123}",
  author    = "Van Der Mee-Marquet, Nathalie and Hernandez, David and Bertrand,
               Xavier and Quentin, Roland and Corvaglia, Anna-Rita and Fran{\c
               c}ois, Patrice",
  abstract  = "ABSTRACT Sequence type 398 (ST398) Staphylococcus aureus was
               originally reported in livestock. We announce the complete
               genome sequence of an ST398 methicillin-susceptible S. aureus
               strain of animal origin, S123. The genome sequence reveals a
               wild-type ...",
  journal   = "Genome Announc.",
  publisher = "Am Soc Microbiol",
  volume    =  1,
  number    =  5,
  pages     = "e00692--13",
  year      =  2013,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
 }

 @ARTICLE{Diene2015-nq,
  title     = "Comparative genomics to investigate the emergence of
               community-associated methicillin-resistant Staphylococcus aureus
               ({CA-MRSA}) {USA300} clone in Geneva, Switzerland",
  author    = "Diene, S M and Von Dach, E and Fankhauser, C and Bonetti, E-J
               and Schrenzel, J and Harbarth, S and Fran{\c c}ois, P",
  abstract  = "... Comparative genomics to investigate the emergence of
               community-associated methicillin-resistant Staphylococcus aureus
               (CA-MRSA) USA300 clone in Geneva, Switzerland. ...
               Solexa-Illumina was used for whole genome sequencing (WGS) of
               all USA300 isolated in 2013. ...",
  journal   = "Antimicrob. Resist. Infect. Control",
  publisher = "BioMed Central",
  volume    =  4,
  number    = "Suppl 1",
  pages     = "P197",
  year      =  2015,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Castillo-Ramirez2012-to,
  title     = "Phylogeographic variation in recombination rates within a global
               clone of {Methicillin-Resistant} Staphylococcus aureus ({MRSA})",
  author    = "Castillo-Ram{\'\i}rez, Santiago and Corander, Jukka and
               Marttinen, Pekka and Aldeljawi, Mona and Hanage, William P and
               Westh, Henrik and Boye, Kit and Gulay, Zeynep and Bentley,
               Stephen D and Parkhill, Julian and Holden, Matthew T and Feil,
               Edward J",
  abstract  = "ABSTRACT: BACKGROUND: Next-generation sequencing (NGS) is a
               powerful tool for understanding both patterns of descent over
               time and space (phylogeography) and the molecular processes
               underpinning genome divergence in pathogenic bacteria. Here, we
               describe a synthesis between these perspectives by employing a
               recently developed Bayesian approach, BRATNextGen, for detecting
               recombination on an expanded NGS dataset of the globally
               disseminated methicillin-resistant Staphylococcus aureus (MRSA)
               clone ST239. RESULTS: The data confirm strong geographical
               clustering at continental, national and city scales and
               demonstrate that the rate of recombination varies significantly
               between phylogeographic sub-groups representing independent
               introductions from Europe. These differences are most striking
               when mobile non-core genes are included, but remain apparent
               even when only considering the stable core genome. The
               monophyletic ST239 sub-group corresponding to isolates from
               South America shows heightened recombination, the sub-group
               predominantly from Asia shows an intermediate level, and a very
               low level of recombination is noted in a third sub-group
               representing a large collection from Turkey. CONCLUSIONS: We
               show that the rapid global dissemination of a single pathogenic
               bacterial clone results in local variation in measured
               recombination rates. Possible explanatory variables include the
               size and time since emergence of each defined sub-population (as
               determined by the sampling frame), variation in transmission
               dynamics due to host movement, and changes in the bacterial
               genome affecting the propensity for recombination.",
  journal   = "Genome Biol.",
  publisher = "biomedcentral.com",
  volume    =  13,
  number    =  12,
  pages     = "R126",
  month     =  dec,
  year      =  2012,
  keywords  = "
               Staphylococcus;recombination;imported\_from\_papers\_14Nov2013;Staph\_evolutionary\_history;bacterial
               comparative genomics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Boyle-Vavra2011-vl,
  title     = "Comparative genome sequencing of an isogenic pair of {USA800}
               clinical methicillin-resistant Staphylococcus aureus isolates
               obtained before and after daptomycin treatment failure",
  author    = "Boyle-Vavra, Susan and Jones, Marcus and Gourley, Brett L and
               Holmes, Michael and Ruf, Rebecca and Balsam, Ashley R and
               Boulware, David R and Kline, Susan and Jawahir, Selina and
               Devries, Aaron and Peterson, Scott N and Daum, Robert S",
  abstract  = "We describe here a clinical daptomycin treatment failure in a
               patient with recurrent methicillin-resistant Staphylococcus
               aureus (MRSA) bacteremia in whom daptomycin was administered
               after a failed empirical treatment course with vancomycin and
               piperacillin-tazobactam. We had the opportunity to compare the
               genome sequences of an isogenic pair of daptomycin-susceptible
               and -resistant MRSA isolates obtained before and after
               initiation of daptomycin therapy, respectively. The genotype of
               both isolates was USA800, ST5, SCCmec type IV, agr type II.
               There was no increase in cell wall thickness in the
               daptomycin-resistant strain despite having decreased
               susceptibility to both vancomycin and daptomycin. By comparing
               the genome sequences by pyrosequencing, we identified a
               polymorphism (S337L) in the tenth transmembrane segment of the
               multiple peptide resistance factor, MprF, encoding lysyl
               phosphatidylglycerol transferase. This enzyme has been shown
               previously to promote repulsion of daptomycin at the cell
               surface by addition of positively charged lysine to
               phosphatidylglycerol. Also, the hlb open reading frame (ORF)
               encoding the $\beta$-toxin was interrupted by a prophage in the
               daptomycin-susceptible strain; this phage was missing in the
               daptomycin-resistant isolate and the hlb ORF was restored. Loss
               of the phage in the resistant isolate also resulted in loss of
               the virulence factor genes clpP, scn, and sak. This is the first
               study to use pyrosequencing to compare the genomes of a
               daptomycin-susceptible/resistant MRSA isolate pair obtained
               during failed daptomycin therapy in humans.",
  journal   = "Antimicrob. Agents Chemother.",
  publisher = "Am Soc Microbiol",
  volume    =  55,
  number    =  5,
  pages     = "2018--2025",
  month     =  may,
  year      =  2011,
  keywords  = "
               Staphylococcus;phage;confirmed\_SA-resistance-mutation;imported\_from\_papers\_14Nov2013;bacterial
               comparative genomics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Judge2015-kn,
  title    = "Early insights into the potential of the Oxford Nanopore {MinION}
              for the detection of antimicrobial resistance genes",
  author   = "Judge, Kim and Harris, Simon R and Reuter, Sandra and Parkhill,
              Julian and Peacock, Sharon J",
  abstract = "OBJECTIVES: Genome sequencing will be increasingly used in the
              clinical setting to tailor antimicrobial prescribing and inform
              infection control outbreaks. A recent technological innovation
              that could reduce the delay between pathogen sampling and data
              generation is single molecule sequencing. An example of this
              technology, which is undergoing evaluation through an early
              access programme, is the Oxford Nanopore MinION. METHODS: We
              undertook a feasibility study on six clinically significant
              pathogens, comparing the MinION to the Illumina MiSeq and PacBio
              RSII platforms. Genomic DNA was prepared and sequenced using the
              MinION as instructed by the manufacturer, and Illumina MiSeq and
              PacBio sequencing was performed using established methods.
              RESULTS: An evaluation of the accuracy of the MinION based on
              sequencing of an MRSA isolate showed that error rates were higher
              in the MinION reads, but provided an even coverage across the
              entire genome length. The MinION detected all of the expected
              carbapenemases and ESBL genes in five Gram-negative isolates and
              the mecA gene in an MRSA isolate. CONCLUSIONS: The MinION can
              detect the presence of acquired resistance genes, but
              improvements in accuracy are needed so that antimicrobial
              resistance associated with mutations in chromosomal genes can be
              identified.",
  journal  = "J. Antimicrob. Chemother.",
  volume   =  70,
  number   =  10,
  pages    = "2775--2778",
  month    =  oct,
  year     =  2015,
  keywords = "antibiotics;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Meric2015-oq,
  title    = "Ecological Overlap and Horizontal Gene Transfer in Staphylococcus
              aureus and Staphylococcus epidermidis",
  author   = "M{\'e}ric, Guillaume and Miragaia, Maria and de Been, Mark and
              Yahara, Koji and Pascoe, Ben and Mageiros, Leonardos and Mikhail,
              Jane and Harris, Llinos G and Wilkinson, Thomas S and Rolo, Joana
              and Lamble, Sarah and Bray, James E and Jolley, Keith A and
              Hanage, William P and Bowden, Rory and Maiden, Martin C J and
              Mack, Dietrich and de Lencastre, Herm{\'\i}nia and Feil, Edward J
              and Corander, Jukka and Sheppard, Samuel K",
  abstract = "The opportunistic pathogens Staphylococcus aureus and
              Staphylococcus epidermidis represent major causes of severe
              nosocomial infection, and are associated with high levels of
              mortality and morbidity worldwide. These species are both common
              commensals on the human skin and in the nasal pharynx, but are
              genetically distinct, differing at 24\% average nucleotide
              divergence in 1,478 core genes. To better understand the genome
              dynamics of these ecologically similar staphylococcal species, we
              carried out a comparative analysis of 324 S. aureus and S.
              epidermidis genomes, including 83 novel S. epidermidis sequences.
              A reference pan-genome approach and whole genome
              multilocus-sequence typing revealed that around half of the
              genome (1,478 genes) was shared between the species. Based on a
              BratNextGen analysis, homologous recombination was found to have
              impacted on 40\% of the core genes in S. epidermidis, but on only
              24\% of the core genes in S. aureus. Homologous recombination
              between the species is rare, with a maximum of 9 gene alleles
              shared between any two S. epidermidis and S. aureus isolates. In
              contrast, considerable interspecies admixture is noted in mobile
              elements, in particular genes associated with the SaPIn1
              pathogenicity island, metal detoxification, and the
              methicillin-resistance island SCCmec. Our data and analysis
              provide a context for considering the nature of recombinational
              boundaries between S. aureus and S. epidermidis and, the
              selective forces that influence realized recombination between
              these species.",
  journal  = "Genome Biol. Evol.",
  volume   =  7,
  number   =  5,
  pages    = "1313--1328",
  month    =  apr,
  year     =  2015,
  keywords = "Staphylococcus; ecology; evolution; nosocomial infections;
              recombination;Staphylococcus;plasmid;recombination;pangenome;Staph\_evolutionary\_history;Staph\_evolutionary\_history/staph
              microbial interactions;bacterial comparative
              genomics;Read-lab-shared;Papers\_for\_Michelle;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers"
 }

 @ARTICLE{Bradley2015-zy,
  title    = "Rapid antibiotic-resistance predictions from genome sequence data
              for Staphylococcus aureus and Mycobacterium tuberculosis",
  author   = "Bradley, Phelim and Gordon, N Claire and Walker, Timothy M and
              Dunn, Laura and Heys, Simon and Huang, Bill and Earle, Sarah and
              Pankhurst, Louise J and Anson, Luke and de Cesare, Mariateresa
              and Piazza, Paolo and Votintseva, Antonina A and Golubchik, Tanya
              and Wilson, Daniel J and Wyllie, David H and Diel, Roland and
              Niemann, Stefan and Feuerriegel, Silke and Kohl, Thomas A and
              Ismail, Nazir and Omar, Shaheed V and Smith, E Grace and Buck,
              David and McVean, Gil and Walker, A Sarah and Peto, Tim E A and
              Crook, Derrick W and Iqbal, Zamin",
  abstract = "The rise of antibiotic-resistant bacteria has led to an urgent
              need for rapid detection of drug resistance in clinical samples,
              and improvements in global surveillance. Here we show how de
              Bruijn graph representation of bacterial diversity can be used to
              identify species and resistance profiles of clinical isolates. We
              implement this method for Staphylococcus aureus and Mycobacterium
              tuberculosis in a software package ('Mykrobe predictor') that
              takes raw sequence data as input, and generates a
              clinician-friendly report within 3 minutes on a laptop. For S.
              aureus, the error rates of our method are comparable to
              gold-standard phenotypic methods, with sensitivity/specificity of
              99.1\%/99.6\% across 12 antibiotics (using an independent
              validation set, n=470). For M. tuberculosis, our method predicts
              resistance with sensitivity/specificity of 82.6\%/98.5\%
              (independent validation set, n=1,609); sensitivity is lower here,
              probably because of limited understanding of the underlying
              genetic mechanisms. We give evidence that minor alleles improve
              detection of extremely drug-resistant strains, and demonstrate
              feasibility of the use of emerging single-molecule nanopore
              sequencing techniques for these purposes.",
  journal  = "Nat. Commun.",
  volume   =  6,
  pages    = "10063",
  month    =  dec,
  year     =  2015,
  keywords = "Staphylococcus;antibiotics;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Garvey2016-cd,
  title    = "Improved understanding of an outbreak of meticillin-resistant
              Staphylococcus aureus in a regional burns centre via whole-genome
              sequencing",
  author   = "Garvey, M I and Pichon, B and Bradley, C W and Moiemen, N S and
              Oppenheim, B and Kearns, A M",
  journal  = "J. Hosp. Infect.",
  month    =  sep,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Bunter2016-ot,
  title    = "Wild type agr-negative livestock-associated {MRSA} exhibits high
              adhesive capacity to human and porcine cells",
  author   = "B{\"u}nter, Julia P and Seth-Smith, Helena M B and R{\"u}egg,
              Simon and Heikinheimo, Annamari and Borel, Nicole and Johler,
              Sophia",
  abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) is one of the
              leading causes of nosocomial infections and a major public health
              concern worldwide. During the last decade, MRSA of CC398 have
              emerged as important colonizers of livestock. These strains also
              represent an increasing cause of human infections. A recent study
              reporting a new dominant spa type among MRSA from Finish
              fattening pigs (CC398/t2741) identified a strain lacking both the
              global virulence regulator gene locus agr and the adhesion gene
              fnbB. The aim of this study was to characterize this
              agr/fnbB-negative livestock-associated MRSA strain in terms of
              growth, hemolysis and adhesive capacity, and to provide data on
              its genomic background. To this end, growth curves and hemolysis
              patterns were generated and adhesion assays on human keratinocyte
              and porcine nasal mucosa cell lines were performed. Whole genome
              sequencing was used to determine the nature and extent of the
              relevant deletions in the livestock strains. For comparison, an
              agr-positive, fnbB-negative CC398/t2741 strain from the same pig
              herd, an agr/fnbB- positive CC398/t034 strain from another pig
              herd and one human MRSA strain and its isogenic $\Delta$agr
              knockout mutant were used. The agr-negative strains adhered
              significantly better to human and porcine host cells than the
              agr-positive control strains. For the agr-positive porcine MRSA
              strains, cytotoxic effects on porcine mucosal cells were
              observed. The strong adhesive capacity of the naturally
              agr-negative livestock-associated MRSA, in combination with
              diminished cytotoxic effects, is likely favorable for inducing
              persistent colonization in pigs. Independently of the host cell
              type, similar adhesive capacities of the naturally agr-negative
              livestock-associated MRSA and the human MRSA strain were shown.
              Our results indicate that loss of agr in the livestock-associated
              MRSA strain investigated in this study may have increased its
              potential to be transmitted to and amongst humans.",
  journal  = "Res. Microbiol.",
  month    =  oct,
  year     =  2016,
  keywords = "Adhesion; Livestock; MRSA; Staphylococcus aureus;
              agr;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Senn2016-of,
  title    = "The Stealthy Superbug: the Role of Asymptomatic Enteric Carriage
              in Maintaining a {Long-Term} Hospital Outbreak of {ST228}
              {Methicillin-Resistant} Staphylococcus aureus",
  author   = "Senn, Laurence and Clerc, Olivier and Zanetti, Giorgio and
              Basset, Patrick and Prod'hom, Guy and Gordon, Nicola C and
              Sheppard, Anna E and Crook, Derrick W and James, Richard and
              Thorpe, Harry A and Feil, Edward J and Blanc, Dominique S",
  abstract = "UNLABELLED: Whole-genome sequencing (WGS) of 228 isolates was
              used to elucidate the origin and dynamics of a long-term outbreak
              of methicillin-resistant Staphylococcus aureus (MRSA) sequence
              type 228 (ST228) SCCmec I that involved 1,600 patients in a
              tertiary care hospital between 2008 and 2012. Combining of the
              sequence data with detailed metadata on patient admission and
              movement confirmed that the outbreak was due to the transmission
              of a single clonal variant of ST228, rather than repeated
              introductions of this clone into the hospital. We note that this
              clone is significantly more frequently recovered from groin and
              rectal swabs than other clones (P < 0.0001) and is also
              significantly more transmissible between roommates (P < 0.01).
              Unrecognized MRSA carriers, together with movements of patients
              within the hospital, also seem to have played a major role. These
              atypical colonization and transmission dynamics can help explain
              how the outbreak was maintained over the long term. This
              ``stealthy'' asymptomatic colonization of the gut, combined with
              heightened transmissibility (potentially reflecting a role for
              environmental reservoirs), means the dynamics of this outbreak
              share some properties with enteric pathogens such as
              vancomycin-resistant enterococci or Clostridium difficile.
              IMPORTANCE: Using whole-genome sequencing, we showed that a large
              and prolonged outbreak of methicillin-resistant Staphylococcus
              aureus was due to the clonal spread of a specific strain with
              genetic elements adapted to the hospital environment.
              Unrecognized MRSA carriers, the movement of patients within the
              hospital, and the low detection with clinical specimens were also
              factors that played a role in this occurrence. The atypical
              colonization of the gut means the dynamics of this outbreak may
              share some properties with enteric pathogens.",
  journal  = "MBio",
  volume   =  7,
  number   =  1,
  pages    = "e02039--15",
  month    =  jan,
  year     =  2016,
  keywords = "
              Staphylococcus;Staph\_evolutionary\_history;Staph\_evolutionary\_history/staph
              microbial interactions;bacterial comparative
              genomics;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Staph\_evolution\_toxins",
  language = "en"
 }

 @ARTICLE{Ishii2015-ur,
  title     = "Phenotypic and genomic comparisons of highly
               vancomycin-resistant Staphylococcus aureus strains developed
               from multiple clinical {MRSA} strains by in vitro mutagenesis",
  author    = "Ishii, Kenichi and Tabuchi, Fumiaki and Matsuo, Miki and
               Tatsuno, Keita and Sato, Tomoaki and Okazaki, Mitsuhiro and
               Hamamoto, Hiroshi and Matsumoto, Yasuhiko and Kaito, Chikara and
               Aoyagi, Tetsuji and Hiramatsu, Keiichi and Kaku, Mitsuo and
               Moriya, Kyoji and Sekimizu, Kazuhisa",
  abstract  = "The development of vancomycin (VCM) resistance in Staphylococcus
               aureus threatens global health. Studies of the VCM-resistance
               mechanism and alternative therapeutic strategies are urgently
               needed. We mutagenized S. aureus laboratory strains and
               methicillin-resistant S. aureus (MRSA) with ethyl
               methanesulfonate, and isolated mutants that exhibited high
               resistance to VCM (minimum inhibitory concentration = 32
               $\mu$g/ml). These VCM-resistant strains were sensitive to
               linezolid and rifampicin, and partly to arbekacin and
               daptomycin. Beta-lactams had synergistic effects with VCM
               against these mutants. VCM-resistant strains exhibited a 2-fold
               increase in the cell wall thickness. Several genes were commonly
               mutated among the highly VCM-resistant mutants. These findings
               suggest that MRSA has a potential to develop high VCM resistance
               with cell wall thickening by the accumulation of mutations.",
  journal   = "Sci. Rep.",
  publisher = "ncbi.nlm.nih.gov",
  volume    =  5,
  pages     = "17092",
  month     =  nov,
  year      =  2015,
  keywords  = "confirmed\_SA-resistance-mutation;Staphylococcus;antibiotics;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Chang2016-oa,
  title    = "Identifying the effect of patient sharing on between-hospital
              genetic differentiation of methicillin-resistant Staphylococcus
              aureus",
  author   = "Chang, Hsiao-Han and Dordel, Janina and Donker, Tjibbe and Worby,
              Colin J and Feil, Edward J and Hanage, William P and Bentley,
              Stephen D and Huang, Susan S and Lipsitch, Marc",
  abstract = "BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is
              one of the most common healthcare-associated pathogens. To
              examine the role of inter-hospital patient sharing on MRSA
              transmission, a previous study collected 2,214 samples from 30
              hospitals in Orange County, California and showed by spa typing
              that genetic differentiation decreased significantly with
              increased patient sharing. In the current study, we focused on
              the 986 samples with spa type t008 from the same population.
              METHODS: We used genome sequencing to determine the effect of
              patient sharing on genetic differentiation between hospitals.
              Genetic differentiation was measured by between-hospital genetic
              diversity, F ST , and the proportion of nearly identical isolates
              between hospitals. RESULTS: Surprisingly, we found very similar
              genetic diversity within and between hospitals, and no
              significant association between patient sharing and genetic
              differentiation measured by F ST . However, in contrast to F ST ,
              there was a significant association between patient sharing and
              the proportion of nearly identical isolates between hospitals. We
              propose that the proportion of nearly identical isolates is more
              powerful at determining transmission dynamics than traditional
              estimators of genetic differentiation (F ST ) when gene flow
              between populations is high, since it is more responsive to
              recent transmission events. Our hypothesis was supported by the
              results from coalescent simulations. CONCLUSIONS: Our results
              suggested that there was a high level of gene flow between
              hospitals facilitated by patient sharing, and that the proportion
              of nearly identical isolates is more sensitive to population
              structure than F ST when gene flow is high.",
  journal  = "Genome Med.",
  volume   =  8,
  number   =  1,
  pages    = "18",
  month    =  feb,
  year     =  2016,
  keywords = "Staphylococcus;Staph\_evolutionary\_history;bacterial comparative
              genomics;Teaching antibiotic resistance
              genomics;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers"
 }

 @ARTICLE{Salipante2015-qz,
  title    = "Application of whole-genome sequencing for bacterial strain
              typing in molecular epidemiology",
  author   = "Salipante, Stephen J and SenGupta, Dhruba J and Cummings, Lisa A
              and Land, Tyler A and Hoogestraat, Daniel R and Cookson, Brad T",
  abstract = "Nosocomial infections pose a significant threat to patient
              health; however, the gold standard laboratory method for
              determining bacterial relatedness (pulsed-field gel
              electrophoresis [PFGE]) remains essentially unchanged 20 years
              after its introduction. Here, we explored bacterial whole-genome
              sequencing (WGS) as an alternative approach for molecular strain
              typing. We compared WGS to PFGE for investigating presumptive
              outbreaks involving three important pathogens:
              vancomycin-resistant Enterococcus faecium (n=19),
              methicillin-resistant Staphylococcus aureus (n=17), and
              Acinetobacter baumannii (n=15). WGS was highly reproducible
              (average$\leq$0.39 differences between technical replicates),
              which enabled a functional, quantitative definition for
              determining clonality. Strain relatedness data determined by PFGE
              and WGS roughly correlated, but the resolution of WGS was
              superior (P=5.6$\times$10(-8) to 0.016). Several discordant
              results were noted between the methods. A total of 28.9\% of
              isolates which were indistinguishable by PFGE were nonclonal by
              WGS. For A. baumannii, a species known to undergo rapid
              horizontal gene transfer, 16.2\% of isolate pairs considered
              nonidentical by PFGE were clonal by WGS. Sequencing whole
              bacterial genomes with single-nucleotide resolution demonstrates
              that PFGE is prone to false-positive and false-negative results
              and suggests the need for a new gold standard approach for
              molecular epidemiological strain typing.",
  journal  = "J. Clin. Microbiol.",
  volume   =  53,
  number   =  4,
  pages    = "1072--1079",
  month    =  apr,
  year     =  2015,
  keywords = "experimental\_design;Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Croucher2016-vz,
  title    = "Horizontal {DNA} Transfer Mechanisms of Bacteria as Weapons of
              Intragenomic Conflict",
  author   = "Croucher, Nicholas J and Mostowy, Rafal and Wymant, Christopher
              and Turner, Paul and Bentley, Stephen D and Fraser, Christophe",
  abstract = "Horizontal DNA transfer (HDT) is a pervasive mechanism of
              diversification in many microbial species, but its primary
              evolutionary role remains controversial. Much recent research has
              emphasised the adaptive benefit of acquiring novel DNA, but here
              we argue instead that intragenomic conflict provides a coherent
              framework for understanding the evolutionary origins of HDT. To
              test this hypothesis, we developed a mathematical model of a
              clonally descended bacterial population undergoing HDT through
              transmission of mobile genetic elements (MGEs) and genetic
              transformation. Including the known bias of transformation toward
              the acquisition of shorter alleles into the model suggested it
              could be an effective means of counteracting the spread of MGEs.
              Both constitutive and transient competence for transformation
              were found to provide an effective defence against parasitic
              MGEs; transient competence could also be effective at permitting
              the selective spread of MGEs conferring a benefit on their host
              bacterium. The coordination of transient competence with
              cell-cell killing, observed in multiple species, was found to
              result in synergistic blocking of MGE transmission through
              releasing genomic DNA for homologous recombination while
              simultaneously reducing horizontal MGE spread by lowering the
              local cell density. To evaluate the feasibility of the functions
              suggested by the modelling analysis, we analysed genomic data
              from longitudinal sampling of individuals carrying Streptococcus
              pneumoniae. This revealed the frequent within-host coexistence of
              clonally descended cells that differed in their MGE infection
              status, a necessary condition for the proposed mechanism to
              operate. Additionally, we found multiple examples of MGEs
              inhibiting transformation through integrative disruption of genes
              encoding the competence machinery across many species, providing
              evidence of an ongoing ``arms race.'' Reduced rates of
              transformation have also been observed in cells infected by MGEs
              that reduce the concentration of extracellular DNA through
              secretion of DNases. Simulations predicted that either mechanism
              of limiting transformation would benefit individual MGEs, but
              also that this tactic's effectiveness was limited by competition
              with other MGEs coinfecting the same cell. A further observed
              behaviour we hypothesised to reduce elimination by transformation
              was MGE activation when cells become competent. Our model
              predicted that this response was effective at counteracting
              transformation independently of competing MGEs. Therefore, this
              framework is able to explain both common properties of MGEs, and
              the seemingly paradoxical bacterial behaviours of transformation
              and cell-cell killing within clonally related populations, as the
              consequences of intragenomic conflict between self-replicating
              chromosomes and parasitic MGEs. The antagonistic nature of the
              different mechanisms of HDT over short timescales means their
              contribution to bacterial evolution is likely to be substantially
              greater than previously appreciated.",
  journal  = "PLoS Biol.",
  volume   =  14,
  number   =  3,
  pages    = "e1002394",
  month    =  mar,
  year     =  2016,
  keywords = "systems\_biology;evolution;recombination;simulated-evolution;theory;Staph\_evolutionary\_history/Teaching\_Prokaryotic\_evolution;Staph\_evolutionary\_history;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Wang2014-uw,
  title    = "Comparative genomics of methicillin-resistant Staphylococcus
              aureus {ST239}: distinct geographical variants in Beijing and
              Hong Kong",
  author   = "Wang, Zheng and Zhou, Haokui and Wang, Hui and Chen, Hongbin and
              Leung, K K and Tsui, Stephen and Ip, Margaret",
  abstract = "BACKGROUND: The ST239 lineage is a globally disseminated,
              multiply drug-resistant hospital-associated methicillin-resistant
              Staphylococcus aureus (HA-MRSA). We performed whole-genome
              sequencing of representative HA-MRSA isolates of the ST239
              lineage from bacteremic patients in hospitals in Hong Kong (HK)
              and Beijing (BJ) and compared them with three published complete
              genomes of ST239, namely T0131, TW20 and JKD6008. Orthologous
              gene group (OGG) analyses of the Hong Kong and Beijing cluster
              strains were also undertaken. RESULTS: Homology analysis, based
              on highest-percentage nucleotide identity, indicated that HK
              isolates were closely related to TW20, whereas BJ isolates were
              more closely related to T0131 from Tianjin. Phylogenetic
              analysis, incorporating a total of 30 isolates from different
              continents, revealed that strains from HK clustered with TW20
              into the 'Asian clade', whereas BJ isolates and T0131 clustered
              closely with strains of the 'Turkish clade' from Eastern Europe.
              HK isolates contained the typical $\varphi$SP$\beta$-like
              prophage with the SasX gene similar to TW20. In contrast, BJ
              isolates contained a unique 15 kb PT1028-like prophage but lacked
              $\varphi$SP$\beta$-like and $\varphi$SA1 prophages. Besides
              distinct mobile genetic elements (MGE) in the two clusters, OGG
              analyses and whole-genome alignment of these clusters highlighted
              differences in genes located in the core genome, including the
              identification of single nucleotide deletions in several genes,
              resulting in frameshift mutations and the subsequent predicted
              truncation of encoded proteins involved in metabolism and
              antimicrobial resistance. CONCLUSIONS: Comparative genomics,
              based on de novo assembly and deep sequencing of HK and BJ
              strains, revealed different origins of the ST239 lineage in
              northern and southern China and identified differences between
              the two clades at single nucleotide polymorphism (SNP), core gene
              and MGE levels. The results suggest that ST239 strains isolated
              in Hong Kong since the 1990s belong to the Asian clade, present
              mainly in southern Asia, whereas those that emerged in northern
              China were of a distinct origin, reflecting the complexity of
              dissemination and the dynamic evolution of this ST239 lineage.",
  journal  = "BMC Genomics",
  volume   =  15,
  pages    = "529",
  month    =  jun,
  year     =  2014,
  keywords = "Staphylococcus;bacterial comparative
              genomics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Mader2016-da,
  title    = "Staphylococcus aureus Transcriptome Architecture: From Laboratory
              to {Infection-Mimicking} Conditions",
  author   = "M{\"a}der, Ulrike and Nicolas, Pierre and Depke, Maren and
              Pan{\'e}-Farr{\'e}, Jan and Debarbouille, Michel and van der
              Kooi-Pol, Magdalena M and Gu{\'e}rin, Cyprien and D{\'e}rozier,
              Sandra and Hiron, Aurelia and Jarmer, Hanne and Leduc,
              Aur{\'e}lie and Michalik, Stephan and Reilman, Ewoud and
              Schaffer, Marc and Schmidt, Frank and Bessi{\`e}res, Philippe and
              Noirot, Philippe and Hecker, Michael and Msadek, Tarek and
              V{\"o}lker, Uwe and van Dijl, Jan Maarten",
  abstract = "Staphylococcus aureus is a major pathogen that colonizes about
              20\% of the human population. Intriguingly, this Gram-positive
              bacterium can survive and thrive under a wide range of different
              conditions, both inside and outside the human body. Here, we
              investigated the transcriptional adaptation of S. aureus HG001, a
              derivative of strain NCTC 8325, across experimental conditions
              ranging from optimal growth in vitro to intracellular growth in
              host cells. These data establish an extensive repertoire of
              transcription units and non-coding RNAs, a classification of 1412
              promoters according to their dependence on the RNA polymerase
              sigma factors SigA or SigB, and allow identification of new
              potential targets for several known transcription factors. In
              particular, this study revealed a relatively low abundance of
              antisense RNAs in S. aureus, where they overlap only 6\% of the
              coding genes, and only 19 antisense RNAs not co-transcribed with
              other genes were found. Promoter analysis and comparison with
              Bacillus subtilis links the small number of antisense RNAs to a
              less profound impact of alternative sigma factors in S. aureus.
              Furthermore, we revealed that Rho-dependent transcription
              termination suppresses pervasive antisense transcription,
              presumably originating from abundant spurious transcription
              initiation in this A+T-rich genome, which would otherwise affect
              expression of the overlapped genes. In summary, our study
              provides genome-wide information on transcriptional regulation
              and non-coding RNAs in S. aureus as well as new insights into the
              biological function of Rho and the implications of spurious
              transcription in bacteria.",
  journal  = "PLoS Genet.",
  volume   =  12,
  number   =  4,
  pages    = "e1005962",
  month    =  apr,
  year     =  2016,
  keywords = "Staphylococcus;rna-seq;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers;microRNA\_in\_bacteria"
 }

 @ARTICLE{Carroll2013-gh,
  title    = "Draft Genome Sequence of Strain {CBD-635}, a
              {Methicillin-Resistant} Staphylococcus aureus {USA100} Isolate",
  author   = "Carroll, Ronan K and Burda, Whittney N and Roberts, Jill C and
              Peak, Kealy K and Cannons, Andrew C and Shaw, Lindsey N",
  abstract = "We present the draft genome sequence of methicillin-resistant
              Staphylococcus aureus strain CBD-635, from the USA100 lineage.
              This is a sepsis isolate obtained from Tampa General Hospital.
              This strain is spa type t003 and multilocus sequence typing
              (MLST) type ST5, and it has been used by our group in the study
              of novel antimicrobial chemotherapeutics.",
  journal  = "Genome Announc.",
  volume   =  1,
  number   =  4,
  month    =  jul,
  year     =  2013,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Wendt2014-oh,
  title    = "Transmission of methicillin-resistant Staphylococcus aureus
              infection through solid organ transplantation: confirmation via
              whole genome sequencing",
  author   = "Wendt, J M and Kaul, D and Limbago, B M and Ramesh, M and Cohle,
              S and Denison, A M and Driebe, E M and Rasheed, J K and Zaki, S R
              and Blau, D M and Paddock, C D and McDougal, L K and Engelthaler,
              D M and Keim, P S and Roe, C C and Akselrod, H and Kuehnert, M J
              and Basavaraju, S V",
  abstract = "We describe two cases of donor-derived methicillin-resistant
              Staphylococcus aureus (MRSA) bacteremia that developed after
              transplantation of organs from a common donor who died from acute
              MRSA endocarditis. Both recipients developed recurrent MRSA
              infection despite appropriate antibiotic therapy, and required
              prolonged hospitalization and hospital readmission. Comparison of
              S. aureus whole genome sequence of DNA extracted from fixed donor
              tissue and recipients' isolates confirmed donor-derived
              transmission. Current guidelines emphasize the risk posed by
              donors with bacteremia from multidrug-resistant organisms. This
              investigation suggests that, particularly in the setting of donor
              endocarditis, even a standard course of prophylactic antibiotics
              may not be sufficient to prevent donor-derived infection.",
  journal  = "Am. J. Transplant",
  volume   =  14,
  number   =  11,
  pages    = "2633--2639",
  month    =  nov,
  year     =  2014,
  keywords = "Staphylococcus;Staph\_evolutionary\_history;bacterial comparative
              genomics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Tong2015-xf,
  title    = "Genome sequencing defines phylogeny and spread of
              methicillin-resistant Staphylococcus aureus in a high
              transmission setting",
  author   = "Tong, Steven Y C and Holden, Matthew T G and Nickerson, Emma K
              and Cooper, Ben S and K{\"o}ser, Claudio U and Cori, Anne and
              Jombart, Thibaut and Cauchemez, Simon and Fraser, Christophe and
              Wuthiekanun, Vanaporn and Thaipadungpanit, Janjira and Hongsuwan,
              Maliwan and Day, Nicholas P and Limmathurotsakul, Direk and
              Parkhill, Julian and Peacock, Sharon J",
  abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) is a major
              cause of nosocomial infection. Whole-genome sequencing of MRSA
              has been used to define phylogeny and transmission in
              well-resourced healthcare settings, yet the greatest burden of
              nosocomial infection occurs in resource-restricted settings where
              barriers to transmission are lower. Here, we study the flux and
              genetic diversity of MRSA on ward and individual patient levels
              in a hospital where transmission was common. We repeatedly
              screened all patients on two intensive care units for MRSA
              carriage over a 3-mo period. All MRSA belonged to multilocus
              sequence type 239 (ST 239). We defined the population structure
              and charted the spread of MRSA by sequencing 79 isolates from 46
              patients and five members of staff, including the first
              MRSA-positive screen isolates and up to two repeat isolates where
              available. Phylogenetic analysis identified a flux of distinct ST
              239 clades over time in each intensive care unit. In total, five
              main clades were identified, which varied in the carriage of
              plasmids encoding antiseptic and antimicrobial resistance
              determinants. Sequence data confirmed intra- and interwards
              transmission events and identified individual patients who were
              colonized by more than one clade. One patient on each unit was
              the source of numerous transmission events, and deep sampling of
              one of these cases demonstrated colonization with a ``cloud'' of
              related MRSA variants. The application of whole-genome sequencing
              and analysis provides novel insights into the transmission of
              MRSA in under-resourced healthcare settings and has relevance to
              wider global health.",
  journal  = "Genome Res.",
  volume   =  25,
  number   =  1,
  pages    = "111--118",
  month    =  jan,
  year     =  2015,
  keywords = "Staphylococcus;bacterial comparative
              genomics;Staph\_evolutionary\_history;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Hernandez2013-xb,
  title     = "{Whole-Genome} Sequences of Staphylococcus aureus {ST398}
               Strains of Animal Origin",
  author    = "Hernandez, David and van der Mee-Marquet, Nathalie and
               Kluytmans, Jan and Donnio, Pierre-Yves and Quentin, Roland and
               Corvaglia, Anna-Rita and Fran{\c c}ois, Patrice",
  abstract  = "Staphylococcus aureus sequence type 398 (ST398) was originally
               associated with animal infections. We announce the complete
               genome sequences of two ST398 methicillin-susceptible S. aureus
               strains from the livestock environment. These genome sequences
               assist in the characterization of interesting ST398 features
               relying on host tropism and epidemiological settings.",
  journal   = "Genome Announc.",
  publisher = "Am Soc Microbiol",
  volume    =  1,
  number    =  5,
  month     =  sep,
  year      =  2013,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
 }

 @ARTICLE{Barrado2013-dt,
  title     = "Draft Genome Sequence of Strain {SA\_ST125\_MupR} of
               {Methicillin-Resistant} Staphylococcus aureus {ST125}, a Major
               Clone in Spain",
  author    = "Barrado, Laura and Viedma, Esther and Vindel, Ana and Otero,
               Joaqu{\'\i}n R and Chaves, Fernando",
  abstract  = "Here, we report the draft genome sequence of a
               methicillin-resistant Staphylococcus aureus (MRSA) strain with
               high-level mupirocin resistance (SA\_ST125\_MupR), isolated from
               a patient with recurrent bacteremia. This strain belonged to
               sequence type ST125, which was responsible for more than 50\% of
               the health care-associated infections caused by MRSA in Spain.",
  journal   = "Genome Announc.",
  publisher = "Am Soc Microbiol",
  volume    =  1,
  number    =  4,
  month     =  aug,
  year      =  2013,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Stegger2013-lf,
  title     = "Genome analysis of Staphylococcus aureus {ST291}, a double locus
               variant of {ST398}, reveals a distinct genetic lineage",
  author    = "Stegger, Marc and Aziz, Maliha and Chroboczek, Tomasz and Price,
               Lance B and Ronco, Troels and Kiil, Kristoffer and Skov, Robert
               L and Laurent, Frederic and Andersen, Paal S",
  abstract  = "Staphylococcus aureus ST291 has been reported as a homologue
               recombinant double locus variant of the livestock associated S.
               aureus ST398. However, whole genome sequencing show that ST291
               is a unique genetic lineage with highly variable content within
               its accessory genome compared to both human and livestock
               associated genome sequenced CC398s.",
  journal   = "PLoS One",
  publisher = "dx.plos.org",
  volume    =  8,
  number    =  5,
  pages     = "e63008",
  month     =  may,
  year      =  2013,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
 }

 @ARTICLE{Wang2012-hj,
  title     = "Whole-genome sequence of Staphylococcus aureus strain
               {LCT-SA112}",
  author    = "Wang, Junfeng and Liu, Yanhong and Wan, Daiwei and Fang,
               Xiangqun and Li, Tianzhi and Guo, Yinghua and Chang, De and Su,
               Longxiang and Wang, Yajuan and Zhao, Jiao and Liu, Changting",
  abstract  = "Staphylococcus aureus is a facultative anaerobic Gram-positive
               coccal bacterium. S. aureus is the most common species of
               Staphylococcus to cause staphylococcal infections, which are
               very common in clinical medicine. Here we report the genome
               sequence of S. aureus strain LCT-SA112, which was isolated from
               S. aureus subsp. aureus CGMCC 1.230.",
  journal   = "J. Bacteriol.",
  publisher = "Am Soc Microbiol",
  volume    =  194,
  number    =  15,
  pages     = "4124",
  month     =  aug,
  year      =  2012,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Golding2012-pq,
  title     = "whole-genome sequence of livestock-associated st398
               methicillin-resistant staphylococcus aureus Isolated from Humans
               in Canada",
  author    = "Golding, George R and Bryden, Louis and Levett, Paul N and
               McDonald, Ryan R and Wong, Alice and Graham, Morag R and Tyler,
               Shaun and Van Domselaar, Gary and Mabon, Philip and Kent,
               Heather and Butaye, Patrick and Smith, Tara C and Kadlec,
               Kristina and Schwarz, Stefan and Weese, Scott J and Mulvey,
               Michael R",
  abstract  = "Despite reports of high colonization rates of ST398
               livestock-associated methicillin-resistant Staphylococcus aureus
               (LA-MRSA) among pigs and pig farmers, the incidence of LA-MRSA
               infection in the general population in Canada appears to be rare
               in comparison to that in some European countries. In this study,
               the complete genome sequence of a Canadian representative
               LA-MRSA isolate (08BA02176) from a human postoperative surgical
               site infection was acquired and compared to the sequenced genome
               of an LA-MRSA isolate (S0385) from Europe to identify genetic
               traits that may explain differences in the success of these
               particular strains in some locales.",
  journal   = "J. Bacteriol.",
  publisher = "Am Soc Microbiol",
  volume    =  194,
  number    =  23,
  pages     = "6627--6628",
  month     =  dec,
  year      =  2012,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
 }

 % The entry below contains non-ASCII chars that could not be converted
 % to a LaTeX equivalent.
 @ARTICLE{Prabhakara2012-aq,
  title     = "Draft genome sequence of Staphylococcus aureus 118 ({ST772)}, a
               major disease clone from India",
  author    = "Prabhakara, Sushma and Khedkar, Supriya and Loganathan, Ramya
               Malarini and Chandana, S and Gowda, Malali and Arakere, Gayathri
               and Seshasayee, Aswin Sai Narain",
  abstract  = "We report the draft genome sequence of an ST772 Staphylococcus
               aureus disease isolate carrying staphylococcal cassette
               chromosome mec (SCCmec) type V from a pyomyositis patient. Our
               de novo short read assembly is ∼2.8 Mb and encodes a unique
               Panton-Valentine leukocidin (PVL) phage with structural genes
               similar to those of ϕ7247PVL and novel lysogenic genes at the N
               termini.",
  journal   = "J. Bacteriol.",
  publisher = "Am Soc Microbiol",
  volume    =  194,
  number    =  14,
  pages     = "3727--3728",
  month     =  jul,
  year      =  2012,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Peleg2012-gx,
  title     = "Whole genome characterization of the mechanisms of daptomycin
               resistance in clinical and laboratory derived isolates of
               Staphylococcus aureus",
  author    = "Peleg, Anton Y and Miyakis, Spiros and Ward, Doyle V and Earl,
               Ashlee M and Rubio, Aileen and Cameron, David R and Pillai,
               Satish and Moellering, Jr, Robert C and Eliopoulos, George M",
  abstract  = "BACKGROUND: Daptomycin remains one of our last-line
               anti-staphylococcal agents. This study aims to characterize the
               genetic evolution to daptomycin resistance in S. aureus.
               METHODS: Whole genome sequencing was performed on a unique
               collection of isogenic, clinical (21 strains) and laboratory (12
               strains) derived strains that had been exposed to daptomycin and
               developed daptomycin-nonsusceptibility. Electron microscopy (EM)
               and lipid membrane studies were performed on selected isolates.
               RESULTS: On average, six coding region mutations were observed
               across the genome in the clinical daptomycin exposed strains,
               whereas only two mutations on average were seen in the
               laboratory exposed pairs. All daptomycin-nonsusceptible strains
               had a mutation in a phospholipid biosynthesis gene. This
               included mutations in the previously described mprF gene, but
               also in other phospholipid biosynthesis genes, including
               cardiolipin synthase (cls2) and
               CDP-diacylglycerol-glycerol-3-phosphate
               3-phosphatidyltransferase (pgsA). EM and lipid membrane
               composition analyses on two clinical pairs showed that the
               daptomycin-nonsusceptible strains had a thicker cell wall and an
               increase in membrane lysyl-phosphatidylglycerol. CONCLUSION:
               Point mutations in genes coding for membrane phospholipids are
               associated with the development of reduced susceptibility to
               daptomycin in S. aureus. Mutations in cls2 and pgsA appear to be
               new genetic mechanisms affecting daptomycin susceptibility in S.
               aureus.",
  journal   = "PLoS One",
  publisher = "dx.plos.org",
  volume    =  7,
  number    =  1,
  pages     = "e28316",
  month     =  jan,
  year      =  2012,
  keywords  = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Gasc2016-sq,
  title    = "Genome Sequence of Staphylococcus aureus Strain {HUK16}, Isolated
              from {Hexachlorocyclohexane-Contaminated} Soil",
  author   = "Gasc, Cyrielle and Richard, Jean-Yves and Peyret, Pierre",
  abstract = "Staphylococcus aureusstrain HUK16 has been isolated from
              hexachlorocyclohexane (HCH)-long-term contaminated soil. The
              genome of strain HUK16 was sequenced to understand the genetic
              basis of its adaptation to HCH and to find the potential
              metabolic pathways allowing it to degrade the pesticide. Here, we
              report the annotated draft genome sequence (~2.7 Mbp) of this
              strain.",
  journal  = "Genome Announc.",
  volume   =  4,
  number   =  2,
  month    =  apr,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Hishinuma2016-wu,
  title    = "Complete Genome Sequence of {Vancomycin-Intermediate}
              Staphylococcus aureus Strain {MI} ({HIP5827})",
  author   = "Hishinuma, Tomomi and Katayama, Yuki and Matsuo, Miki and Sasaki,
              Takashi and Hiramatsu, Keiichi",
  abstract = "We report the complete genome sequence of vancomycin-intermediate
              Staphylococcus aureus (VISA) strain MI (HIP5827).",
  journal  = "Genome Announc.",
  volume   =  4,
  number   =  2,
  month    =  mar,
  year     =  2016,
  keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Marques2016-wq,
  title    = "Genome Sequence of a Clinical Staphylococcus aureus Strain from a
              Prosthetic Joint Infection",
  author   = "Marqu{\`e}s, Claire and Franceschi, Christine and Collin,
              Val{\'e}rie and Laurent, Fr{\'e}d{\'e}ric and Chatellier, Sonia
              and Forestier, Christiane",
  abstract = "Here, we report the genome sequence ofStaphylococcus
              aureusLYO-S2, an isolate with sequence type (ST) 45 that was
              isolated in 2001 from a prosthetic joint infection.",
  journal  = "Genome Announc.",
  volume   =  4,
  number   =  2,
  month    =  apr,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Silva2016-il,
  title    = "Erratum for Silva et al., Draft Genome Sequences of
              Staphylococcus aureus Strains Isolated from Subclinical Bovine
              Mastitis in Brazil",
  author   = "Silva, Danielle Mendes and da Silva, M{\^o}nica Pacheco and
              Vidigal, Pedro M Pereira and Barcelos, Rafael Mazioli and Klein,
              Raphael Contelli and Aguilar, Ananda Pereira and Fabres-Klein,
              Mary Hellen and Oliveira, Guilherme and Ribon, Andr{\'e}a
              Oliveira Barros",
  journal  = "Genome Announc.",
  volume   =  4,
  number   =  2,
  month    =  apr,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Abaev2016-sf,
  title    = "Draft Genome Sequences of Exfoliative Toxin {A-Producing}
              Staphylococcus aureus Strains {B-7772} and {B-7777}
              ({CC8/ST2993}) and {B-7774} ({CC15/ST2126)}, Isolated in a
              Maternity Hospital in the Central Federal District of Russia",
  author   = "Abaev, Igor and Skryabin, Yury and Kislichkina, Angelina and
              Bogun, Alexandr and Korobova, Olga and Mayskaya, Nadezhda and
              Shemyakin, Igor and Dyatlov, Ivan",
  abstract = "Staphylococcus aureus clonal complex 8 (CC8) has not been
              associated with staphylococcal scalded-skin syndrome (SSSS) in
              newborns and exfoliative toxin genes. Here, we report the draft
              genome sequences of exfoliative toxin A-producing B-7772, B-7777
              (both CC8), and B-7774 (CC15) strains associated with SSSS in
              newborns.",
  journal  = "Genome Announc.",
  volume   =  4,
  number   =  2,
  month    =  mar,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Nielsen2016-bg,
  title    = "Fatal Septicemia Linked to Transmission of {MRSA} Clonal Complex
              398 in Hospital and Nursing Home, Denmark",
  author   = "Nielsen, Rikke Thoft and Kemp, Michael and Holm, Anette and Skov,
              Marianne Nielsine and Detlefsen, Mette and Hasman, Henrik and
              Aarestrup, Frank M{\o}ller and Kaas, Rolf Sommer and Nielsen,
              Jesper Boye and Westh, Henrik and Kolmos, Hans J{\o}rn",
  abstract = "We describe 2 fatal cases of methicillin-resistant Staphylococcus
              aureus (MRSA) clonal complex 398 septicemia in persons who had no
              contact with livestock. Whole-genome sequencing of the isolated
              MRSA strains strongly suggest that both were of animal origin and
              that the patients had been infected through 2 independent
              person-to-person transmission chains.",
  journal  = "Emerg. Infect. Dis.",
  volume   =  22,
  number   =  5,
  pages    = "900--902",
  month    =  may,
  year     =  2016,
  keywords = "antimicrobial resistance; bacteremia; bacteria; bacterial
              infections; disease transmission; infectious; livestock;
              methicillin-resistant Staphylococcus aureus; molecular
              epidemiology; spa typing;
              staphylococci;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Stine2016-na,
  title    = "Transmission Clusters of {Methicillin-Resistant} Staphylococcus
              Aureus in {Long-Term} Care Facilities Based on {Whole-Genome}
              Sequencing",
  author   = "Stine, O Colin and Burrowes, Shana and David, Sophia and Johnson,
              J Kristie and Roghmann, Mary-Claire",
  abstract = "OBJECTIVE To define how often methicillin-resistant
              Staphylococcus aureus (MRSA) is spread from resident to resident
              in long-term care facilities using whole-genome sequencing DESIGN
              Prospective cohort study SETTING A long-term care facility
              PARTICIPANTS Elderly residents in a long-term care facility
              METHODS Cultures for MRSA were obtained weekly from multiple body
              sites from residents with known MRSA colonization over 12-week
              study periods. Simultaneously, cultures to detect MRSA
              acquisition were obtained weekly from 2 body sites in residents
              without known MRSA colonization. During the first 12-week cycle
              on a single unit, we sequenced 8 MRSA isolates per swab for 2
              body sites from each of 6 residents. During the second 12-week
              cycle, we sequenced 30 MRSA isolates from 13 residents with known
              MRSA colonization and 3 residents who had acquired MRSA
              colonization. RESULTS MRSA isolates from the same swab showed
              little genetic variation between isolates with the exception of
              isolates from wounds. The genetic variation of isolates between
              body sites on an individual was greater than that within a single
              body site with the exception of 1 sample, which had 2 unrelated
              strains among the 8 isolates. In the second cycle, 10 of 16
              residents colonized with MRSA (63\%) shared 1 of 3 closely
              related strains. Of the 3 residents with newly acquired MRSA, 2
              residents harbored isolates that were members of these clusters.
              CONCLUSIONS Point prevalence surveys with whole-genome sequencing
              of MRSA isolates may detect resident-to-resident transmission
              more accurately than routine surveillance cultures for MRSA in
              long-term care facilities. Infect. Control Hosp. Epidemiol.
              2016;1-7.",
  journal  = "Infect. Control Hosp. Epidemiol.",
  pages    = "1--7",
  month    =  mar,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Davis2016-zc,
  title    = "Complete genome of Staphylococcus aureus Tager 104 provides
              evidence of its relation to modern systemic hospital-acquired
              strains",
  author   = "Davis, 4th, Richard W and Brannen, Andrew D and Hossain, Mohammad
              J and Monsma, Scott and Bock, Paul E and Nahrendorf, Matthias and
              Mead, David and Lodes, Michael and Liles, Mark R and Panizzi,
              Peter",
  abstract = "BACKGROUND: Staphylococcus aureus (S. aureus) infections range in
              severity due to expression of certain virulence factors encoded
              on mobile genetic elements (MGE). As such, characterization of
              these MGE, as well as single nucleotide polymorphisms, is of high
              clinical and microbiological importance. To understand the
              evolution of these dangerous pathogens, it is paramount to define
              reference strains that may predate MGE acquisition. One such
              candidate is S. aureus Tager 104, a previously uncharacterized
              strain isolated from a patient with impetigo in 1947. RESULTS: We
              show here that S. aureus Tager 104 can survive in the bloodstream
              and infect na{\"\i}ve organs. We also demonstrate a procedure to
              construct and validate the assembly of S. aureus genomes, using
              Tager 104 as a proof-of-concept. In so doing, we bridged
              confounding gap regions that limited our initial attempts to
              close this 2.82 Mb genome, through integration of data from
              Illumina Nextera paired-end, PacBio RS, and Lucigen NxSeq
              mate-pair libraries. Furthermore, we provide independent
              confirmation of our segmental arrangement of the Tager 104 genome
              by the sole use of Lucigen NxSeq libraries filled by paired-end
              MiSeq reads and alignment with SPAdes software. Genomic analysis
              of Tager 104 revealed limited MGE, and a $\nu$Sa$\beta$ island
              configuration that is reminiscent of other hospital acquired S.
              aureus genomes. CONCLUSIONS: Tager 104 represents an
              early-branching ancestor of certain hospital-acquired strains.
              Combined with its earlier isolation date and limited content of
              MGE, Tager 104 can serve as a viable reference for future
              comparative genome studies.",
  journal  = "BMC Genomics",
  volume   =  17,
  number   =  1,
  pages    = "179",
  month    =  mar,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Silva2016-rh,
  title    = "Draft Genome Sequences of Staphylococcus aureus Strains Isolated
              from Subclinical Bovine Mastitis in Brazil",
  author   = "Silva, Danielle Mendes and da Silva, M{\^o}nica Pacheco and
              Vidigal, Pedro M Pereira and Barcelos, Rafael Mazioli and Klein,
              Raphael Contelli and Aguilar, Ananda Pereira and Fabres-Klein,
              Mary Hellen and Oliveira, Guilherme and Ribon, Andr{\'e}a
              Oliveira Barros",
  abstract = "Here, we present the draft genome sequences of four
              Staphylococcus aureus strains isolated from mastitic milk
              collected from animals with subclinical manifestations. Three of
              them were typed as sequence type 126 (ST126), a genotype with no
              genome sequence available. ST126 is found in several herds of
              southern Brazil and is described as a bovine pathogen strongly
              associated with milk around the world.",
  journal  = "Genome Announc.",
  volume   =  4,
  number   =  1,
  month    =  feb,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Greninger2016-yp,
  title    = "{Whole-Genome} Sequencing of {Methicillin-Resistant}
              Staphylococcus aureus Resistant to {Fifth-Generation}
              Cephalosporins Reveals Potential {Non-mecA} Mechanisms of
              Resistance",
  author   = "Greninger, Alexander L and Chatterjee, Som S and Chan, Liana C
              and Hamilton, Stephanie M and Chambers, Henry F and Chiu, Charles
              Y",
  abstract = "Fifth-generation cephalosporins, ceftobiprole and ceftaroline,
              are promising drugs for treatment of bacterial infections from
              methicillin-resistant Staphylococcus aureus (MRSA). These
              antibiotics are able to bind native PBP2a, the penicillin-binding
              protein encoded by the mecA resistance determinant that mediates
              broad class resistance to nearly all other beta-lactam
              antibiotics, at clinically achievable concentrations. Mechanisms
              of resistance to ceftaroline based on mecA mutations have been
              previously described. Here we compare the genomes of 11 total
              parent-daughter strains of Staphylococcus aureus for which
              specific selection by serial passaging with ceftaroline or
              ceftobiprole was used to identify novel non-mecA mechanisms of
              resistance. All 5 ceftaroline-resistant strains, derived from 5
              different parental strains, contained mutations directly upstream
              of the pbp4 gene (coding for the PBP4 protein), including four
              with the same thymidine insertion located 377 nucleotides
              upstream of the promoter site. In 4 of 5 independent
              ceftaroline-driven selections, we also isolated mutations to the
              same residue (Asn138) in PBP4. In addition, mutations in
              additional candidate genes such as ClpX endopeptidase, PP2C
              protein phosphatase and transcription terminator Rho, previously
              undescribed in the context of resistance to ceftaroline or
              ceftobiprole, were detected in multiple selections. These genomic
              findings suggest that non-mecA mechanisms, while yet to be
              encountered in the clinical setting, may also be important in
              mediating resistance to 5th-generation cephalosporins.",
  journal  = "PLoS One",
  volume   =  11,
  number   =  2,
  pages    = "e0149541",
  month    =  feb,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Khan2016-ez,
  title    = "Draft Genome Sequences of Two {Methicillin-Resistant} Clinical
              Staphylococcus aureus Isolates",
  author   = "Khan, Saeed and Sung, Kidon and Iram, Saira and Nawaz, Mohamed
              and Xu, Joshua and Marasa, Bernard",
  abstract = "Here, we report the draft genome sequences of two
              methicillin-resistant Staphylococcus aureus (MRSA) clinical
              isolates, hospital-associated perirectal isolate 32S (ST 239)
              from a colitis tracheostomy patient and community-associated MRSA
              isolate 42S (ST 772) from a hepatic-splenomegaly patient in
              Rawalpindi, Pakistan.",
  journal  = "Genome Announc.",
  volume   =  4,
  number   =  1,
  month    =  feb,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Holmes2016-yn,
  title    = "Genomic Analysis of Companion Rabbit Staphylococcus aureus",
  author   = "Holmes, Mark A and Harrison, Ewan M and Fisher, Elizabeth A and
              Graham, Elizabeth M and Parkhill, Julian and Foster, Geoffrey and
              Paterson, Gavin K",
  abstract = "In addition to being an important human pathogen, Staphylococcus
              aureus is able to cause a variety of infections in numerous other
              host species. While the S. aureus strains causing infection in
              several of these hosts have been well characterised, this is not
              the case for companion rabbits (Oryctolagus cuniculus), where
              little data are available on S. aureus strains from this host. To
              address this deficiency we have performed antimicrobial
              susceptibility testing and genome sequencing on a collection of
              S. aureus isolates from companion rabbits. The findings show a
              diverse S. aureus population is able to cause infection in this
              host, and while antimicrobial resistance was uncommon, the
              isolates possess a range of known and putative virulence factors
              consistent with a diverse clinical presentation in companion
              rabbits including severe abscesses. We additionally show that
              companion rabbit isolates carry polymorphisms within dltB as
              described as underlying host-adaption of S. aureus to farmed
              rabbits. The availability of S. aureus genome sequences from
              companion rabbits provides an important aid to understanding the
              pathogenesis of disease in this host and in the clinical
              management and surveillance of these infections.",
  journal  = "PLoS One",
  volume   =  11,
  number   =  3,
  pages    = "e0151458",
  month    =  mar,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
 }

 @ARTICLE{Kong2016-eb,
  title    = "{Whole-Genome} Sequencing for the Investigation of a Hospital
              Outbreak of {MRSA} in China",
  author   = "Kong, Zhenzhen and Zhao, Peipei and Liu, Haibing and Yu, Xiang
              and Qin, Yanyan and Su, Zhaoliang and Wang, Shengjun and Xu,
              Huaxi and Chen, Jianguo",
  abstract = "Staphylococcus aureus is a globally disseminated drug-resistant
              bacterial species. It remains a leading cause of
              hospital-acquired infection, primarily among immunocompromised
              patients. In 2012, the Affiliated People's Hospital of Jiangsu
              University experienced a putative outbreak of
              methicillin-resistant S. aureus (MRSA) that affected 12 patients
              in the Neurosurgery Department. In this study, whole-genome
              sequencing (WGS) was used to gain insight into the epidemiology
              of the outbreak caused by MRSA, and traditional bacterial
              genotyping approaches were also applied to provide supportive
              evidence for WGS. We sequenced the DNA from 6 isolates associated
              with the outbreak. Phylogenetic analysis was constructed by
              comparing single-nucleotide polymorphisms (SNPs) in the core
              genome of 6 isolates in the present study and another 3
              referenced isolates from GenBank. Of the 6 MRSA sequences in the
              current study, 5 belonged to the same group, clustering with
              T0131, while the other one clustered closely with TW20. All of
              the isolates were identified as ST239-SCCmecIII clones.
              Whole-genome analysis revealed that four of the outbreak isolates
              were more tightly clustered into a group and SA13002 together
              with SA13009 were distinct from the outbreak strains, which were
              considered non-outbreak strains. Based on the sequencing results,
              the antibiotic-resistance gene status (present or absent) was
              almost perfectly concordant with the results of phenotypic
              susceptibility testing. Various toxin genes were also analyzed
              successfully. Our analysis demonstrates that using traditional
              molecular methods and WGS can facilitate the identification of
              outbreaks and help to control nosocomial transmission.",
  journal  = "PLoS One",
  volume   =  11,
  number   =  3,
  pages    = "e0149844",
  month    =  mar,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Sidjabat2015-nx,
  title    = "Draft Genome Sequences of Burkholderia pseudomallei and
              Staphylococcus aureus, Isolated from a Patient with Chronic
              Rhinosinusitis",
  author   = "Sidjabat, Hanna E and Cottrell, Kyra and Cervin, Anders",
  abstract = "Here, we report the draft genome sequences of Burkholderia
              pseudomallei and Staphylococcus aureus causing chronic
              rhinosinusitis. Whole-genome sequencing determined the B.
              pseudomallei as sequence type (ST) 1381 and the S. aureus as ST8.
              B. pseudomallei possessed the blaOXA-59 gene. This study
              illustrates the potential emergence of B. pseudomallei in cases
              of chronic rhinosinusitis.",
  journal  = "Genome Announc.",
  volume   =  3,
  number   =  5,
  month    =  oct,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Sharma2015-mr,
  title    = "Draft Genome Sequence of a Staphylococcus aureus Strain Isolated
              from a Cow with Clinical Mastitis",
  author   = "Sharma, Paresh and Reddy, D Peddi and Kumar, P Anand and
              Gadicherla, Ramya and George, Neena and Bhandari, Vasundhra",
  abstract = "We report here the draft genome of Staphylococcus aureus causing
              clinical mastitis in a cow from India. It is a major causative
              agent of mastitis and, further, livestock-associated strains are
              emerging as a potential threat to public health, thereby
              warranting studies to understand the genome of this deadly
              pathogen.",
  journal  = "Genome Announc.",
  volume   =  3,
  number   =  4,
  month    =  aug,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Soni2015-tm,
  title    = "Draft Genome Sequence of {Methicillin-Sensitive} Staphylococcus
              aureus {ATCC} 29213",
  author   = "Soni, Isha and Chakrapani, Harinath and Chopra, Sidharth",
  abstract = "Staphylococcus aureus subsp. aureus ATCC 29213 is one of the most
              commonly used strains in drug discovery research and for quality
              control. We report the completed draft genome sequence for the
              strain.",
  journal  = "Genome Announc.",
  volume   =  3,
  number   =  5,
  month    =  sep,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Marasa2015-ve,
  title    = "Draft Genome Sequence of {Methicillin-Resistant} Clinical
              Staphylococcus aureus Isolate {51S} (Sequence Type 291)",
  author   = "Marasa, Bernard S and Khan, Saeed and Iram, Saira and Sung, Kidon
              and Xu, Joshua",
  abstract = "We report the draft genome sequence of a methicillin-resistant
              clinical Staphylococcus aureus isolate with a novel spa type and
              sequence type (ST291), isolated from a renal failure patient in
              Rawalpindi, Pakistan.",
  journal  = "Genome Announc.",
  volume   =  3,
  number   =  5,
  month    =  sep,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Budd2015-ry,
  title    = "Extensive Genomic Diversity among {Bovine-Adapted} Staphylococcus
              aureus: Evidence for a Genomic Rearrangement within {CC97}",
  author   = "Budd, Kathleen E and McCoy, Finola and Monecke, Stefan and
              Cormican, Paul and Mitchell, Jennifer and Keane, Orla M",
  abstract = "Staphylococcus aureus is an important pathogen associated with
              both human and veterinary disease and is a common cause of bovine
              mastitis. Genomic heterogeneity exists between S. aureus strains
              and has been implicated in the adaptation of specific strains to
              colonise particular mammalian hosts. Knowledge of the factors
              required for host specificity and virulence is important for
              understanding the pathogenesis and management of S. aureus
              mastitis. In this study, a panel of mastitis-associated S. aureus
              isolates (n = 126) was tested for resistance to antibiotics
              commonly used to treat mastitis. Over half of the isolates (52\%)
              demonstrated resistance to penicillin and ampicillin but all were
              susceptible to the other antibiotics tested. S. aureus isolates
              were further examined for their clonal diversity by Multi-Locus
              Sequence Typing (MLST). In total, 18 different sequence types
              (STs) were identified and eBURST analysis demonstrated that the
              majority of isolates grouped into clonal complexes CC97, CC151 or
              sequence type (ST) 136. Analysis of the role of recombination
              events in determining S. aureus population structure determined
              that ST diversification through nucleotide substitutions were
              more likely to be due to recombination compared to point
              mutation, with regions of the genome possibly acting as
              recombination hotspots. DNA microarray analysis revealed a large
              number of differences amongst S. aureus STs in their variable
              genome content, including genes associated with capsule and
              biofilm formation and adhesion factors. Finally, evidence for a
              genomic arrangement was observed within isolates from CC97 with
              the ST71-like subgroup showing evidence of an IS431 insertion
              element having replaced approximately 30 kb of DNA including the
              ica operon and histidine biosynthesis genes, resulting in
              histidine auxotrophy. This genomic rearrangement may be
              responsible for the diversification of ST71 into an emerging
              bovine adapted subgroup.",
  journal  = "PLoS One",
  volume   =  10,
  number   =  8,
  pages    = "e0134592",
  month    =  aug,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Shiroma2015-ho,
  title    = "First Complete Genome Sequences of Staphylococcus aureus subsp.
              aureus Rosenbach 1884 ({DSM} 20231T), Determined by {PacBio}
              {Single-Molecule} {Real-Time} Technology",
  author   = "Shiroma, Akino and Terabayashi, Yasunobu and Nakano, Kazuma and
              Shimoji, Makiko and Tamotsu, Hinako and Ashimine, Noriko and
              Ohki, Shun and Shinzato, Misuzu and Teruya, Kuniko and Satou,
              Kazuhito and Hirano, Takashi",
  abstract = "The first complete genome sequences of Staphylococcus aureus
              subsp. aureus Rosenbach 1884 strain DSM 20231(T), the type strain
              of the bacterium causing staphylococcal disease, were determined
              using PacBio RS II. The sequences represent the chromosome
              (2,755,072 bp long; G+C content, 32.86\%) and a plasmid (27,490
              bp long; G+C content, 30.69\%).",
  journal  = "Genome Announc.",
  volume   =  3,
  number   =  4,
  month    =  jul,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Stephens2015-kc,
  title    = "Draft Genome Sequence of a {Community-Associated}
              {Methicillin-Resistant} {Panton-Valentine} {Leukocidin-Positive}
              Staphylococcus aureus Sequence Type 30 Isolate from a Pediatric
              Patient with a Lung Infection in Brazil",
  author   = "Stephens, Craig and Cho, Paul Jang-Yeon and Afonso de Araujo,
              Veronica and Gomes, Ivete Martins and de Azevedo Sias, Selma
              Maria and Ara{\'u}jo Cardoso, Claudete A and Riley, Lee W and
              Aguiar-Alves, F{\'a}bio",
  abstract = "The sequence of methicillin-resistant Staphylococcus aureus
              strain B6 (sequence type 30 [ST30], spa type t433, staphylococcal
              chromosomal cassette mec element [SCCmec] type IVc,
              Panton-Valentine leukocidin [PVL] positive), isolated from a
              pediatric patient with a lung infection in Niter{\'o}i, Rio de
              Janeiro, Brazil, is described here. The draft genome sequence
              includes a 2.8-Mb chromosome, accompanied by a 20-kb plasmid
              containing blaZ and two small cryptic plasmids.",
  journal  = "Genome Announc.",
  volume   =  3,
  number   =  4,
  month    =  aug,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Nemet2015-mo,
  title    = "Draft Genome Sequence of a Highly Virulent Rabbit Staphylococcus
              aureus Strain",
  author   = "N{\'e}met, Zolt{\'a}n and Albert, Ervin and Nagy, Tibor and
              Olasz, Ferenc and Barta, Endre and Kiss, J{\'a}nos and D{\'a}n,
              {\'A}d{\'a}m and B{\'a}nyai, Kriszti{\'a}n and Hermans, Katleen
              and Biksi, Imre",
  abstract = "We report the draft genome sequence of Staphylococcus aureus
              Sp17, a typical highly virulent (HV) rabbit strain. As current
              medicine apparently fails to effectively reduce disease and
              economical losses caused by this organism, it is essential to
              gain better insight on its genomic arrangement.",
  journal  = "Genome Announc.",
  volume   =  3,
  number   =  4,
  month    =  jul,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Driebe2015-ia,
  title    = "Using Whole Genome Analysis to Examine Recombination across
              Diverse Sequence Types of Staphylococcus aureus",
  author   = "Driebe, Elizabeth M and Sahl, Jason W and Roe, Chandler and
              Bowers, Jolene R and Schupp, James M and Gillece, John D and
              Kelley, Erin and Price, Lance B and Pearson, Talima R and Hepp,
              Crystal M and Brzoska, Pius M and Cummings, Craig A and Furtado,
              Manohar R and Andersen, Paal S and Stegger, Marc and Engelthaler,
              David M and Keim, Paul S",
  abstract = "Staphylococcus aureus is an important clinical pathogen worldwide
              and understanding this organism's phylogeny and, in particular,
              the role of recombination, is important both to understand the
              overall spread of virulent lineages and to characterize
              outbreaks. To further elucidate the phylogeny of S. aureus, 35
              diverse strains were sequenced using whole genome sequencing. In
              addition, 29 publicly available whole genome sequences were
              included to create a single nucleotide polymorphism (SNP)-based
              phylogenetic tree encompassing 11 distinct lineages. All strains
              of a particular sequence type fell into the same clade with clear
              groupings of the major clonal complexes of CC8, CC5, CC30, CC45
              and CC1. Using a novel analysis method, we plotted the homoplasy
              density and SNP density across the whole genome and found
              evidence of recombination throughout the entire chromosome, but
              when we examined individual clonal lineages we found very little
              recombination. However, when we analyzed three branches of
              multiple lineages, we saw intermediate and differing levels of
              recombination between them. These data demonstrate that in S.
              aureus, recombination occurs across major lineages that
              subsequently expand in a clonal manner. Estimated mutation rates
              for the CC8 and CC5 lineages were different from each other.
              While the CC8 lineage rate was similar to previous studies, the
              CC5 lineage was 100-fold greater. Fifty known virulence genes
              were screened in all genomes in silico to determine their
              distribution across major clades. Thirty-three genes were present
              variably across clades, most of which were not constrained by
              ancestry, indicating horizontal gene transfer or gene loss.",
  journal  = "PLoS One",
  volume   =  10,
  number   =  7,
  pages    = "e0130955",
  month    =  jul,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Cameron2015-vs,
  title    = "Draft Genome Sequences of Clinical {Daptomycin-Nonsusceptible}
              {Methicillin-Resistant} Staphylococcus aureus Strain {APS211} and
              Its {Daptomycin-Susceptible} Progenitor {APS210}",
  author   = "Cameron, David R and Jiang, Jhih-Hang and Abbott, Iain J and
              Spelman, Denis W and Peleg, Anton Y",
  abstract = "To assess the genetic factors contributing to daptomycin
              resistance in Staphylococcus aureus, the draft genome of a
              clinically derived daptomycin-nonsusceptible isolate APS211 was
              generated and compared to the draft sequence of its susceptible
              progenitor strain APS210. Four genetic differences were
              identified including a previously described mutation within the
              mprF gene.",
  journal  = "Genome Announc.",
  volume   =  3,
  number   =  3,
  month    =  jun,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Crovadore2015-vb,
  title    = "{Whole-Genome} Sequences of 15 Strains of Staphylococcus aureus
              subsp. aureus Isolated from Foodstuff and Human Clinical Samples",
  author   = "Crovadore, Julien and Calmin, Gautier and Tonacini, Jenna and
              Chablais, Romain and Baumgartner, Andreas and Schnyder, Bruno and
              Hodille, Elisabeth and Lefort, Fran{\c c}ois",
  abstract = "The whole-genome sequences of 15 strains of Staphylococcus aureus
              (10 strains isolated from foodstuff samples in Switzerland and
              five from human clinical samples) were obtained by Illumina
              sequencing. Most strains fit within the known diversity for the
              species, but one (SA-120) possessed a higher G+C content and a
              higher number of genes than usual.",
  journal  = "Genome Announc.",
  volume   =  3,
  number   =  3,
  month    =  jun,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 % The entry below contains non-ASCII chars that could not be converted
 % to a LaTeX equivalent.
 @ARTICLE{Botka2015-wl,
  title    = "Complete genome analysis of two new bacteriophages isolated from
              impetigo strains of Staphylococcus aureus",
  author   = "Botka, Tibor and R{\r u}{\v z}i{\v c}kov{\'a}, Vladislava and
              Kone{\v c}n{\'a}, Hana and Pant{\r u}{\v c}ek, Roman and
              Rychl{\'\i}k, Ivan and Zdr{\'a}hal, Zbyn{\v e}k and Petr{\'a}{\v
              s}, Petr and Do{\v s}ka{\v r}, Ji{\v r}{\'\i}",
  abstract = "Exfoliative toxin A (ETA)-coding temperate bacteriophages are
              leading contributors to the toxic phenotype of impetigo strains
              of Staphylococcus aureus. Two distinct eta gene-positive
              bacteriophages isolated from S. aureus strains which recently
              caused massive outbreaks of pemphigus neonatorum in Czech
              maternity hospitals were characterized. The phages, designated
              ϕB166 and ϕB236, were able to transfer the eta gene into a
              prophageless S. aureus strain which afterwards converted into an
              ETA producer. Complete phage genome sequences were determined,
              and a comparative analysis of five designed genomic regions
              revealed major variances between them. They differed in the
              genome size, number of open reading frames, genome architecture,
              and virion protein patterns. Their high mutual sequence
              similarity was detected only in the terminal regions of the
              genome. When compared with the so far described eta phage
              genomes, noticeable differences were found. Thus, both phages
              represent two new lineages of as yet not characterized
              bacteriophages of the Siphoviridae family having impact on
              pathogenicity of impetigo strains of S. aureus.",
  journal  = "Virus Genes",
  volume   =  51,
  number   =  1,
  pages    = "122--131",
  month    =  aug,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Planet2015-jk,
  title    = "Parallel Epidemics of {Community-Associated}
              {Methicillin-Resistant} Staphylococcus aureus {USA300} Infection
              in North and South America",
  author   = "Planet, Paul J and Diaz, Lorena and Kolokotronis, Sergios-Orestis
              and Narechania, Apurva and Reyes, Jinnethe and Xing, Galen and
              Rincon, Sandra and Smith, Hannah and Panesso, Diana and Ryan,
              Chanelle and Smith, Dylan P and Guzman, Manuel and Zurita,
              Jeannete and Sebra, Robert and Deikus, Gintaras and Nolan, Rathel
              L and Tenover, Fred C and Weinstock, George M and Robinson, D
              Ashley and Arias, Cesar A",
  abstract = "BACKGROUND: The community-associated methicillin-resistant
              Staphylococcus aureus (CA-MRSA) epidemic in the United States is
              attributed to the spread of the USA300 clone. An epidemic of
              CA-MRSA closely related to USA300 has occurred in northern South
              America (USA300 Latin-American variant, USA300-LV). Using
              phylogenomic analysis, we aimed to understand the relationships
              between these 2 epidemics. METHODS: We sequenced the genomes of
              51 MRSA clinical isolates collected between 1999 and 2012 from
              the United States, Colombia, Venezuela, and Ecuador. Phylogenetic
              analysis was used to infer the relationships and times since the
              divergence of the major clades. RESULTS: Phylogenetic analyses
              revealed 2 dominant clades that segregated by geographical
              region, had a putative common ancestor in 1975, and originated in
              1989, in North America, and in 1985, in South America. Emergence
              of these parallel epidemics coincides with the independent
              acquisition of the arginine catabolic mobile element (ACME) in
              North American isolates and a novel copper and mercury resistance
              (COMER) mobile element in South American isolates. CONCLUSIONS:
              Our results reveal the existence of 2 parallel USA300 epidemics
              that shared a recent common ancestor. The simultaneous rapid
              dissemination of these 2 epidemic clades suggests the presence of
              shared, potentially convergent adaptations that enhance fitness
              and ability to spread.",
  journal  = "J. Infect. Dis.",
  volume   =  212,
  number   =  12,
  pages    = "1874--1882",
  month    =  dec,
  year     =  2015,
  keywords = "MRSA; USA300; USA300-LV;
              epidemics;Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers"
 }

 @ARTICLE{Khokhlova2015-lr,
  title    = "Healthcare- and {Community-Associated} {Methicillin-Resistant}
              Staphylococcus aureus ({MRSA}) and Fatal Pneumonia with Pediatric
              Deaths in Krasnoyarsk, Siberian Russia: Unique {MRSA's} Multiple
              Virulence Factors, Genome, and Stepwise Evolution",
  author   = "Khokhlova, Olga E and Hung, Wei-Chun and Wan, Tsai-Wen and Iwao,
              Yasuhisa and Takano, Tomomi and Higuchi, Wataru and Yachenko,
              Svetlana V and Teplyakova, Olga V and Kamshilova, Vera V and
              Kotlovsky, Yuri V and Nishiyama, Akihito and Reva, Ivan V and
              Sidorenko, Sergey V and Peryanova, Olga V and Reva, Galina V and
              Teng, Lee-Jene and Salmina, Alla B and Yamamoto, Tatsuo",
  abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) is a common
              multidrug-resistant (MDR) pathogen. We herein discussed MRSA and
              its infections in Krasnoyarsk, Siberian Russia between 2007 and
              2011. The incidence of MRSA in 3,662 subjects was 22.0\% and
              2.9\% for healthcare- and community-associated MRSA (HA- and
              CA-MRSA), respectively. The 15-day mortality rates for MRSA
              hospital- and community-acquired pneumonia (HAP and CAP) were
              6.5\% and 50\%, respectively. MRSA CAP cases included pediatric
              deaths; of the MRSA pneumonia episodes available, $\geq$27.3\%
              were associated with bacteremia. Most cases of HA-MRSA examined
              exhibited ST239/spa3(t037)/SCCmecIII.1.1.2 (designated as
              ST239Kras), while all CA-MRSA cases examined were
              ST8/spa1(t008)/SCCmecIV.3.1.1(IVc) (designated as ST8Kras).
              ST239Kras and ST8Kras strongly expressed cytolytic peptide
              (phenol-soluble modulin $\alpha$, PSM$\alpha$; and
              $\delta$-hemolysin, Hld) genes, similar to CA-MRSA. ST239Kras
              pneumonia may have been attributed to a unique set of multiple
              virulence factors (MVFs): toxic shock syndrome toxin-1 (TSST-1),
              elevated PSM$\alpha$/Hld expression, $\alpha$-hemolysin, the
              staphylococcal enterotoxin SEK/SEQ, the immune evasion factor
              SCIN/SAK, and collagen adhesin. Regarding ST8Kras, SEA was
              included in MVFs, some of which were common to ST239Kras. The
              ST239Kras (strain OC3) genome contained: a completely unique
              phage, $\varphi$Sa7-like (W), with no att repetition; S. aureus
              pathogenicity island SaPI2R, the first TSST-1 gene-positive
              (tst+) SaPI in the ST239 lineage; and a super copy of IS256
              ($\geq$22 copies/genome). ST239Kras carried the Brazilian
              SCCmecIII.1.1.2 and United Kingdom-type tst. ST239Kras and
              ST8Kras were MDR, with the same levofloxacin resistance
              mutations; small, but transmissible chloramphenicol resistance
              plasmids spread widely enough to not be ignored. These results
              suggest that novel MDR and MVF+ HA- and CA-MRSA (ST239Kras and
              ST8Kras) emerged in Siberian Russia (Krasnoyarsk) associated with
              fatal pneumonia, and also with ST239Kras, a new (Siberian
              Russian) clade of the ST239 lineage, which was created through
              stepwise evolution during its potential transmission route of
              Brazil-Europe-Russia/Krasnoyarsk, thereby selective advantages
              from unique MVFs and the MDR.",
  journal  = "PLoS One",
  volume   =  10,
  number   =  6,
  pages    = "e0128017",
  month    =  jun,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Aalbaek2015-be,
  title    = "{Whole-Genome} Sequence of Staphylococcus aureus {S54F9} Isolated
              from a Chronic Disseminated Porcine Lung Abscess and Used in
              Human Infection Models",
  author   = "Aalb{\ae}k, Bent and Jensen, Louise Kruse and Jensen, Henrik
              Elvang and Olsen, John Elmerdahl and Christensen, Henrik",
  abstract = "We obtained a draft genome sequence of Staphylococcus aureus
              strain S54F9, which was isolated from a chronic disseminated
              porcine lung abscess and used in porcine infection models. Genes
              coding for a number of toxins, including enterotoxins and
              superantigen, were demonstrated in this strain.",
  journal  = "Genome Announc.",
  volume   =  3,
  number   =  5,
  month    =  oct,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Chang2015-gk,
  title    = "Isolation and Genome Characterization of the Virulent
              Staphylococcus aureus Bacteriophage {SA97}",
  author   = "Chang, Yoonjee and Shin, Hakdong and Lee, Ju-Hoon and Park, Chul
              Jong and Paik, Soon-Young and Ryu, Sangryeol",
  abstract = "A novel bacteriophage that infects S. aureus, SA97, was isolated
              and characterized. The phage SA97 belongs to the Siphoviridae
              family, and the cell wall teichoic acid (WTA) was found to be a
              host receptor of the phage SA97. Genome analysis revealed that
              SA97 contains 40,592 bp of DNA encoding 54 predicted open reading
              frames (ORFs), and none of these genes were related to virulence
              or drug resistance. Although a few genes associated with lysogen
              formation were detected in the phage SA97 genome, the phage SA97
              produced neither lysogen nor transductant in S. aureus. These
              results suggest that the phage SA97 may be a promising candidate
              for controlling S. aureus.",
  journal  = "Viruses",
  volume   =  7,
  number   =  10,
  pages    = "5225--5242",
  month    =  oct,
  year     =  2015,
  keywords = "Staphylococcus aureus; bacteriophage; genome
              analysis;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Richards2015-mm,
  title    = "Persistent Staphylococcus aureus isolates from two independent
              cases of bacteremia display increased bacterial fitness and novel
              immune evasion phenotypes",
  author   = "Richards, R L and Haigh, R D and Pascoe, B and Sheppard, S K and
              Price, F and Jenkins, D and Rajakumar, K and Morrissey, J A",
  abstract = "Staphylococcus aureus bacteremia cases are complicated by
              bacterial persistence and treatment failure despite the confirmed
              in vitro susceptibility of the infecting strain to administered
              antibiotics. A high incidence of methicillin-resistant S. aureus
              (MRSA) bacteremia cases are classified as persistent and are
              associated with poorer patient outcomes. It is still unclear how
              S. aureus evades the host immune system and resists antibiotic
              treatment for the prolonged duration of a persistent infection.
              In this study, the genetic changes and associated phenotypic
              traits specific to S. aureus persistent bacteremia were
              identified by comparing temporally dispersed isolates from
              persistent infections (persistent isolates) originating from two
              independent persistent S. aureus bacteremia cases with the
              initial infection isolates and with three resolved S. aureus
              bacteremia isolates from the same genetic background. Several
              novel traits were associated specifically with both independent
              sets of persistent S. aureus isolates compared to both the
              initial isolates and the isolates from resolved infections
              (resolved isolates). These traits included (i) increased growth
              under nutrient-poor conditions; (ii) increased tolerance of iron
              toxicity; (iii) higher expression of cell surface proteins
              involved in immune evasion and stress responses; and (iv)
              attenuated virulence in a Galleria mellonella larva infection
              model that was not associated with small-colony variation or
              metabolic dormancy such as had been seen previously. Whole-genome
              sequence analysis identified different single nucleotide
              mutations within the mprF genes of all the isolates with the
              adaptive persistence traits from both independent cases. Overall,
              our data indicate a novel role for MprF function during
              development of S. aureus persistence by increasing bacterial
              fitness and immune evasion.",
  journal  = "Infect. Immun.",
  volume   =  83,
  number   =  8,
  pages    = "3311--3324",
  month    =  aug,
  year     =  2015,
  keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;biometals;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers"
 }

 @ARTICLE{Sabat2015-jb,
  title    = "Whole-genome analysis of an oxacillin-susceptible {CC80}
              mecA-positive Staphylococcus aureus clinical isolate: insights
              into the mechanisms of cryptic methicillin resistance",
  author   = "Sabat, Artur J and Pournaras, Spyros and Akkerboom, Viktoria and
              Tsakris, Athanassios and Grundmann, Hajo and Friedrich, Alexander
              W",
  abstract = "OBJECTIVES: The mec and bla systems, among other genetic factors,
              are critical in regulating the expression of methicillin
              resistance in Staphylococcus aureus. We examined by WGS a
              naturally occurring oxacillin-susceptible mecA-positive S. aureus
              isolate to identify the mechanism conferring oxacillin
              susceptibility. METHODS: The mecA-positive oxacillin-susceptible
              S. aureus isolate GR2 (penicillin and oxacillin MICs 0.094 and 1
              mg/L, respectively), belonging to clonal complex 80, was
              characterized. DNA fragment libraries were sequenced on Roche 454
              and Illumina MiSeq sequencers and de novo assembly of the genome
              was generated using SeqMan NGen software. Plasmid curing was
              conducted by SDS treatment. Expression of mecA was quantified
              without/with $\beta$-lactam pressure. RESULTS: The genome of GR2
              consisted of a 2 792 802 bp chromosome and plasmids pGR2A (28 895
              bp) and pGR2B (2473 bp). GR2 carried SCCmec type IV, with a
              truncated/non-functional mecR1 gene and no mecI. A single copy of
              the bla system, with an organization unique for S. aureus, was
              found, harboured by plasmid pGR2A. Particularly, the blaZ gene
              was orientated like its regulatory genes, blaI and blaR1, and a
              gene encoding transposase IS66 was integrated between blaZ and
              the regulatory genes deleting the 5'-end of blaR1; blaI, encoding
              blaZ/mecA repressor, was intact. After plasmid loss, GR2 became
              penicillin and oxacillin resistant (MICs 0.5 and 6 mg/L,
              respectively). CONCLUSIONS: We can conclude that after exposure
              to $\beta$-lactams, the non-functional BlaR1 does not cleave the
              mecA repressor BlaI, derepression does not occur and mecA is not
              efficiently expressed. Removal of the bla system after curing of
              pGR2A allows constitutive expression of mecA, resulting in
              oxacillin and penicillin resistance.",
  journal  = "J. Antimicrob. Chemother.",
  volume   =  70,
  number   =  11,
  pages    = "2956--2964",
  month    =  nov,
  year     =  2015,
  keywords = "Staphylococcus;oxacillin;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Hamed2015-om,
  title    = "Whole genome sequence typing and microarray profiling of nasal
              and blood stream methicillin-resistant Staphylococcus aureus
              isolates: Clues to phylogeny and invasiveness",
  author   = "Hamed, Mohamed and Nitsche-Schmitz, Daniel Patric and Ruffing,
              Ulla and Steglich, Matthias and Dordel, Janina and Nguyen, Duy
              and Brink, Jan-Hendrik and Chhatwal, Gursharan Singh and
              Herrmann, Mathias and N{\"u}bel, Ulrich and Helms, Volkhard and
              von M{\"u}ller, Lutz",
  abstract = "Hospital-associated methicillin-resistant Staphylococcus aureus
              (MRSA) infections are frequently caused by predominant clusters
              of closely related isolates that cannot be discriminated by
              conventional diagnostic typing methods. Whole genome sequencing
              (WGS) and DNA microarray (MA) now allow for better discrimination
              within a prevalent clonal complex (CC). This single center
              exploratory study aims to distinguish invasive (blood stream
              infection) and non-invasive (nasal colonization) MRSA isolates of
              the same CC5 into phylogenetic- and virulence-associated
              genotypic subgroups by WGS and MA. A cohort of twelve blood
              stream and fifteen nasal MRSA isolates of CC5 (spa-types t003 and
              t504) was selected. Isolates were propagated at the same period
              of time from unrelated patients treated at the University of
              Saarland Medical Center, Germany. Rooted phylotyping based on WGS
              with core-genome single nucleotide polymorphism (SNP) analysis
              revealed two local clusters of closely related CC5 subgroups
              (t504 and Clade1 t003) which were separated from other local t003
              isolates and from unrelated CC5 MRSA reference isolates of German
              origin. Phylogenetic subtyping was not associated with
              invasiveness when comparing blood stream and nasal isolates.
              Clustering based on MA profiles was not concordant with WGS
              phylotyping, but MA profiles may identify subgroups of isolates
              with nasal and blood stream origin. Among the new putative
              virulence associated genes identified by WGS, the strongest
              association with blood stream infections was shown for ebhB
              mutants. Analysis of the core-genome together with the accessory
              genome enables subtyping of closely related MRSA isolates
              according to phylogeny and presumably also to the potential
              virulence capacity of isolates.",
  journal  = "Infect. Genet. Evol.",
  volume   =  36,
  pages    = "475--482",
  month    =  dec,
  year     =  2015,
  keywords = "DNA microarray; Invasiveness; MRSA; Phylogeny; Staphylococcus
              aureus; Whole genome
              sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Steinig2015-si,
  title    = "Single-molecule sequencing reveals the molecular basis of
              multidrug-resistance in {ST772} methicillin-resistant
              Staphylococcus aureus",
  author   = "Steinig, Eike J and Andersson, Patiyan and Harris, Simon R and
              Sarovich, Derek S and Manoharan, Anand and Coupland, Paul and
              Holden, Matthew T G and Parkhill, Julian and Bentley, Stephen D
              and Robinson, D Ashley and Tong, Steven Y C",
  abstract = "BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is
              a major cause of hospital-associated infection, but there is
              growing awareness of the emergence of multidrug-resistant
              lineages in community settings around the world. One such lineage
              is ST772-MRSA-V, which has disseminated globally and is
              increasingly prevalent in India. Here, we present the complete
              genome sequence of DAR4145, a strain of the ST772-MRSA-V lineage
              from India, and investigate its genomic characteristics in
              regards to antibiotic resistance and virulence factors. RESULTS:
              Sequencing using single-molecule real-time technology resulted in
              the assembly of a single continuous chromosomal sequence, which
              was error-corrected, annotated and compared to nine draft genome
              assemblies of ST772-MRSA-V from Australia, Malaysia and India. We
              discovered numerous and redundant resistance genes associated
              with mobile genetic elements (MGEs) and known core genome
              mutations that explain the highly antibiotic resistant phenotype
              of DAR4145. Staphylococcal toxins and superantigens, including
              the leukotoxin Panton-Valentinin Leukocidin, were predominantly
              associated with genomic islands and the phage
              $\varphi$-IND772PVL. Some of these mobile resistance and
              virulence factors were variably present in other strains of the
              ST772-MRSA-V lineage. CONCLUSIONS: The genomic characteristics
              presented here emphasize the contribution of MGEs to the
              emergence of multidrug-resistant and highly virulent strains of
              community-associated MRSA. Antibiotic resistance was further
              augmented by chromosomal mutations and redundancy of resistance
              genes. The complete genome of DAR4145 provides a valuable
              resource for future investigations into the global dissemination
              and phylogeography of ST772-MRSA-V.",
  journal  = "BMC Genomics",
  volume   =  16,
  pages    = "388",
  month    =  may,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Stipetic2015-tc,
  title    = "Draft Genome Sequence of Isolate Staphylococcus aureus
              {LHSKBClinical}, Isolated from an Infected Hip",
  author   = "Stipetic, Laurence H and Hamilton, Graham and Dalby, Matthew J
              and Davies, Robert L and Meek, R M Dominic and Ramage, Gordon and
              Smith, David G E and Burgess, Karl E V",
  abstract = "We report here the genome sequence of a clinical isolate of
              Staphylococcus aureus from an orthopedic infection.
              Phenotypically diverse Staphylococcus aureus strains are
              associated with orthopedic infections and subsequent implant
              failure, and some are highly resistant to antibiotics. This
              genome sequence will support further analyses of strains causing
              orthopedic infections.",
  journal  = "Genome Announc.",
  volume   =  3,
  number   =  2,
  month    =  apr,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Cazares-Dominguez2015-re,
  title    = "Vancomycin tolerant, methicillin-resistant Staphylococcus aureus
              reveals the effects of vancomycin on cell wall thickening",
  author   = "C{\'a}zares-Dom{\'\i}nguez, Vicenta and Cruz-C{\'o}rdova,
              Ariadnna and Ochoa, Sara A and Escalona, Gerardo and
              Arellano-Galindo, Jos{\'e} and Rodr{\'\i}guez-Leviz, Alejandra
              and Hern{\'a}ndez-Castro, Rigoberto and L{\'o}pez-Villegas, Edgar
              O and Xicohtencatl-Cortes, Juan",
  abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) is an
              important opportunistic pathogen that causes both healthcare- and
              community-acquired infections. An increase in the incidence of
              these infections may lead to a substantial change in the rate of
              vancomycin usage. Incidence of reduced susceptibility to
              vancomycin has been increasing worldwide for the last few years,
              conferring different levels of resistance to vancomycin as well
              as producing changes in the cell wall structure. The aim of the
              present study was to determine the effect of vancomycin on cell
              wall thickening in clinical isolates of vancomycin-tolerant (VT)
              MRSA obtained from pediatric patients. From a collection of 100
              MRSA clinical isolates from pediatric patients, 12\% (12/100)
              were characterized as VT-MRSA, and from them, 41.66\% (5/12)
              exhibited the heterogeneous vancomycin-intermediate S. aureus
              (hVISA) phenotype. Multiplex-PCR assays revealed 66.66\% (8/12),
              25\% (3/12), and 8.33\% (1/12) of the VT-MRSA isolates were
              associated with agr group II, I, and III polymorphisms,
              respectively; the II-mec gene was amplified from 83.3\% (10/12)
              of the isolates, and the mecIVa gene was amplified from 16.66\%
              (2/12) of the isolates. Pulsed field electrophoresis (PFGE)
              fingerprint analysis showed 62\% similarity among the VT-MRSA
              isolates. Thin transverse sections analyzed by transmission
              electron microscopy (TEM) revealed an average increase of 24 nm
              (105.55\%) in the cell wall thickness of VT-MRSA compared with
              untreated VT-MRSA isolates. In summary, these data revealed that
              the thickened cell walls of VT-MRSA clinical isolates with agr
              type II and SCCmec group II polymorphisms are associated with an
              adaptive resistance to vancomycin.",
  journal  = "PLoS One",
  volume   =  10,
  number   =  3,
  pages    = "e0118791",
  month    =  mar,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Yamaguchi2015-vn,
  title    = "Evolution and single-nucleotide polymorphisms in
              methicillin-resistant Staphylococcus aureus strains with reduced
              susceptibility to vancomycin and daptomycin, based on
              determination of the complete genome",
  author   = "Yamaguchi, Tetsuo and Suzuki, Shingo and Okamura, Sakiko and
              Miura, Yuri and Tsukimori, Ayaka and Nakamura, Itaru and Ito,
              Norihiko and Masuya, Anri and Shiina, Takashi and Matsumoto,
              Tetsuya",
  abstract = "We obtained a series of methicillin-resistant Staphylococcus
              aureus isolates, including both daptomycin-susceptible strain TD1
              and daptomycin-resistant strain TD4, from a patient. We
              determined the complete genome sequences of TD1 and TD4 using
              next-generation sequencing, and only four single-nucleotide
              polymorphisms (SNPs) were identified, one each in capB (E58K),
              rpoB (H481Y), lytN (I16V), and mprF (V351E). We determined that
              these four SNPs were sufficient to cause the strains to develop
              daptomycin, vancomycin, and rifampin resistance.",
  journal  = "Antimicrob. Agents Chemother.",
  volume   =  59,
  number   =  6,
  pages    = "3585--3587",
  month    =  mar,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Daum2015-li,
  title    = "{Whole-Genome} Sequence for {Methicillin-Resistant}
              Staphylococcus aureus Strain {ATCC} {BAA-1680}",
  author   = "Daum, Luke T and Bumah, Violet V and Masson-Meyers, Daniela S and
              Khubbar, Manjeet and Rodriguez, John D and Fischer, Gerald W and
              Enwemeka, Chukuka S and Gradus, Steve and Bhattacharyya, Sanjib",
  abstract = "We report here the whole-genome sequence of the USA300 strain of
              methicillin-resistant Staphylococcus aureus (MRSA), designated
              ATCC BAA-1680, and commonly referred to as community-associated
              MRSA (CA-MRSA). This clinical MRSA isolate is commercially
              available from the American Type Culture Collection (ATCC) and is
              widely utilized as a control strain for research applications and
              clinical diagnosis. The isolate was propagated in ATCC medium 18,
              tryptic soy agar, and has been utilized as a model S. aureus
              strain in several studies, including MRSA genetic analysis after
              irradiation with 470-nm blue light.",
  journal  = "Genome Announc.",
  volume   =  3,
  number   =  2,
  month    =  mar,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Anderson2014-qt,
  title    = "Whole Genome Sequencing of a {Methicillin-Resistant}
              Staphylococcus aureus {Pseudo-Outbreak} in a Professional
              Football Team",
  author   = "Anderson, Deverick J and Harris, Simon R and Godofsky, Eliot and
              Toriscelli, Todd and Rude, Thomas H and Elder, Kevin and Sexton,
              Daniel J and Pellman, Elliot J and Mayer, Thom and Fowler, Jr,
              Vance G and Peacock, Sharon J",
  abstract = "Two American football players on the same team were diagnosed
              with methicillin-resistant Staphylococcus aureus (MRSA) skin and
              soft tissue infections on the same day. Our investigation,
              including whole genome sequencing, confirmed that players did not
              transmit MRSA to one another nor did they acquire the MRSA from a
              single source within the training facility.",
  journal  = "Open Forum Infect Dis",
  volume   =  1,
  number   =  3,
  pages    = "ofu096",
  month    =  dec,
  year     =  2014,
  keywords = "American football; MRSA; outbreak investigation; whole genome
              sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 % The entry below contains non-ASCII chars that could not be converted
 % to a LaTeX equivalent.
 @ARTICLE{Hattangady2015-we,
  title    = "Genomic, Transcriptomic and Metabolomic Studies of Two
              {Well-Characterized}, {Laboratory-Derived}
              {Vancomycin-Intermediate} Staphylococcus aureus Strains Derived
              from the Same Parent Strain",
  author   = "Hattangady, Dipti S and Singh, Atul K and Muthaiyan, Arun and
              Jayaswal, Radheshyam K and Gustafson, John E and Ulanov,
              Alexander V and Li, Zhong and Wilkinson, Brian J and Pfeltz,
              Richard F",
  abstract = "Complete genome comparisons, transcriptomic and metabolomic
              studies were performed on two laboratory-selected,
              well-characterized vancomycin-intermediate Staphylococcus aureus
              (VISA) derived from the same parent MRSA that have changes in
              cell wall composition and decreased autolysis. A variety of
              mutations were found in the VISA, with more in strain
              13136p(-)m⁺V20 (vancomycin MIC = 16 µg/mL) than strain
              13136p(-)m⁺V5 (MIC = 8 µg/mL). Most of the mutations have not
              previously been associated with the VISA phenotype; some were
              associated with cell wall metabolism and many with stress
              responses, notably relating to DNA damage. The genomes and
              transcriptomes of the two VISA support the importance of gene
              expression regulation to the VISA phenotype. Similarities in
              overall transcriptomic and metabolomic data indicated that the
              VISA physiologic state includes elements of the stringent
              response, such as downregulation of protein and nucleotide
              synthesis, the pentose phosphate pathway and nutrient transport
              systems. Gene expression for secreted virulence determinants was
              generally downregulated, but was more variable for
              surface-associated virulence determinants, although capsule
              formation was clearly inhibited. The importance of activated
              stress response elements could be seen across all three analyses,
              as in the accumulation of osmoprotectant metabolites such as
              proline and glutamate. Concentrations of potential cell wall
              precursor amino acids and glucosamine were increased in the VISA
              strains. Polyamines were decreased in the VISA, which may
              facilitate the accrual of mutations. Overall, the studies confirm
              the wide variability in mutations and gene expression patterns
              that can lead to the VISA phenotype.",
  journal  = "Antibiotics (Basel)",
  volume   =  4,
  number   =  1,
  pages    = "76--112",
  month    =  feb,
  year     =  2015,
  keywords = "Staphylococcus aureus; VISA; genomics; metabolomics;
              transcriptomics;Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Fluit2015-cw,
  title    = "Comparison of an {ST80} {MRSA} strain from the {USA} with
              European {ST80} strains",
  author   = "Fluit, Ad C and Carpaij, Neeltje and Majoor, Eline A M and
              Weinstein, Robert A and Aroutcheva, Alla and Rice, Thomas W and
              Bonten, Marc J M and Willems, Rob J L",
  abstract = "OBJECTIVES: A number of community-acquired MRSA (CA-MRSA) clonal
              lineages dominate worldwide. ST80 was dominant in Europe and has
              increasingly been described from the Middle East. Here we report
              the whole genome sequence of the first ST80 CA-MRSA from the USA.
              METHODS: CA-MRSA isolate S0924 was obtained from a patient
              admitted to Cook County Hospital (Chicago, IL, USA) who came from
              Syria; the isolate belonged to spa type t044 and ST80. The whole
              genome sequence of S0924 was determined and compared with three
              previously published whole genome sequences of ST80 CA-MRSA from
              Europe and a newly sequenced ST80 CA-MRSA from the Netherlands
              (S1475). RESULTS: Based on spa typing, SCCmec type and virulence
              gene profile, this US ST80 isolate is indistinguishable from the
              European CA-MRSA ST80 clone. SNP analysis within the conserved
              core genome showed clear differences between the strains with up
              to 144 SNPs differing between S0924 and strain S1800, an ST80
              MRSA from Greece. The gene content showed 21 regions of
              difference between the US and European isolates, although these
              were largely restricted to mobile genetic elements. Phylogenetic
              reconstruction indicated that the European strains were more
              closely related to each other than to the US strain. The SNP data
              suggest that a common ancestor existed around two decades ago,
              indicating that the US and European ST80 strains are clonally
              linked. CONCLUSIONS: These data combined with the country of
              origin of the patient suggest that ST80 S0924 was probably
              relatively recently introduced into the USA from Syria.",
  journal  = "J. Antimicrob. Chemother.",
  volume   =  70,
  number   =  3,
  pages    = "664--669",
  month    =  mar,
  year     =  2015,
  keywords = "CA-MRSA; US; whole genome
              sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Guo2015-yz,
  title    = "Use of genome sequencing to assess nucleotide structure variation
              of Staphylococcus aureus strains cultured in spaceflight on
              {Shenzhou-X}, under simulated microgravity and on the ground",
  author   = "Guo, Jun and Han, Na and Zhang, Yuanyuan and Wang, Haiyin and
              Zhang, Xuelin and Su, Longxiang and Liu, Chao and Li, Jia and
              Chen, Chen and Liu, Changting",
  abstract = "The extreme environment of space could affect microbial behavior
              and may increase the risk of infectious disease during
              spaceflight. However, the molecular genetic changes of
              methicillin-resistant Staphylococcus aureus (MRSA) in response to
              the spaceflight environment have not been fully clarified. In the
              present study, we determined the draft genome sequences for an
              ancestral S. aureus strain (LCT-SAO) isolated from a clinical
              sample and three derivative strains, LCT-SAS, LCT-SAM and
              LCT-SAG, cultured in parallel during the spaceflight Shenzhou-X,
              under simulated microgravity and on the ground, respectively. To
              evaluate the impact of short-term spaceflight on the MRSA
              strains, comparative genomic analysis was implemented.
              Genome-based mapping of toxin genes and antibiotic resistance
              genes confirmed that these strains have the conventional
              pathogenicity and resistance to drugs, as none of the strains
              showed significant changes in these regions after culturing in
              the three different environments; this result suggests that
              spaceflight may not change bacterial virulence or drug
              resistance. Thirty-nine strain-specific sequence variants (SVs)
              were identified throughout the genomes, and the three derivatives
              exhibited almost the same mutation rates. Fifty-nine percent of
              SVs were located in the intergenic regions of the genomes,
              indicating that S. aureus may have an extremely robust repair
              mechanism responsible for recognizing and repairing DNA
              replication mismatches. It is noteworthy that strain LCT-SAS,
              cultured in space, presented the most unique SVs (n=9) and shared
              the fewest SVs with LCT-SAM (n=5) and LCT-SAG (n=4). Furthermore,
              we identified 10 potential deletion regions and 2 potential
              insertion regions, with LCT-SAS appearing more fragile than other
              strains by this measure. These results suggest that the
              environment of space is inherently complicated, with multiple
              variables, and cannot be simulated in a simple manner. Our
              results represent the first analysis of nucleotide structure
              variation of S. aureus strains in a spaceflight environment and
              also provide a valuable insight for understanding the mutation
              strategies of MRSA on earth.",
  journal  = "Microbiol. Res.",
  volume   =  170,
  pages    = "61--68",
  month    =  jan,
  year     =  2015,
  keywords = "Genome; High-throughput; SNP; Spaceflight; Staphylococcus
              aureus;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Ramaraj2014-yk,
  title    = "Draft Genome Sequences of {Vancomycin-Susceptible} Staphylococcus
              aureus Related to Heterogeneous {Vancomycin-Intermediate} S.
              aureus",
  author   = "Ramaraj, Thiruvarangan and Matyi, Stephanie A and Sundararajan,
              Anitha and Lindquist, Ingrid E and Devitt, Nicolas P and
              Schilkey, Faye D and Lamichhane-Khadka, Reena and Hoyt, Peter R
              and Mudge, Joann and Gustafson, John E",
  abstract = "We report the draft genome sequences of three
              vancomycin-susceptible methicillin-resistant Staphylococcus
              aureus strains. S. aureus strain MV8 is a sequence type 8 (ST-8)
              staphylococcal cassette chromosome mec element type IV (SCCmec
              IV) derivative, while the other two strains (S. aureus MM25 and
              MM61) are ST-5 SCCmec II strains. MM61 is also closely related to
              the heterogeneous vancomycin-intermediate S. aureus strain MM66.",
  journal  = "Genome Announc.",
  volume   =  2,
  number   =  5,
  month    =  oct,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Kropp2014-ci,
  title    = "Draft Genome Sequence of a Staphylococcus aureus Isolate Taken
              from the Blood of a Preterm Neonatal Blood Sepsis Patient",
  author   = "Kropp, K A and Lucid, A and Carroll, J and Belgrudov, V and
              Walsh, P and Kelly, B and Templeton, K and Smith, C and
              Dickinson, P and O'Driscoll, A and Ghazal, P and Sleator, R D",
  abstract = "Herein, we report the draft genome sequence of Staphylococcus
              aureus ED-NGS-1006, cultivated from a blood sample taken from a
              neonatal sepsis patient at the Royal Infirmary in Edinburgh,
              Scotland, United Kingdom.",
  journal  = "Genome Announc.",
  volume   =  2,
  number   =  5,
  month    =  sep,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Stegger2014-wr,
  title    = "Origin and evolution of European community-acquired
              methicillin-resistant Staphylococcus aureus",
  author   = "Stegger, Marc and Wirth, Thierry and Andersen, Paal S and Skov,
              Robert L and De Grassi, Anna and Sim{\~o}es, Patricia Martins and
              Tristan, Anne and Petersen, Andreas and Aziz, Maliha and Kiil,
              Kristoffer and Cirkovi{\'c}, Ivana and Udo, Edet E and del Campo,
              Rosa and Vuopio-Varkila, Jaana and Ahmad, Norazah and Tokajian,
              Sima and Peters, Georg and Schaumburg, Frieder and
              Olsson-Liljequist, Barbro and Givskov, Michael and Driebe,
              Elizabeth E and Vigh, Henrik E and Shittu, Adebayo and
              Ramdani-Bougessa, Nadjia and Rasigade, Jean-Philippe and Price,
              Lance B and Vandenesch, Francois and Larsen, Anders R and
              Laurent, Frederic",
  abstract = "UNLABELLED: Community-acquired methicillin-resistant
              Staphylococcus aureus (CA-MRSA) was recognized in Europe and
              worldwide in the late 1990s. Within a decade, several genetically
              and geographically distinct CA-MRSA lineages carrying the small
              SCCmec type IV and V genetic elements and the Panton-Valentine
              leukocidin (PVL) emerged around the world. In Europe, the
              predominant CA-MRSA strain belongs to clonal complex 80 (CC80)
              and is resistant to kanamycin/amikacin and fusidic acid. CC80 was
              first reported in 1993 but was relatively rare until the late
              1990s. It has since been identified throughout North Africa, the
              Middle East, and Europe, with recent sporadic reports in
              sub-Saharan Africa. While strongly associated with skin and soft
              tissue infections, it is rarely found among asymptomatic
              carriers. Methicillin-sensitive S. aureus (MSSA) CC80 strains are
              extremely rare except in sub-Saharan Africa. In the current
              study, we applied whole-genome sequencing to a global collection
              of both MSSA and MRSA CC80 isolates. Phylogenetic analyses
              strongly suggest that the European epidemic CA-MRSA lineage is
              derived from a PVL-positive MSSA ancestor from sub-Saharan
              Africa. Moreover, the tree topology suggests a single acquisition
              of both the SCCmec element and a plasmid encoding the fusidic
              acid resistance determinant. Four canonical SNPs distinguish the
              derived CA-MRSA lineage and include a nonsynonymous mutation in
              accessory gene regulator C (agrC). These changes were associated
              with a star-like expansion into Europe, the Middle East, and
              North Africa in the early 1990s, including multiple cases of
              cross-continent imports likely driven by human migrations.
              IMPORTANCE: With increasing levels of CA-MRSA reported from most
              parts of the Western world, there is a great interest in
              understanding the origin and factors associated with the
              emergence of these epidemic lineages. To trace the origin,
              evolution, and dissemination pattern of the European CA-MRSA
              clone (CC80), we sequenced a global collection of strains of the
              S. aureus CC80 lineage. Our study determined that a single
              descendant of a PVL-positive methicillin-sensitive ancestor
              circulating in sub-Saharan Africa rose to become the dominant
              CA-MRSA clone in Europe, the Middle East, and North Africa. In
              the transition from a methicillin-susceptible lineage to a
              successful CA-MRSA clone, it simultaneously became resistant to
              fusidic acid, a widely used antibiotic for skin and soft tissue
              infections, thus demonstrating the importance of antibiotic
              selection in the success of this clone. This finding furthermore
              highlights the significance of horizontal gene acquisitions and
              underscores the combined importance of these factors for the
              success of CA-MRSA.",
  journal  = "MBio",
  volume   =  5,
  number   =  5,
  pages    = "e01044--14",
  month    =  aug,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Matyi2014-ug,
  title    = "Draft Genomes of Heterogeneous {Vancomycin-Intermediate}
              Staphylococcus aureus Strain {MM66} and {MM66} Derivatives with
              Altered Vancomycin Resistance Levels",
  author   = "Matyi, Stephanie A and Ramaraj, Thiruvarangan and Sundararajan,
              Anitha and Lindquist, Ingrid E and Devitt, Nicolas P and
              Schilkey, Faye D and Lamichhane-Khadka, Reena and Hoyt, Peter R
              and Mudge, Joann and Gustafson, John E",
  abstract = "The draft genomes of heterogeneous vancomycin-intermediate
              Staphylococcus aureus (hVISA) strain MM66 and MM66 isolates
              demonstrating altered vancomycin resistance levels were produced
              in an effort to provide information on mutations contributing to
              the vancomycin resistance levels observed in these strains.",
  journal  = "Genome Announc.",
  volume   =  2,
  number   =  4,
  month    =  jul,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Jeon2014-nu,
  title    = "Complete Genome Sequence of the Siphoviral Bacteriophage
              {YMC/09/04/R1988} {MRSA} {BP}: A lytic phage from a
              methicillin-resistant Staphylococcus aureus isolate",
  author   = "Jeon, Jongsoo and D'Souza, Roshan and Hong, Sung Kuk and Lee,
              Yangsoon and Yong, Dongeun and Choi, Jongrak and Lee, Kyungwon
              and Chong, Yunsop",
  abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) is an
              increasing cause of serious infection, both in the community and
              hospital settings. Despite sophisticated strategies and efforts,
              the antibiotic options for treating MRSA infection have been
              narrowed due to the limited number of newly developed
              antimicrobials. Herein, we analyze the completely sequenced
              genome of a novel virulent phage YMC/09/04/R1988 MRSA BP as a
              potential alternative anti-MRSA agent, which lysed clinical
              isolates from a patient admitted to the hospital due to hip
              disarticulation. The phage contains a linear double-stranded DNA
              genome of 44,459 bp in length, with 33.37\% GC content, 62
              predicted open reading frames (ORFs), and annotated functions of
              only 23 ORFs that are associated with structural assembly, host
              lysis, DNA replication, and modification. It showed a broad host
              range (17 of 30 strains) against MRSA strains in clinical
              isolates. This article is protected by copyright. All rights
              reserved.",
  journal  = "FEMS Microbiol. Lett.",
  month    =  aug,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 % The entry below contains non-ASCII chars that could not be converted
 % to a LaTeX equivalent.
 @ARTICLE{Keary2014-ke,
  title    = "Genome analysis of the staphylococcal temperate phage {DW2} and
              functional studies on the endolysin and tail hydrolase",
  author   = "Keary, Ruth and McAuliffe, Olivia and Ross, R Paul and Hill,
              Colin and O'Mahony, Jim and Coffey, Aidan",
  abstract = "This study describes the genome of temperate Siphoviridae phage
              DW2, which is routinely propagated on Staphylococcus aureus
              DPC5246. The 41941 bp genome revealed an open reading frame
              (ORF1) which has a high level of homology with members of the
              resolvase subfamily of site-specific serine recombinase, involved
              in chromosomal integration and excision. In contrast, the
              majority of staphylococcal phages reported to date encode
              tyrosine recombinases. Two putative genes encoded by phage DW2
              (ORF15 and ORF24) were highly homologous to the NWMN0273 and
              NWMN0280 genes encoding virulence factors carried on the genome
              of ϕNM4, a prophage in the genome of S. aureus Newman. Phage DW2
              also encodes proteins highly homologous to two well-characterized
              Staphylococcus aureus pathogenicity island derepressors encoded
              by the staphylococcal helper phage 80$\alpha$ indicating that it
              may similarly act as a helper phage for mobility of pathogenicity
              islands in S. aureus. This study also focused on the enzybiotic
              potential of phage DW2. The structure of the putative endolysin
              and tail hydrolase were investigated and used as the basis for a
              cloning strategy to create recombinant peptidoglycan hydrolyzing
              proteins. After overexpression in E. coli, four of these proteins
              (LysDW2, THDW2, CHAPE1-153, and CHAPE1-163) were demonstrated to
              have hydrolytic activity against peptidoglycan of S. aureus and
              thus represent novel candidates for exploitation as enzybiotics.",
  journal  = "Bacteriophage",
  volume   =  4,
  pages    = "e28451",
  month    =  mar,
  year     =  2014,
  keywords = "Staphylococcus; bacteriophage; endolysin; serine recombinase;
              virion-associated peptidoglycan hydrolase;
              virulence;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 % The entry below contains non-ASCII chars that could not be converted
 % to a LaTeX equivalent.
 @ARTICLE{SenGupta2014-is,
  title    = "Whole-genome sequencing for high-resolution investigation of
              methicillin-resistant Staphylococcus aureus epidemiology and
              genome plasticity",
  author   = "SenGupta, Dhruba J and Cummings, Lisa A and Hoogestraat, Daniel R
              and Butler-Wu, Susan M and Shendure, Jay and Cookson, Brad T and
              Salipante, Stephen J",
  abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) infections
              pose a major challenge in health care, yet the limited
              heterogeneity within this group hinders molecular investigations
              of related outbreaks. Pulsed-field gel electrophoresis (PFGE) has
              been the gold standard approach but is impractical for many
              clinical laboratories and is often replaced with PCR-based
              methods. Regardless, both approaches can prove problematic for
              identifying subclonal outbreaks. Here, we explore the use of
              whole-genome sequencing for clinical laboratory investigations of
              MRSA molecular epidemiology. We examine the relationships of 44
              MRSA isolates collected over a period of 3 years by using
              whole-genome sequencing and two PCR-based methods, multilocus
              variable-number tandem-repeat analysis (MLVA) and spa typing. We
              find that MLVA offers higher resolution than spa typing, as it
              resolved 17 versus 12 discrete isolate groups, respectively. In
              contrast, whole-genome sequencing reproducibly cataloged genomic
              variants (131,424 different single nucleotide polymorphisms and
              indels across the strain collection) that uniquely identified
              each MRSA clone, recapitulating those groups but enabling
              higher-resolution phylogenetic inferences of the epidemiological
              relationships. Importantly, whole-genome sequencing detected a
              significant number of variants, thereby distinguishing between
              groups that were considered identical by both spa typing
              (minimum, 1,124 polymorphisms) and MLVA (minimum, 193
              polymorphisms); this suggests that these more conventional
              approaches can lead to false-positive identification of outbreaks
              due to inappropriate grouping of genetically distinct strains. An
              analysis of the distribution of variants across the MRSA genome
              reveals 47 mutational hot spots (comprising ∼ 2.5\% of the
              genome) that account for 23.5\% of the observed polymorphisms,
              and the use of this selected data set successfully recapitulates
              most epidemiological relationships in this pathogen group.",
  journal  = "J. Clin. Microbiol.",
  volume   =  52,
  number   =  8,
  pages    = "2787--2796",
  month    =  aug,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Dordel2014-pp,
  title    = "Novel determinants of antibiotic resistance: identification of
              mutated loci in highly methicillin-resistant subpopulations of
              methicillin-resistant Staphylococcus aureus",
  author   = "Dordel, Janina and Kim, Choonkeun and Chung, Marilyn and Pardos
              de la G{\'a}ndara, Mar{\'\i}a and Holden, Matthew T J and
              Parkhill, Julian and de Lencastre, Herm{\'\i}nia and Bentley,
              Stephen D and Tomasz, Alexander",
  abstract = "We identified mutated genes in highly resistant subpopulations of
              methicillin-resistant Staphylococcus aureus (MRSA) that are most
              likely responsible for the historic failure of the $\beta$-lactam
              family of antibiotics as therapeutic agents against these
              important pathogens. Such subpopulations are produced during
              growth of most clinical MRSA strains, including the four
              historically early MRSA isolates studied here. Chromosomal DNA
              was prepared from the highly resistant cells along with DNA from
              the majority of cells (poorly resistant cells) followed by full
              genome sequencing. In the highly resistant cells, mutations were
              identified in 3 intergenic sequences and 27 genes representing a
              wide range of functional categories. A common feature of these
              mutations appears to be their capacity to induce high-level
              $\beta$-lactam resistance and increased amounts of the resistance
              protein PBP2A in the bacteria. The observations fit a recently
              described model in which the ultimate controlling factor of the
              phenotypic expression of $\beta$-lactam resistance in MRSA is a
              RelA-mediated stringent response. IMPORTANCE It has been well
              established that the level of antibiotic resistance (i.e.,
              minimum concentration of a $\beta$-lactam antibiotic needed to
              inhibit growth) of a methicillin-resistant Staphylococcus aureus
              (MRSA) strain depends on the transcription and translation of the
              resistance protein PBP2A. Here we describe mutated loci in an
              additional novel set of genetic determinants that appear to be
              essential for the unusually high resistance levels typical of
              subpopulations of staphylococci that are produced with unique low
              frequency in most MRSA clinical isolates. We propose that
              mutations in these determinants can trigger induction of the
              stringent stress response which was recently shown to cause
              increased transcription/translation of the resistance protein
              PBP2A in parallel with the increased level of resistance.",
  journal  = "MBio",
  volume   =  5,
  number   =  2,
  pages    = "e01000",
  month    =  apr,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Baines2015-ms,
  title    = "Convergent Adaptation in the Dominant Global Hospital Clone
              {ST239} of {Methicillin-Resistant} Staphylococcus aureus",
  author   = "Baines, Sarah L and Holt, Kathryn E and Schultz, Mark B and
              Seemann, Torsten and Howden, Brian O and Jensen, Slade O and van
              Hal, Sebastiaan J and Coombs, Geoffrey W and Firth, Neville and
              Powell, David R and Stinear, Timothy P and Howden, Benjamin P",
  abstract = "UNLABELLED: Infections caused by highly successful clones of
              hospital-associated methicillin-resistant Staphylococcus aureus
              (HA-MRSA) are a major public health burden. The globally dominant
              sequence type 239 (ST239) HA-MRSA clone has persisted in the
              health care setting for decades, but the basis of its success has
              not been identified. Taking a collection of 123 ST239 isolates
              spanning 32 years, we have used population-based functional
              genomics to investigate the evolution of this highly persistent
              and successful clone. Phylogenetic reconstruction and population
              modeling uncovered a previously unrecognized distinct clade of
              ST239 that was introduced into Australia from Asia and has
              perpetuated the epidemic in this region. Functional analysis
              demonstrated attenuated virulence and enhanced resistance to
              last-line antimicrobials, the result of two different phenomena,
              adaptive evolution within the original Australian ST239 clade and
              the introduction of a new clade displaying shifts in both
              phenotypes. The genetic diversity between the clades allowed us
              to employ genome-wide association testing and identify mutations
              in other essential regulatory systems, including walKR, that
              significantly associate with and may explain these key
              phenotypes. The phenotypic convergence of two independently
              evolving ST239 clades highlights the very strong selective
              pressures acting on HA-MRSA, showing that hospital environments
              have favored the accumulation of mutations in essential MRSA
              genes that increase resistance to antimicrobials, attenuate
              virulence, and promote persistence in the health care
              environment. Combinations of comparative genomics and careful
              phenotypic measurements of longitudinal collections of clinical
              isolates are giving us the knowledge to intelligently address the
              impact of current and future antibiotic usage policies and
              practices on hospital pathogens globally. IMPORTANCE:
              Methicillin-resistant Staphylococcus aureus (MRSA) is responsible
              for innumerable drug-resistant health care-associated infections
              globally. This study, the first to investigate the evolutionary
              response of hospital-associated MRSA (HA-MRSA) over many decades,
              demonstrates how MRSA can persist in a region through the
              reintroduction of a previously unrecognized distinct clade. This
              study also demonstrates the crucial adaptive responses of HA-MRSA
              to the highly selective environment of the health care system,
              the evolution of MRSA isolates to even higher levels of
              antibiotic resistance at the cost of attenuated virulence.
              However, in vivo persistence is maintained, resulting in a clone
              of HA-MRSA able to resist almost all antimicrobial agents and
              still cause invasive disease in the heavily compromised hosts
              found in modern health care settings.",
  journal  = "MBio",
  volume   =  6,
  number   =  2,
  pages    = "e00080",
  month    =  may,
  year     =  2015,
  keywords = "Staphylococcus;Staph\_evolutionary\_history;bacterial comparative
              genomics;antibiotcs-evolution-fitness;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;GWAS-bacteria"
 }

 @ARTICLE{Qu2014-cf,
  title    = "Whole genome analysis of a community-associated
              methicillin-resistant Staphylococcus aureus {ST59} isolate from a
              case of human sepsis and severe pneumonia in China",
  author   = "Qu, Tingting and Feng, Ye and Jiang, Yan and Zhu, Peiqiong and
              Wei, Zeqing and Chen, Yan and Otto, Michael and Yu, Yunsong",
  abstract = "We report a case of necrotizing pneumonia in a young patient
              caused by community acquired-methicillin resistant Staphylococcus
              aureus (CA-MRSA) in a teaching hospital in the People's Republic
              of China. The patient had a typical clinical presentation and was
              successfully treated with antibiotics and intravenous
              immunoglobulin. A CA-MRSA strain, named SA268, was isolated from
              the blood of the patient. The isolate was susceptible to most
              antimicrobial agents, except cephalosporins, penicillins, and
              $\beta$-lactamase inhibitor combinations. Multi-locus sequence
              typing (MLST) assigned SA268 to ST59, a clone widely spread in
              eastern Asia. The strain was positive for Panton Valentine
              Leukocidin (PVL)-encoding genes and SCCmec type V. We sequenced
              the complete genome of the SA268 isolate. The genome of SA268 was
              almost identical to that of the Taiwanese ST59 CA-MRSA strains
              M013 and SA957. However, we observed several differences in gene
              composition, which included differences in the SCCmec element and
              several lipoprotein genes that were present in the Taiwanese
              strains but absent from SA268.",
  journal  = "PLoS One",
  volume   =  9,
  number   =  2,
  pages    = "e89235",
  month    =  feb,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Elbir2013-tl,
  title    = "Staphylococcus aureus subsp. anaerobius strain {ST1464} genome
              sequence",
  author   = "Elbir, Haitham and Robert, Catherine and Nguyen, Ti Thien and
              Gimenez, Gr{\'e}gory and El Sanousi, Sulieman M and Flock,
              Jan-Ingmar and Raoult, Didier and Drancourt, Michel",
  abstract = "Staphylococcus aureus subsp. anaerobius is responsible for
              Morel's disease in animals and a cause of abscess in humans. It
              is characterized by a microaerophilic growth, contrary to the
              other strains of S. aureus. The 2,604,446-bp genome (32.7\% GC
              content) of S. anaerobius ST1464 comprises one chromosome and no
              plasmids. The chromosome contains 2,660 open reading frames
              (ORFs), 49 tRNAs and three complete rRNAs, forming one complete
              operon. The size of ORFs ranges between 100 to 4,600 bp except
              for two ORFs of 6,417 and 7,173 bp encoding segregation ATPase
              and non-ribosomal peptide synthase, respectively. The chromosome
              harbors Staphylococcus phage 2638A genome and incomplete
              Staphylococcus phage genome PT1028, but no detectable CRISPRS.
              The antibiotic resistance gene for tetracycline was found
              although Staphylococcus aureus subsp. anaerobius is susceptible
              to tetracycline in-vitro. Intact oxygen detoxification genes
              encode superoxide dismutase and cytochrome quinol oxidase whereas
              the catalase gene is impaired by a stop codon. Based on the
              genome, in-silico multilocus sequence typing indicates that S.
              aureus subsp. anaerobius emerged as a clone separated from all
              other S. aureus strains, illustrating host-adaptation linked to
              missing functions. Availability of S. aureus subsp. anaerobius
              genome could prompt the development of post-genomic tools for its
              rapid discrimination from S. aureus.",
  journal  = "Stand. Genomic Sci.",
  volume   =  9,
  number   =  1,
  pages    = "1--13",
  month    =  oct,
  year     =  2013,
  keywords = "Morel's disease; SOLiD; Staphylococcus aureus subsp. anaerobius;
              genome;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Monecke2013-fe,
  title    = "Genome sequencing and molecular characterisation of
              Staphylococcus aureus {ST772-MRSA-V}, ``Bengal Bay Clone''",
  author   = "Monecke, Stefan and Baier, Vico and Coombs, Geoffrey W and
              Slickers, Peter and Ziegler, Albrecht and Ehricht, Ralf",
  abstract = "BACKGROUND: The PVL-positive ST772-MRSA-V is an emerging
              community-associated (CA-) MRSA clone that has been named Bengal
              Bay Clone since most patients have epidemiological connections to
              the Indian subcontinent. It is found increasingly common in other
              areas of the world. METHODS: One isolate of ST772-MRSA-V was
              sequenced using the Illumina Genome Analyzer System. After
              initial assembling the multiple sequence contigs were analysed
              using different in-house annotation scripts. Results were
              compared to microarray hybridisation results of clinical isolates
              of ST772-MRSA-V, of related strains and to another ST772-MRSA-V
              genome sequence. RESULTS: According to MLST e-burst analysis,
              ST772-MRSA-V belongs to Clonal Complex (CC)1, differing from ST1
              only in one MLST allele (pta-22). However, there are several
              additional differences including agr alleles (group II rather
              than III), capsule type (5 rather than 8), the presence of the
              egc enterotoxin gene cluster and of the enterotoxin homologue ORF
              CM14 as well as the absence of the enterotoxin H gene seh.
              Enterotoxin genes sec and sel are present. ST772-MRSA-V harbours
              the genes encoding enterotoxin A (sea) and PVL (lukS/F-PV). Both
              are located on the same prophage. CONCLUSIONS: ST772-MRSA-V may
              have emerged from the same lineage as globally spread CC1 and CC5
              strains. It has acquired a variety of virulence factors, and for
              a CA-MRSA strain it has an unusually high number of genes
              associated with antibiotic resistance.",
  journal  = "BMC Res. Notes",
  volume   =  6,
  pages    = "548",
  month    =  dec,
  year     =  2013,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Baek2013-yj,
  title    = "Genetic variation in the Staphylococcus aureus 8325 strain
              lineage revealed by whole-genome sequencing",
  author   = "B{\ae}k, Kristoffer T and Frees, Dorte and Renzoni, Adriana and
              Barras, Christine and Rodriguez, Natalia and Manzano, Caroline
              and Kelley, William L",
  abstract = "Staphylococcus aureus strains of the 8325 lineage, especially
              8325-4 and derivatives lacking prophage, have been used
              extensively for decades of research. We report herein the results
              of our deep sequence analysis of strain 8325-4. Assignment of
              sequence variants compared with the reference strain 8325
              (NRS77/PS47) required correction of errors in the 8325 reference
              genome, and reassessment of variation previously attributed to
              chemical mutagenesis of the restriction-defective RN4220. Using
              an extensive strain pedigree analysis, we discovered that 8325-4
              contains 16 single nucleotide polymorphisms (SNP) arising prior
              to the construction of RN4220. We identified 5 indels in 8325-4
              compared with 8325. Three indels correspond to expected $\Phi$11,
              12, 13 excisions, one indel is explained by a sequence assembly
              artifact, and the final indel ($\Delta$63bp) in the spa-sarS
              intergenic region is common to only a sub-lineage of 8325-4
              strains including SH1000. This deletion was found to
              significantly decrease (75\%) steady state sarS but not spa
              transcript levels in post-exponential phase. The sub-lineage
              8325-4 was also found to harbor 4 additional SNPs. We also found
              large sequence variation between 8325, 8325-4 and RN4220 in a
              cluster of repetitive hypothetical proteins (SA0282 homologs)
              near the Ess secretion cluster. The overall 8325-4 SNP set
              results in 17 alterations within coding sequences. Remarkably, we
              discovered that all tested strains of the 8325-4 lineage lack
              phenol soluble modulin $\alpha$3 (PSM$\alpha$3), a virulence
              determinant implicated in neutrophil chemotaxis, biofilm
              architecture and surface spreading. Collectively, our results
              clarify and define the 8325-4 pedigree and reveal clear evidence
              that mutations existing throughout all branches of this lineage,
              including the widely used RN6390 and SH1000 strains, could
              conceivably impact virulence regulation.",
  journal  = "PLoS One",
  volume   =  8,
  number   =  9,
  pages    = "e77122",
  month    =  sep,
  year     =  2013,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Matsuo2013-qu,
  title    = "Comprehensive identification of mutations responsible for
              heterogeneous vancomycin-intermediate Staphylococcus aureus
              ({hVISA)-to-VISA} conversion in laboratory-generated {VISA}
              strains derived from {hVISA} clinical strain Mu3",
  author   = "Matsuo, Miki and Cui, Longzhu and Kim, Jeeyoung and Hiramatsu,
              Keiichi",
  abstract = "Heterogeneous vancomycin-intermediate Staphylococcus aureus
              (hVISA) spontaneously produces VISA cells within its cell
              population at a frequency of 10(-6) or greater. We established a
              total of 45 VISA mutant strains independently obtained from hVISA
              Mu3 and its related strains by one-step vancomycin selection. We
              then performed high-throughput whole-genome sequencing of the 45
              strains and their parent strains to identify the genes involved
              in the hVISA-to-VISA phenotypic conversion. A comparative genome
              study showed that all the VISA strains tested carried a unique
              set of mutations. All of the 45 VISA strains carried 1 to 4
              mutations possibly affecting the expression of a total of 48
              genes. Among them, 32 VISA strains carried only one gene affected
              by a single mutation. As many as 20 genes in more than eight
              functional categories were affected in the 32 VISA strains, which
              explained the extremely high rates of the hVISA-to-VISA
              phenotypic conversion. Five genes, rpoB, rpoC, walK, pbp4, and
              pp2c, were previously reported as being involved in vancomycin
              resistance. Fifteen remaining genes were newly identified as
              associated with vancomycin resistance in this study. The gene
              most frequently affected (6 out of 32 strains) was cmk, which
              encodes cytidylate kinase, followed closely by rpoB (5 out of
              32), encoding the $\beta$ subunit of RNA polymerase. A mutation
              prevalence study also revealed a sizable number of cmk mutants
              among clinical VISA strains (7 out of 38 [18\%]). Reduced
              cytidylate kinase activity in cmk mutant strains is proposed to
              contribute to the hVISA-to-VISA phenotype conversion by
              thickening the cell wall and reducing the cell growth rate.",
  journal  = "Antimicrob. Agents Chemother.",
  volume   =  57,
  number   =  12,
  pages    = "5843--5853",
  month    =  dec,
  year     =  2013,
  keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Chen2013-cu,
  title    = "Complete genome sequence of a {Pant{\'o}n-Valentine}
              leukocidin-negative community-associated methicillin-resistant
              Staphylococcus aureus strain of sequence type 72 from Korea",
  author   = "Chen, Yan and Chatterjee, Som S and Porcella, Stephen F and Yu,
              Yun-Song and Otto, Michael",
  abstract = "In the past decade, community-associated (CA-) infections with
              methicillin-resistant Staphylococcus aureus (MRSA) have emerged
              throughout the world. Different CA-MRSA strains dominate in
              different geographical locations. Many CA-MRSA lineages contain
              genes coding for the Pant{\'o}n-Valentine leukocidin. However,
              the role of this leukotoxin in CA-MRSA pathogenesis is still
              controversial. The genome sequences of two key PVL-positive
              CA-MRSA strains (USA300, USA400) have been reported, but we lack
              information on the more recently found PVL-negative CA-MRSA
              strains. One such strain is the PVL-negative ST72, the main cause
              of CA-MRSA infections in Korea. Here, we report the entire genome
              sequence of CA-MRSA ST72 and analyze its gene content with a
              focus on virulence factors. Our results show that this strain
              does not have considerable differences in virulence factor
              content compared to other CA-MRSA strains (USA300, USA400),
              indicating that other toxins do not substitute for the lack of
              PVL in ST72. This finding is in accordance with the notion that
              differential expression of widespread virulence determinants,
              rather than the acquisition of additional virulence factors on
              mobile genetic elements, such as PVL, is responsible for the
              increased virulence of CA- compared to hospital-associated MRSA.",
  journal  = "PLoS One",
  volume   =  8,
  number   =  8,
  pages    = "e72803",
  month    =  aug,
  year     =  2013,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Yoon2013-gy,
  title    = "Characterization and genomic analysis of two Staphylococcus
              aureus bacteriophages isolated from poultry/livestock farms",
  author   = "Yoon, Hyunjin and Yun, Jiae and Lim, Jeong-A and Roh, Eunjung and
              Jung, Kyu-Seok and Chang, Yoonjee and Ryu, Sangryeol and Heu,
              Sunggi",
  abstract = "Staphylococcus aureus is one of the most important pathogens,
              causing various diseases in humans and animals. As
              methicillin-resistant S. aureus (MRSA) has become increasingly
              prevalent, controlling this pathogen with standard antibiotic
              treatment has become challenging. Bacteriophages (phages) have
              attracted interest as alternative antibacterial agents to control
              MRSA. In this study, we isolated six S. aureus phages from soils
              of poultry/livestock farms. Based on the results of host range
              determination with 150 S. aureus strains and restriction enzyme
              treatment of phage DNA, two phages, designated SP5 and SP6, were
              selected for further characterization and genome sequencing. Both
              SP5 and SP6 were classified as members of the family
              Siphoviridae. The genome of SP5 comprises 43 305 bp and contains
              63 ORFs, while the SP6 genome comprises 42 902 bp and contains 61
              ORFs. Although they have different host spectra, the phage
              genomes exhibit high nucleotide similarity to each other.
              Adsorption assay results suggested that the host range
              determinants of the two phages are involved in both adsorption
              and infection. Comparative genomic analyses of the two phages
              provided evidence that the lysogenic/lytic control module and
              tail proteins may be important for host specificity.",
  journal  = "J. Gen. Virol.",
  volume   =  94,
  number   = "Pt 11",
  pages    = "2569--2576",
  month    =  nov,
  year     =  2013,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Botelho2016-yb,
  title    = "Complete genome sequence of an agr-dysfunctional variant of the
              {ST239} lineage of the methicillin-resistant Staphylococcus
              aureus strain {GV69} from Brazil",
  author   = "Botelho, Ana M N and Costa, Maiana O C and Beltrame, Cristiana O
              and Ferreira, Fabienne A and C{\^o}rtes, Marina F and Bandeira,
              Paula T and Lima, Nicholas C B and Souza, Rangel C and Almeida,
              Luiz G P and Vasconcelos, Ana T R and Nicol{\'a}s, Marisa F and
              Figueiredo, Agnes M S",
  abstract = "Staphylococcus aureus is a versatile Gram-positive coccus
              frequently found colonizing the skin and nasal membranes of
              humans. The acquisition of the staphylococcal cassette chromosome
              mec was a major milestone in the evolutionary path of
              methicillin-resistant S. aureus. This genetic element carries the
              mecA gene, the main determinant of methicillin resistance. MRSA
              is involved in a plethora of opportunistic infectious diseases.
              The accessory gene regulator is the major S. aureus quorum
              sensing system, playing an important role in staphylococcal
              virulence, including the development of biofilms. We report the
              complete genome sequence (NCBI BioProject ID: PRJNA264181) of the
              methicillin-resistant S. aureus strain GV69 (= CMVRS P4521), a
              variant of the ST239 lineage that presents with a natural
              attenuation of agr-RNAIII transcription and a moderate
              accumulation of biofilm.",
  journal  = "Stand. Genomic Sci.",
  volume   =  11,
  pages    = "34",
  month    =  may,
  year     =  2016,
  keywords = "Complete genome sequence; Methicillin-resistant Staphylococcus
              aureus; ST239; Skin hospital infection; agr
              dysfunction;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Gaviria-Agudelo2015-oi,
  title    = "Genomic Heterogeneity of Methicillin Resistant Staphylococcus
              aureus Associated with Variation in Severity of Illness among
              Children with Acute Hematogenous Osteomyelitis",
  author   = "Gaviria-Agudelo, Claudia and Aroh, Chukwuemika and Tareen,
              Naureen and Wakeland, Edward K and Kim, Minsoo and Copley, Lawson
              A",
  abstract = "INTRODUCTION: The association between severity of illness of
              children with osteomyelitis caused by Methicillin-resistant
              Staphylococcus aureus (MRSA) and genomic variation of the
              causative organism has not been previously investigated. The
              purpose of this study is to assess genomic heterogeneity among
              MRSA isolates from children with osteomyelitis who have diverse
              severity of illness. MATERIALS AND METHODS: Children with
              osteomyelitis were prospectively studied between 2010 and 2011.
              Severity of illness of the affected children was determined from
              clinical and laboratory parameters. MRSA isolates were analyzed
              with next generation sequencing (NGS) and optical mapping.
              Sequence data was used for multi-locus sequence typing (MLST),
              phylogenetic analysis by maximum likelihood (PAML), and
              identification of virulence genes and single nucleotide
              polymorphisms (SNP) relative to reference strains. RESULTS: The
              twelve children studied demonstrated severity of illness scores
              ranging from 0 (mild) to 9 (severe). All isolates were USA300, ST
              8, SCC mec IVa MRSA by MLST. The isolates differed from reference
              strains by 2 insertions (40 Kb each) and 2 deletions (10 and 25
              Kb) but had no rearrangements or copy number variations. There
              was a higher occurrence of virulence genes among study isolates
              when compared to the reference strains (p = 0.0124). There were
              an average of 11 nonsynonymous SNPs per strain. PAML demonstrated
              heterogeneity of study isolates from each other and from the
              reference strains. DISCUSSION: Genomic heterogeneity exists among
              MRSA isolates causing osteomyelitis among children in a single
              community. These variations may play a role in the pathogenesis
              of variation in clinical severity among these children.",
  journal  = "PLoS One",
  volume   =  10,
  number   =  6,
  pages    = "e0130415",
  month    =  jun,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Aswani2016-td,
  title    = "Complete Genome Sequence of Staphylococcus aureus {MCRF184}, a
              Necrotizing {Fasciitis-Causing} {Methicillin-Sensitive} Sequence
              Type 45 Staphylococcus Strain",
  author   = "Aswani, Vijay and Mau, Bob and Shukla, Sanjay K",
  abstract = "We report here the complete genome sequence of a highly virulent
              methicillin-sensitive Staphylococcus aureus strain, MCRF184,
              belonging to sequence type 45. This staphylococcal strain was
              isolated from a surgical biopsy specimen from a patient with
              necrotizing fasciitis.",
  journal  = "Genome Announc.",
  volume   =  4,
  number   =  3,
  month    =  may,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Johnston2016-tz,
  title    = "Genomic Signatures of Experimental Adaptation to Antimicrobial
              Peptides in Staphylococcus aureus",
  author   = "Johnston, Paul R and Dobson, Adam J and Rolff, Jens",
  abstract = "The evolution of resistance against antimicrobial peptides has
              long been considered unlikely due to their mechanism of action,
              yet experimental selection with AMPs results in rapid evolution
              of resistance in several species of bacteria. Although numerous
              studies have utilized mutant screens to identify loci that
              determine AMP susceptibility, there is a dearth of data
              concerning the genomic changes which accompany experimental
              evolution of AMP resistance. Using genome re-sequencing we
              analysed the mutations which arise during experimental evolution
              of resistance to the cationic AMPs iseganan, melittin and
              pexiganan, as well as to a combination of melittin and pexiganan,
              or to the aminoglycoside antibiotic streptomycin. Analysis of 17
              independently replicated Staphylococcus aureus selection lines,
              including unselected controls, showed that each AMP selected for
              mutations at distinct loci. We identify mutations in genes
              involved in the synthesis and maintenance of the cell envelope.
              This includes genes previously identified from mutant screens for
              AMP resistance, and genes involved in the response to AMPs and
              cell-wall-active antibiotics. Furthermore, transposon insertion
              mutants were used to verify that a number of the identified genes
              are directly involved in determining AMP susceptibility. Strains
              selected for AMP resistance under controlled experimental
              evolution displayed consistent AMP-specific mutations in genes
              which determine AMP susceptibility. This suggests that different
              routes to evolve resistance are favored within a controlled
              genetic background.",
  journal  = "G3",
  month    =  apr,
  year     =  2016,
  keywords = "Staphylococcus aureus; antimicrobial peptide resistance;
              experimental
              evolution;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Ugolotti2016-br,
  title    = "Whole-genome sequencing as standard practice for the analysis of
              clonality in outbreaks of meticillin-resistant Staphylococcus
              aureus in a paediatric setting",
  author   = "Ugolotti, E and Larghero, P and Vanni, I and Bandettini, R and
              Tripodi, G and Melioli, G and Di Marco, E and Raso, A and
              Biassoni, R",
  abstract = "Meticillin-resistant Staphylococcus aureus (MRSA) is one of the
              leading causes of hospital-associated infections. This study
              investigated the potential use of whole-genome sequencing (WGS)
              for surveillance purposes by re-examining MRSA strains related to
              past outbreaks among hospitalized paediatric patients. WGS data
              ameliorated the genotypic profile previously obtained with Sanger
              sequencing and pulsed-field gel electrophoresis typing, and
              discriminated between strains that were related and unrelated to
              the outbreaks. This allowed strain clonality to be defined with a
              higher level of resolution than achieved previously. This study
              demonstrates the potential of WGS to trace hospital outbreaks,
              which may lead to WGS becoming standard practice in outbreak
              investigations.",
  journal  = "J. Hosp. Infect.",
  month    =  apr,
  year     =  2016,
  keywords = "Hospital-associated infections; MRSA; Paediatric hospital
              outbreak; Whole-genome
              sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Iguchi2016-kk,
  title    = "Rapid Acquisition of Linezolid Resistance in
              {Methicillin-Resistant} Staphylococcus aureus: Role of
              Hypermutation and Homologous Recombination",
  author   = "Iguchi, Shigekazu and Mizutani, Tomonori and Hiramatsu, Keiichi
              and Kikuchi, Ken",
  abstract = "BACKGROUND: We previously reported the case of a 64-year-old man
              with mediastinitis caused by Staphylococcus aureus in which the
              infecting bacterium acquired linezolid resistance after only 14
              days treatment with linezolid. We therefore investigated relevant
              clinical isolates for possible mechanisms of this rapid
              acquisition of linezolid resistance. METHODS: Using clinical S.
              aureus isolates, we assessed the in vitro mutation rate and
              performed stepwise selection for linezolid resistance. To
              investigate homologous recombination, sequences were determined
              for each of the 23S ribosomal RNA (23S rRNA) loci; analyzed
              sequences spanned the entirety of each 23S rRNA gene, including
              domain V, as well as the 16S-23S intergenic spacer regions. We
              additionally performed next-generation sequencing on clinical
              strains to identify single-nucleotide polymorphisms compared to
              the N315 genome. RESULTS: Strains isolated from the patient prior
              to linezolid exposure (M5-M7) showed higher-level linezolid
              resistance than N315, and the pre-exposure strain (M2) exhibited
              more rapid acquisition of linezolid resistance than did N315.
              However, the mutation rates of these and contemporaneous clinical
              isolates were similar to those of N315, and the isolates did not
              exhibit any mutations in hypermutation-related genes. Sequences
              of the 23S rRNA genes and 16S-23S intergenic spacer regions were
              identical among the pre- and post-exposure clinical strains.
              Notably, all of the pre-exposure isolates harbored a recQ
              missense mutation (Glu69Asp) with respect to N315; such a lesion
              may have affected short sequence recombination (facilitating, for
              example, recombination among rrn loci). We hypothesize that this
              mechanism contributed to rapid acquisition of linezolid
              resistance. CONCLUSIONS: Hypermutation and homologous
              recombination of the ribosomal RNA genes, including 23S rRNA
              genes, appear not to have been sources of the accelerated
              acquisition of linezolid resistance observed in our clinical
              case. Increased frequency of short sequence recombination may
              have resulted from a recQ variant in the infecting organism.",
  journal  = "PLoS One",
  volume   =  11,
  number   =  5,
  pages    = "e0155512",
  month    =  may,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Ward2016-qy,
  title    = "Identification of source and sink populations for the emergence
              and global spread of the {East-Asia} clone of
              community-associated {MRSA}",
  author   = "Ward, Melissa J and Goncheva, Mariya and Richardson, Emily and
              McAdam, Paul R and Raftis, Emma and Kearns, Angela and Daum,
              Robert S and David, Michael Z and Lauderdale, Tsai Ling and
              Edwards, Giles F and Nimmo, Graeme R and Coombs, Geoffrey W and
              Huijsdens, Xander and Woolhouse, Mark E J and Fitzgerald, J Ross",
  abstract = "BACKGROUND: Our understanding of the factors influencing the
              emergence, dissemination and global distribution of epidemic
              clones of bacteria is limited. ST59 is a major epidemic clone of
              community-associated MRSA in East Asia, responsible for extensive
              morbidity and mortality, but has a much lower prevalence in other
              parts of the world. The geographic origin of ST59 and its
              international routes of dissemination are unclear and disputed in
              the literature. RESULTS: To investigate the origin and spread of
              the ST59 clone, we obtained whole genome sequences of isolates
              from four continents, sampled over more than a decade, and
              carried out a time-scaled phylogeographic analysis. We discover
              that two distinct ST59 clades emerged concurrently, in East Asia
              and the USA, but underwent clonal expansion at different times.
              The East Asia clade was strongly enriched for gene determinants
              associated with antibiotic resistance, consistent with regional
              differences in antibiotic usage. Both clones spread independently
              to Australia and Europe, and we found evidence of the persistence
              of multi-drug resistance following export from East Asia. Direct
              transfer of strains between Taiwan and the USA was not observed
              in either direction, consistent with geographic niche exclusion.
              CONCLUSIONS: Our results resolve a longstanding controversy
              regarding the origin of the ST59 clone, revealing the major
              global source and sink populations and routes for the spread of
              multi-drug resistant clones. Additionally, our findings indicate
              that diversification of the accessory genome of epidemic clones
              partly reflects region-specific patterns of antibiotic usage,
              which may influence bacterial fitness after transmission to
              different geographic locations.",
  journal  = "Genome Biol.",
  volume   =  17,
  number   =  1,
  pages    = "160",
  month    =  jul,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Lozano2012-xl,
  title    = "Expansion of a Plasmid Classification System for {Gram-Positive}
              Bacteria and Determination of the Diversity of Plasmids in
              Staphylococcus aureus Strains of Human, Animal, and Food Origins",
  author   = "Lozano, C and Garcia-Migura, L and Aspiroz, C and Zarazaga, M and
              Torres, C and Aarestrup, F M",
  journal  = "Appl. Environ. Microbiol.",
  volume   =  78,
  number   =  16,
  pages    = "5948--5955",
  month    =  aug,
  year     =  2012,
  keywords = "Staphylococcus;plasmid;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Bosi2016-fz,
  title    = "Comparative genome-scale modelling of Staphylococcus aureus
              strains identifies strain-specific metabolic capabilities linked
              to pathogenicity",
  author   = "Bosi, Emanuele and Monk, Jonathan M and Aziz, Ramy K and Fondi,
              Marco and Nizet, Victor and Palsson, Bernhard {\O}",
  abstract = "Staphylococcus aureus is a preeminent bacterial pathogen capable
              of colonizing diverse ecological niches within its human host. We
              describe here the pangenome of S. aureus based on analysis of
              genome sequences from 64 strains of S. aureus spanning a range of
              ecological niches, host types, and antibiotic resistance
              profiles. Based on this set, S. aureus is expected to have an
              open pangenome composed of 7,411 genes and a core genome composed
              of 1,441 genes. Metabolism was highly conserved in this core
              genome; however, differences were identified in amino acid and
              nucleotide biosynthesis pathways between the strains.
              Genome-scale models (GEMs) of metabolism were constructed for the
              64 strains of S. aureus These GEMs enabled a systems approach to
              characterizing the core metabolic and panmetabolic capabilities
              of the S. aureus species. All models were predicted to be
              auxotrophic for the vitamins niacin (vitamin B3) and thiamin
              (vitamin B1), whereas strain-specific auxotrophies were predicted
              for riboflavin (vitamin B2), guanosine, leucine, methionine, and
              cysteine, among others. GEMs were used to systematically analyze
              growth capabilities in more than 300 different growth-supporting
              environments. The results identified metabolic capabilities
              linked to pathogenic traits and virulence acquisitions. Such
              traits can be used to differentiate strains responsible for mild
              vs. severe infections and preference for hosts (e.g., animals vs.
              humans). Genome-scale analysis of multiple strains of a species
              can thus be used to identify metabolic determinants of virulence
              and increase our understanding of why certain strains of this
              deadly pathogen have spread rapidly throughout the world.",
  journal  = "Proc. Natl. Acad. Sci. U. S. A.",
  month    =  jun,
  year     =  2016,
  keywords = "core genome; mathematical modeling; pangenome; pathogenicity;
              systems
              biology;Staphylococcus;pangenome;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Jaton2016-ll,
  title    = "Common skin infection due to {Panton-Valentine}
              leucocidin-producing Staphylococcus aureus strains in asylum
              seekers from Eritrea: a genome-based investigation of a suspected
              outbreak",
  author   = "Jaton, L and Pillonel, T and Jaton, K and Dory, E and Prod'hom, G
              and Blanc, D S and Tissot, F and Bodenmann, P and Greub, G",
  abstract = "OBJECTIVES: Since late 2014, multiple cases of abscesses and
              boils due to methicillin susceptible Staphylococcus aureus (MSSA)
              expressing the Panton-Valentine leukocidin (PVL) were observed in
              Eritrean asylum seekers in Lausanne, Switzerland. Strains
              isolated from infected Eritrean and non-Eritrean patients were
              compared by whole genome sequencing (WGS) to determine whether
              these numerous cases results from an outbreak. METHODS: The
              genome of S. aureus PVL-producing strains were sequenced and
              compared. Clinical and epidemiological characteristics of
              patients infected by PVL-producing strains were investigated.
              RESULTS: This work reports 15 cases of infections due to
              PVL-producing strains affecting mostly asylum seekers (n=10),
              people working with refugees and/or exposed to Africans (n=3).
              Most infections were due to closely related strains of CC152
              (n=8) and CC15 (n=3), two distantly related (>34,000 core single
              nucleotide polymorphisms [SNPs]) clonal complexes.
              Epidemiological link between the 15 cases could be ruled out by
              WGS (33 to 172 core SNPs between the different strains of a given
              complex). Altogether, these results reflect the probable high
              incidence of CC15 and CC152 PVL-producing strains in eastern
              Africa. CONCLUSIONS: Clinicians facing unusual skin infections in
              African refugees (or in any person returning from this high
              endemic region) should consider S. aureus PVL-producer before
              suspecting rare infections such as leishmaniosis or
              rickettsiosis. Clinicians should also remember that PVL are
              frequently expressed by MSSA in some regions of the world and
              that antibiotics efficient on the toxin expression, such as
              clindamycin, represent the best therapeutic option.",
  journal  = "Clin. Microbiol. Infect.",
  month    =  jun,
  year     =  2016,
  keywords = "Panton-Valentine leukocidin; ST132; Staphylococcus aureus; genome
              sequence; migrants; skin
              infection;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Winstel2013-hw,
  title    = "Wall teichoic acid structure governs horizontal gene transfer
              between major bacterial pathogens",
  author   = "Winstel, Volker and Liang, Chunguang and Sanchez-Carballo,
              Patricia and Steglich, Matthias and Munar, Marta and Br{\"o}ker,
              Barbara M and Penad{\'e}s, Jose R and N{\"u}bel, Ulrich and
              Holst, Otto and Dandekar, Thomas and Peschel, Andreas and Xia,
              Guoqing",
  abstract = "Mobile genetic elements (MGEs) encoding virulence and resistance
              genes are widespread in bacterial pathogens, but it has remained
              unclear how they occasionally jump to new host species.
              Staphylococcus aureus clones exchange MGEs such as S. aureus
              pathogenicity islands (SaPIs) with high frequency via helper
              phages. Here we report that the S. aureus ST395 lineage is
              refractory to horizontal gene transfer (HGT) with typical S.
              aureus but exchanges SaPIs with other species and genera
              including Staphylococcus epidermidis and Listeria monocytogenes.
              ST395 produces an unusual wall teichoic acid (WTA) resembling
              that of its HGT partner species. Notably, distantly related
              bacterial species and genera undergo efficient HGT with typical
              S. aureus upon ectopic expression of S. aureus WTA. Combined with
              genomic analyses, these results indicate that a 'glycocode' of
              WTA structures and WTA-binding helper phages permits HGT even
              across long phylogenetic distances thereby shaping the evolution
              of Gram-positive pathogens.",
  journal  = "Nat. Commun.",
  volume   =  4,
  pages    = "2345",
  year     =  2013,
  keywords = "Staphylococcus;evolution;recombination;phage;Staph\_evolutionary\_history;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Azarian2016-ta,
  title    = "Intrahost Evolution of {Methicillin-Resistant} Staphylococcus
              aureus {USA300} Among Individuals With Reoccurring Skin and
              {Soft-Tissue} Infections",
  author   = "Azarian, Taj and Daum, Robert S and Petty, Lindsay A and
              Steinbeck, Jenny L and Yin, Zachary and Nolan, David and
              Boyle-Vavra, Susan and Hanage, W P and Salemi, Marco and David,
              Michael Z",
  abstract = "BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA)
              USA300 is the leading cause of MRSA infections in the United
              States and has caused an epidemic of skin and soft-tissue
              infections. Recurrent infections with USA300 MRSA are common, yet
              intrahost evolution during persistence on an individual has not
              been studied. This gap hinders the ability to clinically manage
              recurrent infections and reconstruct transmission networks.
              METHODS: To characterize bacterial intrahost evolution, we
              examined the clinical courses of 4 subjects with 3-6 recurrent
              USA300 MRSA infections, using patient clinical data, including
              antibiotic exposure history, and whole-genome sequencing and
              phylogenetic analysis of all available MRSA isolates (n = 29).
              RESULTS: Among sequential isolates, we found variability in
              diversity, accumulation of mutations, and mobile genetic
              elements. Selection for antimicrobial-resistant populations was
              observed through both an increase in the number of plasmids
              conferring multidrug resistance and strain replacement by a
              resistant population. Two of 4 subjects had strain replacement
              with a genetically distinct USA300 MRSA population. DISCUSSIONS:
              During a 5-year period in 4 subjects, we identified development
              of antimicrobial resistance, intrahost evolution, and strain
              replacement among isolates from patients with recurrent MRSA
              infections. This calls into question the efficacy of
              decolonization to prevent recurrent infections and highlights the
              adaptive potential of USA300 and the need for effective sampling.",
  journal  = "J. Infect. Dis.",
  volume   =  214,
  number   =  6,
  pages    = "895--905",
  month    =  sep,
  year     =  2016,
  keywords = "MRSA; Staphylococcus aureus; USA300; antibiotic resistance;
              evolution; intrahost; phylogenetic; recurrent infections; skin
              and soft-tissue infections; whole-genome sequencing; within
              host;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Spoor2015-ub,
  title     = "Recombination-mediated remodelling of host--pathogen
               interactions during Staphylococcus aureus niche adaptation",
  author    = "Spoor, Laura E and Richardson, Emily and Richards, Amy C and
               Wilson, Gillian J and Mendonca, Chriselle and Gupta, Ravi Kr and
               McAdam, Paul R and Nutbeam-Tuffs, Stephen and Black, Nikki S and
               O'Gara, James P and Lee, Chia Y and Corander, Jukka and Ross
               Fitzgerald, J",
  abstract  = "Large-scale recombination events have led to the emergence of
               epidemic clones of several major bacterial pathogens. However,
               the functional impact of the recombination on clonal success is
               not understood. Here, we identified a novel widespread hybrid
               clone (ST71) of livestock-associated Staphylococcus aureus that
               evolved from an ancestor belonging to the major bovine lineage
               CC97, through multiple large-scale recombination events with
               other S. aureus lineages occupying the same ruminant niche. The
               recombination events, affecting a 329 kb region of the
               chromosome spanning the origin of replication, resulted in
               allele replacement and loss or gain of an array of genes
               influencing host--pathogen interactions. Of note, molecular
               functional analyses revealed that the ST71 hybrid clone has
               acquired multiple novel pathogenic traits associated with
               acquired and innate immune evasion and bovine extracellular
               matrix adherence. These findings provide a paradigm for the
               impact of large-scale recombination events on the rapid
               evolution of bacterial pathogens within defined ecological
               niches.",
  journal   = "Microbial Genomics",
  publisher = "Microbiology Society",
  volume    =  1,
  number    =  4,
  month     =  oct,
  year      =  2015,
  keywords  = "recombination; remodelling; Staphylococcus aureus;
               host--pathogen interactions; niche
               adaptation;recombination;Staphylococcus;host-pathogen;Staph\_evolutionary\_history;Staph\_evolutionary\_history/staph
               microbial interactions;Staphylococcus\_aureus\_genome\_papers"
 }

 @UNPUBLISHED{Thorpe2016-nj,
  title    = "The large majority of intergenic sites in bacteria are
              selectively constrained, even when known regulatory elements are
              excluded",
  author   = "Thorpe, Harry A and Bayliss, Sion C and Hurst, Laurence D and
              Feil, Edward J",
  abstract = "There are currently no broad estimates of the overall strength
              and direction of selection operating on intergenic variation in
              bacteria. Here we address this using large whole genome sequence
              datasets representing six diverse bacterial species; Escherichia
              coli, Staphylococcus aureus, Salmonella enterica, Streptococcus
              pneumoniae, Klebsiella pneumoniae, and Mycobacterium
              tuberculosis. Excluding M. tuberculosis, we find that a high
              proportion (62\%-79\%; mean 70\%) of intergenic sites are
              selectively constrained, relative to synonymous sites. Non-coding
              RNAs tend to be under stronger selective constraint than
              promoters, which in turn are typically more constrained than
              rho-independent terminators. Even when these regulatory elements
              are excluded, the mean proportion of constrained intergenic sites
              only falls to 69\%; thus our current understanding of the
              functionality of intergenic regions (IGRs) in bacteria is
              severely limited. Consistent with a role for positive as well as
              negative selection on intergenic sites, we present evidence for
              strong positive selection in Mycobacterium tuberculosis
              promoters, underlining the key role of regulatory changes as an
              adaptive mechanism in this highly monomorphic pathogen.",
  journal  = "bioRxiv",
  pages    = "069708",
  month    =  jan,
  year     =  2016,
  keywords = "evolution;Staphylococcus;bacterial comparative
              genomics;Staph\_evolutionary\_history/Teaching\_Prokaryotic\_evolution;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;microRNA\_in\_bacteria",
  language = "en"
 }

 @ARTICLE{Santos2016-wg,
  title    = "Draft Genome Sequence of the Aureocin {A53-Producing} Strain
              Staphylococcus aureus {A53}",
  author   = "Santos, Olinda Cabral Silva and Duarte, Andreza Freitas Souza and
              Albano, Rodolpho Mattos and Bastos, Maria Carmo Freire",
  abstract = "Here, we present the 2,658,363-bp draft genome sequence of the
              aureocin A53-producing strain Staphylococcus aureus A53. This
              genome information may contribute to the optimal and rational
              exploitation of aureocin A53 as an antimicrobial agent and to its
              production in large scale.",
  journal  = "Genome Announc.",
  volume   =  4,
  number   =  4,
  month    =  aug,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Ward2016-pz,
  title    = "Identification of source and sink populations for the emergence
              and global spread of the {East-Asia} clone of
              community-associated {MRSA}",
  author   = "Ward, Melissa J and Goncheva, Mariya and Richardson, Emily and
              McAdam, Paul R and Raftis, Emma and Kearns, Angela and Daum,
              Robert S and David, Michael Z and Lauderdale, Tsai Ling and
              Edwards, Giles F and Nimmo, Graeme R and Coombs, Geoffrey W and
              Huijsdens, Xander and Woolhouse, Mark E J and Fitzgerald, J Ross",
  abstract = "Our understanding of the factors influencing the emergence,
              dissemination and global distribution of epidemic clones of
              bacteria is limited. ST59 is a major epidemic clone of
              community-associated MRSA in East Asia, responsible for extensive
              morbidity and mortality, but has a much lower prevalence in other
              parts of the world. The geographic origin of ST59 and its
              international routes of dissemination are unclear and disputed in
              the literature.",
  journal  = "Genome Biol.",
  volume   =  17,
  number   =  1,
  pages    = "1--13",
  year     =  2016,
  keywords = "
              Staphylococcus;antibiotics;Staph\_evolutionary\_history;bacterial
              comparative
              genomics;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers;Staph-animal-human"
 }

 @ARTICLE{Weber2016-fq,
  title    = "Complete Genome Sequences of Two {Methicillin-Sensitive}
              Staphylococcus aureus Isolates Representing a Population Subset
              Highly Prevalent in Human Colonization",
  author   = "Weber, Robert E and Layer, Franziska and Fuchs, Stephan and
              Bender, Jennifer K and Fiedler, Stefan and Werner, Guido and
              Strommenger, Birgit",
  abstract = "Here, we report the high-quality draft genome sequences of two
              methicillin-susceptible Staphylococcus aureus isolates, 08-02119
              and 08-02300. Belonging to sequence type 582 (ST582) and ST7,
              both isolates are representatives of clonal lineages often
              associated with asymptomatic colonization of humans.",
  journal  = "Genome Announc.",
  volume   =  4,
  number   =  4,
  month    =  jul,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Senghore2016-mp,
  title    = "Whole-genome sequencing reveals transmission of Staphylococcus
              aureus from humans to green monkeys in The Gambia",
  author   = "Senghore, Madikay and Bayliss, Sion C and Kwambana-Adams, Brenda
              A and Foster-Nyarko, Ebenezer and Manneh, Jainaba and Dione,
              Michel and Badji, Henry and Ebruke, Chinelo and Doughty, Emma L
              and Thorpe, Harry A and Jasinska, Anna J and Schmitt, Christopher
              A and Cramer, Jennifer D and Turner, Trudy R and Weinstock,
              George and Freimer, Nelson B and Pallen, Mark J and Feil, Edward
              J and Antonio, Martin",
  abstract = "Staphylococcus aureus is an important pathogen of humans and
              animals. We genome-sequenced ninety S. aureus isolates from the
              Gambia: 46 isolates from invasive disease in humans, 13 human
              carriage isolates and 31 monkey carriage isolates. We inferred
              multiple anthroponotic transmissions of S. aureus from humans to
              green monkeys, Chlorocebus sabaeus in The Gambia over different
              timescales. We report a novel monkey-associated clade of S.
              aureus that emerged from a human-to-monkey switch estimated to
              have occurred 2,700 years ago. Adaptation of this lineage to the
              monkey host is accompanied by loss of phage-encoded genes that
              are known to play an important role in human colonisation. We
              also report recent anthroponotic transmission of the
              well-characterised human lineages, ST6 and ST15, to monkeys,
              probably because of steadily increasing encroachment of humans
              into the monkeys' habitat. Although we have found no evidence of
              transmission of S. aureus from monkeys to humans, as the two
              species come into ever-closer contact there might be an increased
              risk of additional inter-species exchanges of potential
              pathogens. IMPORTANCE: The population structures of
              Staphylococcus aureus in humans and monkeys in sub-Saharan Africa
              have been previously described using MLST. However, these data
              lack the power to accurately infer details regarding the origin
              and maintenance of new adaptive lineages. Here, we describe the
              use of whole genome sequencing to detect transmission of S.
              aureus between humans and non-human primates and to document the
              genetic changes accompanying host adaptation. We note that human
              to monkey switches tend to be more common than the reverse, and
              that a novel monkey associated clade is likely to have emerged
              from such a switch approximately 2700 years ago. Moreover,
              analysis of the accessory genome provides important clues as to
              the genetic changes underpinning host adaptation, and in
              particular show that human to monkey switches tend to be
              associated with the loss of genes known to confer adaptation to
              the human host.",
  journal  = "Appl. Environ. Microbiol.",
  month    =  jul,
  year     =  2016,
  keywords = "Staphylococcus;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Monecke2015-ob,
  title    = "A clonal complex 12 methicillin-resistant Staphylococcus aureus
              strain, West Australian {MRSA-59}, harbors a novel
              {pseudo-SCCmec} element",
  author   = "Monecke, Stefan and Coombs, Geoffrey W and Pearson, Julie and
              Hotzel, Helmut and Slickers, Peter and Ehricht, Ralf",
  abstract = "A West Australian methicillin-resistant Staphylococcus aureus
              strain (WA MRSA-59) was characterized by microarray and
              sequencing. Its pseudo-staphylococcal cassette chromosome mec
              (SCCmec) element comprised dcs, Q9XB68-dcs, mvaS-SCC, Q5HJW6,
              dru, ugpQ, ydeM, mecA-mecR-mecI, txbi mecI, tnp IS431, copA2-mco
              (copper resistance), ydhK, arsC-arsB-arsR (arsenic resistance),
              open reading frame PT43, and per-2. Recombinase genes, xylR
              (mecR2), and PSM-mec (phenol-soluble modulin) were absent. We
              suggest that mec complex A should be split into two subtypes. One
              harbors PSM-mec and xylR (mecR2). It is found in SCCmec types II,
              III, and VIII. The second subtype, described herein, is present
              in WA MRSA-59 and some coagulase-negative staphylococci.",
  journal  = "Antimicrob. Agents Chemother.",
  volume   =  59,
  number   =  11,
  pages    = "7142--7144",
  month    =  nov,
  year     =  2015,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Davis2015-op,
  title    = "Genome sequencing reveals strain dynamics of
              methicillin-resistant Staphylococcus aureus in the same household
              in the context of clinical disease in a person and a dog",
  author   = "Davis, Meghan F and Misic, Ana M and Morris, Daniel O and Moss,
              John T and Tolomeo, Pam and Beiting, Daniel P and Nachamkin,
              Irving and Lautenbach, Ebbing and Rankin, Shelley C",
  abstract = "The strain dynamics of methicillin-resistant Staphylococcus
              aureus (MRSA) isolates from people and the household dog were
              investigated. The isolates were identified in the context of a
              randomized controlled trial that tested household-wide
              decolonization of people. Genotypic comparison of MRSA isolates
              obtained from two household members, the dog, and home surfaces
              over a three-month period failed to implicate the pet or the home
              environment in recurrent colonization of the household members.
              However, it did implicate the pet's bed in exposure of the dog
              prior to the dog's infection. Whole genome sequencing was
              performed to differentiate the isolates. This report also
              describes introduction of diverse strains of MRSA into the
              household within six weeks of cessation of harmonized
              decolonization treatment of people and treatment for infection in
              the dog. These findings suggest that community sources outside
              the home may be important for recurrent MRSA colonization or
              infection.",
  journal  = "Vet. Microbiol.",
  volume   =  180,
  number   = "3-4",
  pages    = "304--307",
  month    =  nov,
  year     =  2015,
  keywords = "Antimicrobial resistance; Canine; MRSA; SSI;
              SSTI;Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
 }

 @ARTICLE{Yan2016-hn,
  title    = "Genetic features of livestock-associated Staphylococcus aureus
              {ST9} isolates from Chinese pigs that carry the lsa(E) gene for
              quinupristin/dalfopristin resistance",
  author   = "Yan, Xiaomei and Li, Zongwei and Chlebowicz, Monika A and Tao,
              Xiaoxia and Ni, Ming and Hu, Yuan and Li, Zhen and Grundmann,
              Hajo and Murray, Susan and Pascoe, Ben and Sheppard, Samuel K and
              Bo, Xiaochen and Dijl, Jan Maarten van and Du, Pengcheng and
              Zhang, Minli and You, Yuanhai and Yu, Xiaojie and Meng, Fanliang
              and Wang, Shengqi and Zhang, Jianzhong",
  abstract = "Whole-genome sequencing (WGS) was used to investigate the genetic
              features of the recently identified lsa(E) gene in porcine S.
              aureus ST9 isolates. Three quinupristin/dalfopristin-resistant
              isolates harboring the lsa(E) gene (two MRSA and one MSSA) were
              sequenced. Phylogenetic analysis of 184S. aureus genomes showed
              that ST9 porcine isolates belong to a distinct sequence cluster.
              Further analysis showed that all isolates were deficient in the
              recently described type IV restriction-modification system and
              SCCmec type XII was identified in the two MRSA isolates, which
              included a rare class C2 mec gene complex. A 24kb $\Psi$SCC
              fragment was found in the MRSA and MSSA isolates sharing 99\%
              nucleotide sequence homology with the $\Psi$SCCJCSC6690 (O-2)
              element of a ST9 MRSA isolate from Thailand (accession number
              AB705453). Comparison of these ST9 isolates with 181 publically
              available S. aureus genomes identified 24 genes present in all
              (100\%) ST9 isolates, that were absent from the most closely
              related human isolate. Our analysis suggests that the sequenced
              quinupristin/dalfopristin-resistant ST9 lineage represent a
              reservoir of mobile genetic elements associated with resistance
              and virulence features.",
  journal  = "Int. J. Med. Microbiol.",
  month    =  aug,
  year     =  2016,
  keywords = "ABC transporters; Livestock-associated;
              Quinupristin/dalfopristin; Resistance; ST9; Staphylococcus
              aureus;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Hughes2015-sf,
  title    = "Clonal variation in high- and low-level phenotypic and genotypic
              mupirocin resistance of {MRSA} isolates in south-east London",
  author   = "Hughes, John and Stabler, Richard and Gaunt, Michael and Karadag,
              Tacim and Desai, Nergish and Betley, Jason and Ioannou, Avgousta
              and Aryee, Anna and Hearn, Pasco and Marbach, Helene and Patel,
              Amita and Otter, Jonathan A and Edgeworth, Jonathan D and Tosas
              Auguet, Olga",
  abstract = "OBJECTIVES: Both low-level mupirocin resistance (LMR) and
              high-level mupirocin resistance (HMR) have been identified. The
              aim of this study was to determine the epidemiology of LMR and
              HMR in MRSA isolates at five hospitals that have used mupirocin
              for targeted decolonization as part of successful institutional
              control programmes. METHODS: All MRSA identified in three
              microbiology laboratories serving five central and south-east
              London hospitals and surrounding communities between November
              2011 and February 2012 were included. HMR and LMR were determined
              by disc diffusion testing. WGS was used to derive multilocus
              sequence types (MLSTs) and the presence of HMR and LMR resistance
              determinants. RESULTS: Prevalence of either HMR or LMR amongst
              first healthcare episode isolates from 795 identified patients
              was 9.69\% (95\% CI 7.72-11.96); LMR was 6.29\% (95\% CI
              4.70-8.21) and HMR was 3.40\% (95\% CI 2.25-4.90). Mupirocin
              resistance was not significantly different in isolates identified
              from inpatients at each microbiology laboratory, but was more
              common in genotypically defined 'hospital' rather than
              'community' isolates (OR 3.17, 95\% CI 1.36-9.30, P = 0.002). LMR
              was associated with inpatient stay, previous history of MRSA and
              age $\geq$65 years; HMR was associated with age $\geq$65 years
              and residential postcode outside London. LMR and HMR varied by
              clone, with both being low in the dominant UK MRSA clone ST22
              compared with ST8, ST36 and ST239/241 for LMR and with ST8 and
              ST36 for HMR. V588F mutation and mupA carriage had high
              specificity (>97\%) and area under the curve (>83\%) to
              discriminate phenotypic mupirocin resistance, but uncertainty
              around the sensitivity point estimate was large (95\% CI
              52.50\%-94.44\%). Mutations in or near the mupA gene were found
              in eight isolates that carried mupA but were not HMR.
              CONCLUSIONS: Mupirocin resistance was identified in <10\% of
              patients and varied significantly by clone, implying that changes
              in clonal epidemiology may have an important role in determining
              the prevalence of resistance in conjunction with selection due to
              mupirocin use.",
  journal  = "J. Antimicrob. Chemother.",
  volume   =  70,
  number   =  12,
  pages    = "3191--3199",
  month    =  dec,
  year     =  2015,
  keywords = "Staphylococcus;antibiotics;confirmed\_SA-resistance-mutation;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 % The entry below contains non-ASCII chars that could not be converted
 % to a LaTeX equivalent.
 @ARTICLE{Mellmann2016-os,
  title    = "{Real-Time} Genome Sequencing of Resistant Bacteria Provides
              Precision Infection Control in an Institutional Setting",
  author   = "Mellmann, Alexander and Bletz, Stefan and B{\"o}king, Thomas and
              Kipp, Frank and Becker, Karsten and Schultes, Anja and Prior,
              Karola and Harmsen, Dag",
  abstract = "The increasing prevalence of multidrug-resistant (MDR) bacteria
              is a serious global challenge. Here, we studied prospectively
              whether bacterial whole-genome sequencing (WGS) for real-time MDR
              surveillance is technical feasible, returns actionable results,
              and is cost-beneficial. WGS was applied to all MDR isolates of
              four species (methicillin-resistant Staphylococcus aureus [MRSA],
              vancomycin-resistant Enterococcus faecium, MDR Escherichia coli,
              and MDR Pseudomonas aeruginosa) at the University Hospital
              Muenster, Muenster, Germany, a tertiary care hospital with 1,450
              beds, during two 6-month intervals. Turnaround times (TAT) were
              measured, and total costs for sequencing per isolate were
              calculated. After cancelling prior policies of preemptive
              isolation of patients harboring certain Gram-negative MDR
              bacteria in risk areas, the second interval was conducted. During
              interval I, 645 bacterial isolates were sequenced. From culture,
              TATs ranged from 4.4 to 5.3 days, and costs were €202.49 per
              isolate. During interval II, 550 bacterial isolates were
              sequenced. Hospital-wide transmission rates of the two most
              common species (MRSA and MDR E. coli) were low during interval I
              (5.8\% and 2.3\%, respectively) and interval II (4.3\% and 5.0\%,
              respectively). Cancellation of isolation of patients infected
              with non-pan-resistant MDR E. coli in risk wards did not increase
              transmission. Comparing sequencing costs with avoided costs
              mostly due to fewer blocked beds during interval II, we saved in
              excess of €200,000. Real-time microbial WGS in our institution
              was feasible, produced precise actionable results, helped us to
              monitor transmission rates that remained low following a
              modification in isolation procedures, and ultimately saved costs.",
  journal  = "J. Clin. Microbiol.",
  volume   =  54,
  number   =  12,
  pages    = "2874--2881",
  month    =  dec,
  year     =  2016,
  keywords = "Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers;Anti-infectives\_course",
  language = "en"
 }

 @ARTICLE{Kleinert2016-mz,
  title    = "Draft Genome Sequences of Three Northern German Epidemic
              Staphylococcus aureus ({ST247}) Strains Containing Multiple
              Copies of {IS256}",
  author   = "Kleinert, Franziska and Kallies, Ren{\'e} and Zweynert, Annegret
              and Bierbaum, Gabriele",
  abstract = "We report the draft genome sequences of three multiresistant
              Staphylococcus aureus strains of sequence type 247 (ST247). The
              methicillin-resistant S. aureus (MRSA) SA1450/94 is vancomycin
              susceptible, while the clinical MRSA isolate S. aureus SA137/93A
              and its spontaneous laboratory mutant SA137/93G are characterized
              by intermediate vancomycin susceptibility.",
  journal  = "Genome Announc.",
  volume   =  4,
  number   =  5,
  month    =  sep,
  year     =  2016,
  keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Papers\_for\_Michelle;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers",
  language = "en"
 }

 @ARTICLE{Cao2016-tc,
  title    = "Identification and functional study of type {III-A} {CRISPR-Cas}
              systems in clinical isolates of Staphylococcus aureus",
  author   = "Cao, Linyan and Gao, Chun-Hui and Zhu, Jiade and Zhao, Liping and
              Wu, Qingfa and Li, Min and Sun, Baolin",
  abstract = "The CRISPR-Cas (clustered regularly interspaced short palindromic
              repeats [CRISPR]-CRISPR associated proteins [Cas]) system can
              provide prokaryote with immunity against invading mobile genetic
              elements (MGEs) such as phages and plasmids, which are the main
              sources of staphylococcal accessory genes. To date, only a few
              Staphylococcus aureus strains containing CRISPR-Cas systems have
              been identified, but no functional study in these strains has
              been reported. In this study, 6 clinical isolates of S. aureus
              with type III-A CRISPR-Cas systems were identified, and
              whole-genome sequencing and functional study were conducted
              subsequently. Genome sequence analysis revealed a close linkage
              between the CRISPR-Cas system and the staphylococcal cassette
              chromosome mec (SCCmec) element in five strains. Comparative
              sequence analysis showed that the type III-A repeats are
              conserved within staphylococci, despite of the decreased
              conservation in trailer-end repeats. Highly homologous sequences
              of some spacers were identified in staphylococcal MGEs, and
              partially complementary sequences of spacers were mostly found in
              the coding strand of lytic regions in staphylococcal phages.
              Transformation experiments showed that S. aureus type III-A
              CRISPR-Cas system can specifically prevent plasmid transfer in a
              transcription-dependent manner. Base paring between crRNA and
              target sequence, the endoribonuclease, and the Csm complex were
              proved to be necessary for type III-A CRISPR-Cas immunity.",
  journal  = "Int. J. Med. Microbiol.",
  month    =  aug,
  year     =  2016,
  keywords = "Prophage; SCCmec; Staphylococcus aureus; Type III-A CRISPR-Cas
              system;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Botelho2016-ed,
  title    = "Complete genome sequence of the {MRSA} isolate {HC1335} from
              {ST239} lineage displaying a truncated {AgrC} histidine kinase
              receptor",
  author   = "Botelho, Ana M N and Costa, Maiana O C and Beltrame, Cristiana O
              and Ferreira, Fabienne A and Lima, Nicholas C B and Costa, Bruno
              S S and de Morais, Guilherme L and Souza, Rangel C and Almeida,
              Luiz G P and Vasconcelos, Ana T R and Nicol{\'a}s, Marisa F and
              Figueiredo, Agnes M S",
  abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) is still one
              of the most important hospital pathogen globally. The
              multiresistant isolates of the ST239-SCCmecIII lineage are spread
              over large geographic regions, colonizing and infecting hospital
              patients in virtually all continents. The balance between fitness
              (adaptability) and virulence potential is likely to represent an
              important issue in the clonal shift dynamics leading the success
              of some specific MRSA clones over another. The accessory gene
              regulator (agr) is the master quorum sensing system of
              staphylococci playing a role in the global regulation of key
              virulence factors. Consequently, agr inactivation in S. aureus
              may represent a significant mechanism of genetic variability in
              the adaptation of this healthcare-associated pathogen. We report
              here the complete genome sequence of the methicillin-resistant S.
              aureus, isolate HC1335, a variant of the ST239 lineage, which
              presents a natural insertion of an IS256 transposase element in
              the agrC gene encoding AgrC histidine kinase receptor.",
  journal  = "Genome Biol. Evol.",
  month    =  sep,
  year     =  2016,
  keywords = "IS256 insertion; ST239 lineage; agrC dysfunction; complete genome
              sequence; methicillin-resistant Staphylococcus
              aureus;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Harrison2016-eo,
  title    = "Transmission of methicillin-resistant Staphylococcus aureus in
              long-term care facilities and their related healthcare networks",
  author   = "Harrison, Ewan M and Ludden, Catherine and Brodrick, Hayley J and
              Blane, Beth and Brennan, Gr{\'a}inne and Morris, Dearbh{\'a}ile
              and Coll, Francesc and Reuter, Sandra and Brown, Nicholas M and
              Holmes, Mark A and O'Connell, Brian and Parkhill, Julian and
              T{\"o}r{\"o}k, M Estee and Cormican, Martin and Peacock, Sharon J",
  abstract = "BACKGROUND: Long-term care facilities (LTCF) are potential
              reservoirs for methicillin-resistant Staphylococcus aureus
              (MRSA), control of which may reduce MRSA transmission and
              infection elsewhere in the healthcare system. Whole-genome
              sequencing (WGS) has been used successfully to understand MRSA
              epidemiology and transmission in hospitals and has the potential
              to identify transmission between these and LTCF. METHODS: Two
              prospective observational studies of MRSA carriage were conducted
              in LTCF in England and Ireland. MRSA isolates were whole-genome
              sequenced and analyzed using established methods. Genomic data
              were available for MRSA isolated in the local healthcare systems
              (isolates submitted by hospitals and general practitioners).
              RESULTS: We sequenced a total of 181 MRSA isolates from the two
              study sites. The majority of MRSA were multilocus sequence type
              (ST)22. WGS identified one likely transmission event between
              residents in the English LTCF and three putative transmission
              events in the Irish LTCF. WGS also identified closely related
              isolates present in colonized Irish residents and their immediate
              environment. Based on phylogenetic reconstruction, closely
              related MRSA clades were identified between the LTCF and their
              healthcare referral network, together with putative MRSA
              acquisition by LTCF residents during hospital admission.
              CONCLUSIONS: These data confirm that MRSA is transmitted between
              residents of LTCF and is both acquired and transmitted to others
              in referral hospitals and beyond. Our data present compelling
              evidence for the importance of environmental contamination in
              MRSA transmission, reinforcing the importance of environmental
              cleaning. The use of WGS in this study highlights the need to
              consider infection control in hospitals and community healthcare
              facilities as a continuum.",
  journal  = "Genome Med.",
  volume   =  8,
  number   =  1,
  pages    = "102",
  month    =  oct,
  year     =  2016,
  keywords = "Long-term care facilities; MRSA; Molecular epidemiology; Nursing
              home; Staphylococcus aureus; Transmission; Whole-genome
              sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Van_Duijkeren2016-pd,
  title    = "Transmission of {MRSA} between humans and animals on duck and
              turkey farms",
  author   = "van Duijkeren, E and Hengeveld, P and Zomer, T P and Landman, F
              and Bosch, T and Haenen, A and van de Giessen, A",
  abstract = "OBJECTIVES: The objectives of this study were to estimate the
              prevalence of MRSA on duck and turkey farms, identify risk
              factors for human carriage and study transmission between animals
              and humans. METHODS: On 10 duck and 10 turkey farms, samples were
              taken from animals, poultry houses, home residences and humans
              and cultured using pre-enrichment and selective enrichment. MRSA
              isolates were typed by spa typing and multiple-locus variable
              number tandem repeat analysis (MLVA) typing. A subset of isolates
              from animals and humans was investigated using whole-genome
              mapping. RESULTS: MRSA was found on one duck farm and three
              turkey farms. On duck farms, all humans were MRSA negative. On
              turkey farms, 5 of 11 farmers, 2 of 32 family members and 15 of
              49 samples from the home residences were MRSA positive.
              Individuals with daily contact with turkeys were significantly
              more often MRSA positive than individuals without daily contact.
              All MRSA isolates belonged to livestock-associated MLVA complex
              398, belonged to spa type t011, were negative for
              Panton-Valentine leucocidin, were mecC negative and were mecA
              positive. Whole-genome mapping proved a valuable tool to study
              the transmission of livestock-associated MRSA and showed that on
              two turkey farms the isolates from the animals and humans were
              indistinguishable or closely related, indicating transmission.
              CONCLUSIONS: MRSA carriage in individuals in daily contact with
              turkeys was significantly higher than that in individuals only
              living on the farms or than in the general Dutch population.
              Therefore, persons with a high degree of contact with turkeys
              have an increased risk of MRSA carriage, and we propose that they
              should be screened prior to hospitalization in order to decrease
              the risk of nosocomial transmission.",
  journal  = "J. Antimicrob. Chemother.",
  volume   =  71,
  number   =  1,
  pages    = "58--62",
  month    =  jan,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Suhaili2016-gq,
  title    = "Draft genome sequence of Staphylococcus aureus {KT/312045}, an
              {ST1-MSSA} {PVL} positive isolated from pus sample in East Coast
              Malaysia",
  author   = "Suhaili, Zarizal and Lean, Soo-Sum and Mohamad, Noor Muzamil and
              Rachman, Abdul R Abdul and Desa, Mohd Nasir Mohd and Yeo, Chew
              Chieng",
  abstract = "Most of the efforts in elucidating the molecular relatedness and
              epidemiology of Staphylococcus aureus in Malaysia have been
              largely focused on methicillin-resistant S. aureus (MRSA).
              Therefore, here we report the draft genome sequence of the
              methicillin-susceptible Staphylococcus aureus (MSSA) with
              sequence type 1 (ST1), spa type t127 with Panton-Valentine
              Leukocidin (pvl) pathogenic determinant isolated from pus sample
              designated as KT/314250 strain. The size of the draft genome is
              2.86 Mbp with 32.7\% of G + C content consisting 2673 coding
              sequences. The draft genome sequence has been deposited in
              DDBJ/EMBL/GenBank under the accession number AOCP00000000.",
  journal  = "Genom Data",
  volume   =  9,
  pages    = "111--112",
  month    =  sep,
  year     =  2016,
  keywords = "Methicillin-susceptible Staphylococcus aureus; Panton-Valentibe
              Leukocidin; ST1-MSSA PVL positive Malaysia
              isolates;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Azarian2016-bd,
  title    = "Genomic Epidemiology of {Methicillin-Resistant} Staphylococcus
              aureus in a Neonatal Intensive Care Unit",
  author   = "Azarian, Taj and Maraqa, Nizar F and Cook, Robert L and Johnson,
              Judith A and Bailey, Christine and Wheeler, Sarah and Nolan,
              David and Rathore, Mobeen H and Morris, Jr, J Glenn and Salemi,
              Marco",
  abstract = "Despite infection prevention efforts, neonatal intensive care
              unit (NICU) patients remain at risk of Methicillin-resistant
              Staphylococcus aureus (MRSA) infection. Modes of transmission for
              healthcare-associated (HA) and community-associated (CA) MRSA
              remain poorly understood and may vary by genotype, hindering the
              development of effective prevention and control strategies. From
              2008-2010, all patients admitted to a level III NICU were
              screened for MRSA colonization, and all available isolates were
              spa-typed. Spa-type t008, the most prevalent CA- genotype in the
              United States, spa-type t045, a HA- related genotype, and a
              convenience sample of strains isolated from 2003-2011, underwent
              whole-genome sequencing and phylodynamic analysis. Patient risk
              factors were compared between colonized and noncolonized infants,
              and virulence and resistance genes compared between spa-type t008
              and non-t008 strains. Epidemiological and genomic data were used
              to estimate MRSA importations and acquisitions through
              transmission reconstruction. MRSA colonization was identified in
              9.1\% (177/1940) of hospitalized infants and associated with low
              gestational age and birth weight. Among colonized infants, low
              gestational age was more common among those colonized with t008
              strains. Our data suggest that approximately 70\% of
              colonizations were the result of transmission events within the
              NICU, with the remainder likely to reflect importations of
              ``outside'' strains. While risk of transmission within the NICU
              was not affected by spa-type, patterns of acquisition and
              importation differed between t008 and t045 strains. Phylodynamic
              analysis showed the effective population size of spa-type t008
              has been exponentially increasing in both community and hospital,
              with spa-type t008 strains possessed virulence genes not found
              among t045 strains; t045 strains, in contrast, appeared to be of
              more recent origin, with a possible hospital source. Our data
              highlight the importance of both intra-NICU transmission and
              recurrent introductions in maintenance of MRSA colonization
              within the NICU environment, as well as spa-type-specific
              differences in epidemiology.",
  journal  = "PLoS One",
  volume   =  11,
  number   =  10,
  pages    = "e0164397",
  month    =  oct,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Wan2016-jx,
  title    = "Complete Circular Genome Sequence of Successful {ST8/SCCmecIV}
              {Community-Associated} {Methicillin-Resistant} Staphylococcus
              aureus ({OC8}) in Russia: {One-Megabase} Genomic Inversion,
              {IS256's} Spread, and Evolution of Russia {ST8-IV}",
  author   = "Wan, Tsai-Wen and Khokhlova, Olga E and Iwao, Yasuhisa and
              Higuchi, Wataru and Hung, Wei-Chun and Reva, Ivan V and Singur,
              Olga A and Gostev, Vladimir V and Sidorenko, Sergey V and
              Peryanova, Olga V and Salmina, Alla B and Reva, Galina V and
              Teng, Lee-Jene and Yamamoto, Tatsuo",
  abstract = "ST8/SCCmecIV community-associated methicillin-resistant
              Staphylococcus aureus (CA-MRSA) has been a common threat, with
              large USA300 epidemics in the United States. The global
              geographical structure of ST8/SCCmecIV has not yet been fully
              elucidated. We herein determined the complete circular genome
              sequence of ST8/SCCmecIVc strain OC8 from Siberian Russia. We
              found that 36.0\% of the genome was inverted relative to USA300.
              Two IS256, oppositely oriented, at IS256-enriched hot spots were
              implicated with the one-megabase genomic inversion (MbIN) and
              vSa$\beta$ split. The behavior of IS256 was flexible: its
              insertion site (att) sequences on the genome and junction
              sequences of extrachromosomal circular DNA were all divergent,
              albeit with fixed sizes. A similar multi-IS256 system was
              detected, even in prevalent ST239 healthcare-associated MRSA in
              Russia, suggesting IS256's strong transmission potential and
              advantage in evolution. Regarding epidemiology, all ST8/SCCmecIVc
              strains from European, Siberian, and Far Eastern Russia, examined
              had MbIN, and geographical expansion accompanied divergent spa
              types and resistance to fluoroquinolones, chloramphenicol, and
              often rifampicin. Russia ST8/SCCmecIVc has been associated with
              life-threatening infections such as pneumonia and sepsis in both
              community and hospital settings. Regarding virulence, the OC8
              genome carried a series of toxin and immune evasion genes, a
              truncated giant surface protein gene, and IS256 insertion
              adjacent to a pan-regulatory gene. These results suggest that
              unique single ST8/spa1(t008)/SCCmecIVc CA-MRSA (clade, Russia
              ST8-IVc) emerged in Russia, and this was followed by large
              geographical expansion, with MbIN as an epidemiological marker,
              and fluoroquinolone resistance, multiple virulence factors, and
              possibly a multi-IS256 system as selective advantages.",
  journal  = "PLoS One",
  volume   =  11,
  number   =  10,
  pages    = "e0164168",
  month    =  oct,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers",
  language = "en"
 }

 @ARTICLE{Bletz2015-ks,
  title    = "Ensuring backwards compatibility: traditional genotyping efforts
              in the era of whole genome sequencing",
  author   = "Bletz, S and Mellmann, A and Rothg{\"a}nger, J and Harmsen, D",
  abstract = "When using next-generation whole genome sequencing (WGS),
              extraction of spa types from WGS data is essential for backwards
              compatibility with Sanger sequencing-based spa typing of
              methicillin-resistant Staphylococcus aureus (MRSA). We evaluated
              WGS-based spa typing with a 2$\times$250 bp protocol in a diverse
              collection of 423 MRSA isolates using two pipelines that executed
              sequence quality-trimming and de novo assembly before spa typing.
              The SeqSphere(+) pipeline correctly typed 419 isolates (99.1\%)
              whereas the CLCbio pipeline succeeded in 249 isolates (58.9\%).
              In summary, WGS combined with an optimized de novo assembly
              enables nearly full compatibility with Sanger sequencing-based
              spa typing data.",
  journal  = "Clin. Microbiol. Infect.",
  volume   =  21,
  number   =  4,
  pages    = "347.e1--4",
  month    =  apr,
  year     =  2015,
  keywords = "Backwards compatibility; Staphylococcus aureus;
              methicillin-resistant Staphylococcus aureus; spa typing; whole
              genome
              sequencing;Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Sarrou2016-yj,
  title    = "Characterization of a Novel lsa(E)- and {lnu(B)-Carrying}
              Structure Located in the Chromosome of a Staphylococcus aureus
              Sequence Type 398 Strain",
  author   = "Sarrou, S and Liakopoulos, A and Tsoumani, K and Sagri, E and
              Mathiopoulos, K D and Tzouvelekis, L S and Miriagou, V and
              Petinaki, E",
  journal  = "Antimicrob. Agents Chemother.",
  volume   =  60,
  number   =  2,
  pages    = "1164--1166",
  month    =  feb,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Kaur2016-ib,
  title    = "Genome sequencing, assembly, annotation and analysis of
              \textit{Staphylococcus xylosus} strain {DMB3-Bh1} reveals genes
              responsible for pathogenicity",
  author   = "Kaur, Gurwinder and Arora, Amit and Sathyabama, Sathyaseelan and
              Mubin, Nida and Verma, Sheenam and Mayilraj, Shanmugam and
              Agrewala, Javed N",
  abstract = "BACKGROUND: Staphylococcus xylosus is coagulase-negative
              staphylococci (CNS), found occasionally on the skin of humans but
              recurrently on other mammals. Recent reports suggest that this
              commensal bacterium may cause diseases in humans and other
              animals. In this study, we present the first report of whole
              genome sequencing of S. xylosus strain DMB3-Bh1, which was
              isolated from the stool of a mouse. RESULTS: The draft genome of
              S. xylosus strain DMB3-Bh1 consisted of 2,81,0255 bp with G+C
              content of 32.7 mol\%, 2623 predicted coding sequences (CDSs) and
              58 RNAs. The final assembly contained 12 contigs of total size
              2,81,0255 bp with N50 contig length of 4,37,962 bp and the
              largest contig assembled measured 7,61,338 bp. Further, an
              interspecies comparative genomic analysis through rapid
              annotation using subsystem technology server was achieved with
              Staphylococcus aureus RF122 that revealed 36 genes having
              similarity with S. xylosus DMB3-Bh1. 35 genes encoded for
              virulence, disease and defense and 1 gene encoded for phages,
              prophages and transposable elements. CONCLUSIONS: These results
              suggest co linearity in genes between S. xylosus DMB3-Bh1 and S.
              aureus RF122 that contribute to pathogenicity and might be the
              result of horizontal gene transfer. The study indicates that S.
              xylosus DMB3-Bh1 may be a potential emerging pathogen for
              rodents.",
  journal  = "Gut Pathog.",
  volume   =  8,
  pages    = "55",
  month    =  nov,
  year     =  2016,
  keywords = "CDSs; Coagulase-negative staphylococci; Disease and defense;
              EzTaxon; Rapid annotation using subsystem technology (RAST);
              Staphylococcus aureus;
              Virulence;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Price2016-vt,
  title     = "Transmission of Staphylococcus aureus between healthcare
               workers, the environment and patients in an intensive care unit:
               a whole-genome sequencing based longitudinal cohort study",
  author    = "Price, J R and Cole, K and Bexley, A and Kostiou, V and Eyre, D
               W and Golubchik, T and Wilson, D and Crook, D W and Walker, A S
               and Peto, T and Llewelyn, M and Paul, J",
  abstract  = "UCL Discovery is UCL's open access repository, showcasing and
               providing access to UCL research outputs from all UCL
               disciplines.",
  journal   = "Lancet Infect. Dis.",
  publisher = "Elsevier",
  month     =  dec,
  year      =  2016,
  keywords  = "Staphylococcus;bacterial comparative
               genomics;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Singh2016-ge,
  title    = "In Vitro Tolerance of A {Drug-Na{\"\i}ve} Staphylococcus aureus
              {FDA209P} towards Vancomycin",
  author   = "Singh, Madhuri and Matsuo, Miki and Sasaki, Takashi and Morimoto,
              Yuh and Hishinuma, Tomomi and Hiramatsu, Keiichi",
  abstract = "The mechanisms underlying bacterial tolerance to antibiotics are
              unclear. A possible adaptation strategy has now been explored by
              exposure of drug-na{\"\i}ve methicillin-susceptible
              Staphylococcus aureus strain FDA209P to vancomycin in vitro
              Vancomycin-survivor strains, which appeared after 96 h of
              exposure, were slow-growing derivatives of the parent strain.
              Although the vancomycin minimum-inhibitory concentrations (MICs)
              with the survivor strains were within the susceptible range, the
              cytokilling effects of vancomycin at 20-fold MIC were
              significantly lower than those in the parent strain. Whole-genome
              sequencing demonstrated that ileS, encoding isoleucyl-tRNA
              synthetase (IleRS), was mutated in two of the three
              vancomycin-survivor strains. The IleRS Y723H mutation is located
              close to the isoleucyl-tRNA contact site, and potentially affects
              the binding affinity of IleRS for isoleucyl-tRNA, thereby
              inhibiting protein synthesis and leading to vancomycin tolerance.
              Introduction of the mutation encoding IleRS Y723H into FDA209P by
              allelic replacement successfully transferred the
              vancomycin-tolerance phenotype. We have identified mutation of
              ileS as one of the bona fide genetic events leading to the
              acquisition of vancomycin tolerance in S. aureus, potentially
              acting via inhibition of the function of IleRS.",
  journal  = "Antimicrob. Agents Chemother.",
  month    =  nov,
  year     =  2016,
  keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Sharma2016-bu,
  title    = "{Livestock-Associated} Methicillin Resistant
              \textit{Staphylococcus aureus} ({LA-MRSA}) Clonal Complex ({CC})
              398 Isolated from {UK} Animals belong to European Lineages",
  author   = "Sharma, Meenaxi and Nunez-Garcia, Javier and Kearns, Angela M and
              Doumith, Michel and Butaye, Patrick R and Argud{\'\i}n, M Angeles
              and Lahuerta-Marin, Angela and Pichon, Bruno and AbuOun, Manal
              and Rogers, Jon and Ellis, Richard J and Teale, Christopher and
              Anjum, Muna F",
  abstract = "In recent years, there has been an increase in the number of
              livestock-associated methicillin resistant Staphylococcus aureus
              (LA-MRSA) clonal complex (CC) 398 recovered from S. aureus
              isolated animals in the UK. To determine possible origins of 12
              LA-MRSA CC398 isolates collected after screening more than a
              thousand S. aureus animal isolates from the UK between 2013 and
              2015, whole genome sequences (WGS) of CC398 European, including
              UK, and non-European isolates from diverse animal hosts were
              compared. Phylogenetic reconstruction applied to WGS data to
              assess genetic relatedness of all 89 isolates, clustered the 12
              UK CC398 LA-MRSA within the European sub-lineages, although on
              different nodes; implicating multiple independent incursions into
              the UK, as opposed to a single introduction followed by clonal
              expansion. Three UK isolates from healthy pigs and one from
              turkey clustered within the cassette chromosome recombinases ccr
              C S. aureus protein A (spa)-type t011 European sub-lineage and
              three UK isolates from horses within the ccrA2B2 t011 European
              sub-lineage. The remaining UK isolates, mostly from pigs,
              clustered within the t034 European lineage. Presence of
              virulence, antimicrobial (AMR), heavy metal (HMR), and
              disinfectant (DR) resistance genes were determined using an
              in-house pipeline. Most, including UK isolates, harbored
              resistance genes to $\geq$3 antimicrobial classes in addition to
              $\beta$-lactams. HMR genes were detected in most European ccrC
              positive isolates, with >80\% harboring czrC, encoding zinc and
              cadmium resistance; in contrast ~60\% ccrC isolates within
              non-European lineages and 6\% ccrA2B2 isolates showed this
              characteristic. The UK turkey MRSA isolate did not harbor
              $\varphi$AV$\beta$ avian prophage genes (SAAV\_2008 and
              SAAV\_2009) present in US MSSA isolates from turkey and pigs.
              Absence of some of the major human-associated MRSA toxigenic and
              virulence genes in the UK LA-MRSA animal isolates was not
              unexpected. Therefore, we can conclude that the 12 UK LA-MRSA
              isolates collected in the past 2 years most likely represent
              separate incursions into the UK from other European countries.
              The presence of zinc and cadmium resistance in all nine food
              animal isolates (pig and poultry), which was absent from the 3
              horse isolates may suggest heavy metal use/exposure has a
              possible role in selection of some MRSA.",
  journal  = "Front. Microbiol.",
  volume   =  7,
  pages    = "1741",
  month    =  nov,
  year     =  2016,
  keywords = "UK CC398s; avian prophage genes; methicillin resistant
              Staphylococcus aureus in animals; whole genome sequencing; zinc
              and cadmium
              resistance;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Meumann2016-kp,
  title     = "Whole genome sequencing to investigate a putative outbreak of
               the virulent community-associated methicillin-resistant
               Staphylococcus aureus {ST93} clone in a remote Indigenous
               community",
  author    = "Meumann, Ella M and Andersson, Patiyan and Yeaman, Fiona and
               Oldfield, Sarah and Lilliebridge, Rachael and Bentley, Stephen D
               and Krause, Vicki and Beaman, Miles and Currie, Bart J and Holt,
               Deborah C and Giffard, Philip M and Tong, Steven Y C",
  abstract  = "We report two cases of severe pneumonia due to ST93 MRSA
               presenting from a remote Australian Indigenous community within
               a 2-week period, and utilised whole genome sequences to
               determine whether these were part of an outbreak. S. aureus was
               isolated from 12 of 92 nasal swabs collected from 25 community
               households (including the two index households); 1 isolate was
               ST93. Three of 5 skin lesion S. aureus isolates obtained at the
               community were ST93. Whole genome sequencing of the ST93
               isolates from this study and a further 20 ST93 isolates from the
               same region suggested that recent transmission and progression
               to disease had not taken place. The proximity in time and space
               of the 2 severe pneumonia cases is likely a reflection of the
               high burden of disease due to ST93 MRSA in this population where
               skin infections and household crowding are common.",
  journal   = "Microbial Genomics",
  publisher = "Microbiology Society",
  month     =  nov,
  year      =  2016,
  keywords  = "colonization;Staphylococcus;bacterial comparative
               genomics;Staphylococcus\_aureus\_genome\_papers",
  language  = "en"
 }

 @ARTICLE{Sabat2017-po,
  title    = "Complete-genome sequencing elucidates outbreak dynamics of
              {CA-MRSA} {USA300} ({ST8-spa} t008) in an academic hospital of
              Paramaribo, Republic of Suriname",
  author   = "Sabat, Artur J and Hermelijn, Sandra M and Akkerboom, Viktoria
              and Juliana, Amadu and Degener, John E and Grundmann, Hajo and
              Friedrich, Alexander W",
  abstract = "We report the investigation of an outbreak situation of
              methicillin-resistant Staphylococcus aureus (MRSA) that occurred
              at the Academic Hospital Paramaribo (AZP) in the Republic of
              Suriname from April to May 2013. We performed whole genome
              sequencing with complete gap closure for chromosomes and plasmids
              on all isolates. The outbreak involved 12 patients and 1
              healthcare worker/nurse at the AZP. In total 24 isolates were
              investigated. spa typing, genome-wide single nucleotide
              polymorphism (SNP) analysis, ad hoc whole genome multilocus
              sequence typing (wgMLST), stable core genome MLST (cgMLST) and in
              silico PFGE were used to determine phylogenetic relatedness and
              to identify transmission. Whole-genome sequencing (WGS) showed
              that all isolates were members of genomic variants of the North
              American USA300 clone. However, WGS revealed a heterogeneous
              population structure of USA300 circulating at the AZP. We
              observed up to 8 SNPs or up to 5 alleles of difference by wgMLST
              when the isolates were recovered from different body sites of the
              same patient or if direct transmission between patients was most
              likely. This work describes the usefulness of complete genome
              sequencing of bacterial chromosomes and plasmids providing an
              unprecedented level of detail during outbreak investigations not
              being visible by using conventional typing methods.",
  journal  = "Sci. Rep.",
  volume   =  7,
  pages    = "41050",
  month    =  jan,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Highlander2007-ff,
  title    = "Subtle genetic changes enhance virulence of methicillin resistant
              and sensitive Staphylococcus aureus",
  author   = "Highlander, Sarah K and Hult{\'e}n, Kristina G and Qin, Xiang and
              Jiang, Huaiyang and Yerrapragada, Shailaja and Mason, Jr, Edward
              O and Shang, Yue and Williams, Tiffany M and Fortunov, R{\'e}gine
              M and Liu, Yamei and Igboeli, Okezie and Petrosino, Joseph and
              Tirumalai, Madhan and Uzman, Akif and Fox, George E and Cardenas,
              Ana Maria and Muzny, Donna M and Hemphill, Lisa and Ding, Yan and
              Dugan, Shannon and Blyth, Peter R and Buhay, Christian J and
              Dinh, Huyen H and Hawes, Alicia C and Holder, Michael and Kovar,
              Christie L and Lee, Sandra L and Liu, Wen and Nazareth, Lynne V
              and Wang, Qiaoyan and Zhou, Jianling and Kaplan, Sheldon L and
              Weinstock, George M",
  abstract = "BACKGROUND: Community acquired (CA) methicillin-resistant
              Staphylococcus aureus (MRSA) increasingly causes disease
              worldwide. USA300 has emerged as the predominant clone causing
              superficial and invasive infections in children and adults in the
              USA. Epidemiological studies suggest that USA300 is more virulent
              than other CA-MRSA. The genetic determinants that render
              virulence and dominance to USA300 remain unclear. RESULTS: We
              sequenced the genomes of two pediatric USA300 isolates: one
              CA-MRSA and one CA-methicillin susceptible (MSSA), isolated at
              Texas Children's Hospital in Houston. DNA sequencing was
              performed by Sanger dideoxy whole genome shotgun (WGS) and 454
              Life Sciences pyrosequencing strategies. The sequence of the
              USA300 MRSA strain was rigorously annotated. In USA300-MRSA 2658
              chromosomal open reading frames were predicted and 3.1 and 27
              kilobase (kb) plasmids were identified. USA300-MSSA contained a
              20 kb plasmid with some homology to the 27 kb plasmid found in
              USA300-MRSA. Two regions found in US300-MRSA were absent in
              USA300-MSSA. One of these carried the arginine deiminase operon
              that appears to have been acquired from S. epidermidis. The
              USA300 sequence was aligned with other sequenced S. aureus
              genomes and regions unique to USA300 MRSA were identified.
              CONCLUSION: USA300-MRSA is highly similar to other MRSA strains
              based on whole genome alignments and gene content, indicating
              that the differences in pathogenesis are due to subtle changes
              rather than to large-scale acquisition of virulence factor genes.
              The USA300 Houston isolate differs from another sequenced USA300
              strain isolate, derived from a patient in San Francisco, in
              plasmid content and a number of sequence polymorphisms. Such
              differences will provide new insights into the evolution of
              pathogens.",
  journal  = "BMC Microbiol.",
  volume   =  7,
  pages    = "99",
  month    =  nov,
  year     =  2007,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Galata2016-sq,
  title    = "Comparing genome versus proteome-based identification of clinical
              bacterial isolates",
  author   = "Galata, Valentina and Backes, Christina and Laczny, C{\'e}dric
              Christian and Hemmrich-Stanisak, Georg and Li, Howard and Smoot,
              Laura and Posch, Andreas Emanuel and Schmolke, Susanne and
              Bischoff, Markus and von M{\"u}ller, Lutz and Plum, Achim and
              Franke, Andre and Keller, Andreas",
  abstract = "Whole-genome sequencing (WGS) is gaining importance in the
              analysis of bacterial cultures derived from patients with
              infectious diseases. Existing computational tools for WGS-based
              identification have, however, been evaluated on previously
              defined data relying thereby unwarily on the available taxonomic
              information.Here, we newly sequenced 846 clinical gram-negative
              bacterial isolates representing multiple distinct genera and
              compared the performance of five tools (CLARK, Kaiju, Kraken,
              DIAMOND/MEGAN and TUIT). To establish a faithful 'gold standard',
              the expert-driven taxonomy was compared with identifications
              based on matrix-assisted laser desorption/ionization
              time-of-flight (MALDI-TOF) mass spectrometry (MS) analysis.
              Additionally, the tools were also evaluated using a data set of
              200 Staphylococcus aureus isolates.CLARK and Kraken (with k =31)
              performed best with 626 (100\%) and 193 (99.5\%) correct species
              classifications for the gram-negative and S aureus isolates,
              respectively. Moreover, CLARK and Kraken demonstrated highest
              mean F-measure values (85.5/87.9\% and 94.4/94.7\% for the two
              data sets, respectively) in comparison with DIAMOND/MEGAN (71 and
              85.3\%), Kaiju (41.8 and 18.9\%) and TUIT (34.5 and 86.5\%).
              Finally, CLARK, Kaiju and Kraken outperformed the other tools by
              a factor of 30 to 170 fold in terms of runtime.We conclude that
              the application of nucleotide-based tools using k-mers-e.g. CLARK
              or Kraken-allows for accurate and fast taxonomic characterization
              of bacterial isolates from WGS data. Hence, our results suggest
              WGS-based genotyping to be a promising alternative to the
              MS-based biotyping in clinical settings. Moreover, we suggest
              that complementary information should be used for the evaluation
              of taxonomic classification tools, as public databases may suffer
              from suboptimal annotations.",
  journal  = "Brief. Bioinform.",
  month    =  dec,
  year     =  2016,
  keywords = "MALDI-TOF MS; bacteria; taxonomy; whole-genome next-generation
              sequencing;Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Bakthavatchalam2016-zq,
  title    = "Novel Observations in 11 Heteroresistant
              {Vancomycin-Intermediate} {Methicillin-Resistant} Staphylococcus
              aureus Strains from South India",
  author   = "Bakthavatchalam, Yamuna Devi and Veeraraghavan, Balaji and Peter,
              John Victor and Rajinikanth, Janakiraman and Inbanathan, Francis
              Yesurajan and Devanga Ragupathi, Naveen Kumar and Rajamani Sekar,
              Suresh Kumar",
  abstract = "We report here the draft genome sequences of 11 heteroresistant
              vancomycin-intermediate Staphylococcus aureus (hVISA) strains
              from bloodstream infection. All strains harbor mutations in
              vraSR, graSR, walKR, and/or tcaRAB and are often implicated as
              the frequently mutated candidate genes in hVISA phenotypes.",
  journal  = "Genome Announc.",
  volume   =  4,
  number   =  6,
  month    =  dec,
  year     =  2016,
  keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Berenger2016-gq,
  title    = "Draft {Whole-Genome} Sequence of a {Catalase-Negative}
              Staphylococcus aureus subsp. aureus (Sequence Type 25) Strain
              Isolated from a Patient with Endocarditis and Septic Arthritis",
  author   = "Berenger, Byron and Chen, Justin and Bernier, Anne-Marie and
              Bernard, Kathryn",
  abstract = "Staphylococcus aureus strains without catalase activity are rare,
              challenging to identify with conventional biochemical methods,
              and, despite a supposed decreased pathogenicity, can still cause
              disease. The first whole-genome sequence of a catalase-negative
              S. aureus isolate causing severe recurrent invasive infection
              with two novel missense mutations in the katA gene is reported
              here.",
  journal  = "Genome Announc.",
  volume   =  4,
  number   =  6,
  month    =  dec,
  year     =  2016,
  keywords = "Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Peng2016-ga,
  title    = "{WalK(S221P)}, a naturally occurring mutation, confers vancomycin
              resistance in {VISA} strain {XN108}",
  author   = "Peng, Huagang and Hu, Qiwen and Shang, Weilong and Yuan, Jizhen
              and Zhang, Xiaopeng and Liu, Hui and Zheng, Ying and Hu, Zhen and
              Yang, Yi and Tan, Li and Li, Shu and Hu, Xiaomei and Li, Ming and
              Rao, Xiancai",
  abstract = "OBJECTIVES: Vancomycin-intermediate Staphylococcus aureus (VISA)
              strains have spread globally. We previously isolated an ST239
              VISA (XN108) with a vancomycin MIC of 12 mg/L. The mechanism for
              XN108 resistance to vancomycin was investigated in this study.
              METHODS: Genome comparison was performed to characterize
              mutations that might contribute to the XN108 resistance
              phenotype. The novel mutation WalK(S221P) was identified and
              investigated using allelic replacement experiments. Vancomycin
              susceptibilities, autolytic activities and morphologies of the
              strains were examined. Autophosphorylation activities of WalK and
              the WalK(S221P) mutant were determined in vitro with
              [$\lambda$-(32)P]ATP, and binding activity of
              WalK(S221P)-activated WalR to the promoter region of its target
              gene lytM was determined by electrophoretic mobility shift assay.
              RESULTS: Genome comparison revealed three mutations, GraS(T136I),
              RpoB(H481N) and WalK(S221P), which might be responsible for
              vancomycin resistance in XN108. The introduction of WalK(S221P)
              to the vancomycin-susceptible strain N315 increased its
              vancomycin MIC from 1.5 to 8 mg/L, whereas the allelic
              replacement of WalK(S221P) with the native N315 WalK allele in
              XN108 decreased its vancomycin MIC from 12 to 4 mg/L. The VISA
              strains have thickened cell walls and decreased autolysis,
              consistent with observed changes in the expression of genes
              involved in cell wall metabolism and virulence regulation.
              WalK(S221P) exhibited reduced autophosphorylation, which may lead
              to reduced phosphorylation of WalR. WalK(S221P)-phosphorylated
              WalR also exhibited a reduced capacity to bind to the lytM
              promoter. CONCLUSIONS: The naturally occurring WalK(S221P)
              mutation plays a key role in vancomycin resistance in XN108.",
  journal  = "J. Antimicrob. Chemother.",
  month    =  dec,
  year     =  2016,
  keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Mellmann2017-go,
  title    = "High Interlaboratory Reproducibility and Accuracy of
              {Next-Generation} {Sequencing-Based} Bacterial Genotyping in a
              {Ring-Trial}",
  author   = "Mellmann, Alexander and Andersen, Paal Skytt and Bletz, Stefan
              and Friedrich, Alexander W and Kohl, Thomas A and Lilje, Berit
              and Niemann, Stefan and Prior, Karola and Rossen, John W and
              Harmsen, Dag",
  abstract = "Today, next-generation whole genome sequencing (WGS) technology
              is increasingly used to determine the genetic relationship of
              bacteria on a nearly whole genome level for infection control
              purposes and molecular surveillance. Here, we conducted a
              multicenter ring-trial comprising five laboratories to determine
              the reproducibility and accuracy of WGS-based typing.The
              participating laboratories sequenced 20 blind-coded
              Staphylococcus aureus DNA samples using the 250 bp paired-end
              chemistry for library preparation in a single sequencing run on
              an Illumina Miseq sequencer. Run acceptance criteria were
              sequencing outputs > 5.6 Gb and Q30 read quality scores > 75\%.
              Subsequently, spa typing, multilocus sequence typing (MLST),
              ribosomal MLST, and core genome (cg)MLST were performed by the
              participants. Moreover, cgMLST target sequence discrepancies in
              comparison to the also included and published sequence of quality
              control strain ATCC25923 were resolved using Sanger
              sequencing.All five laboratories fulfilled the run acceptance
              criteria in a single sequencing run without any repetition. Of
              the in total 400 possible typing results, 394 reported spa types,
              sequence types (ST), rSTs, and cgMLST cluster types were correct
              and identical among all laboratories; only six typing results
              were missing. Analysis of cgMLST allelic profiles corroborated
              this high reproducibility: only 3 (0.0016\%) of in total 183,927
              cgMLST allele calls were wrong. Sanger sequencing confirmed all
              the 12 discrepancies of the ring-trial results in comparison to
              the published sequence of ATCC25923.In summary, this ring-trial
              demonstrated the high reproducibility and accuracy of current
              NGS-based bacterial typings for molecular surveillance when done
              with nearly completely locked down methods.",
  journal  = "J. Clin. Microbiol.",
  month    =  jan,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Kawada-Matsuo2016-tq,
  title    = "{C55} bacteriocin produced by {ETB-plasmid} positive
              Staphylococcus aureus strains is a key factor for competition
              with S. aureus strains",
  author   = "Kawada-Matsuo, Miki and Shammi, Fariha and Oogai, Yuichi and
              Nakamura, Norifumi and Sugai, Motoyuki and Komatsuzawa, Hitoshi",
  abstract = "Exfoliative toxin (ET) produced by Staphylococcus aureus is
              closely associated with the onset of bullous impetigo. To date,
              three ETs (ETA, ETB and ETD) have been identified. The gene
              encoding ETB is located in a plasmid designated pETB. Bacteriocin
              synthesis genes are also located in this plasmid and
              pETB-positive strains reportedly produce the C55 bacteriocin. In
              this study, the antibacterial activity against S. aureus strains
              of the bacteriocin produced by the pETB-positive strain TY4 was
              investigated. This bacteriocin demonstrated antibacterial
              activity against all pETB-negative but not pETB-positive strains,
              including TY4. Additionally, a TY4- strain from which the pETB
              plasmid had been deleted exhibited susceptibility to the
              bacteriocin. Further experiments revealed that two immunity
              factors (orf 46-47 and orf 48) downstream of the bacteriocin
              synthesis genes in the pETB plasmid are associated with immunity
              against the bacteriocin produced by TY4. The TY4- with orf46-47
              strain exhibited complete resistance to bacteriocin, whereas the
              TY4- with orf48 strain exhibited partial resistance. Whether
              bacteriocin affects the proportion of each strain when
              co-cultured with S. aureus strains was also investigated. When
              TY4 or TY4- was co-cultured with 209P strain, which is
              susceptible to the bacteriocin, the proportion of 209P
              co-cultured with TY4 was significantly less than when 209P was
              co-cultured with TY4-, whereas the proportion of TY4- with
              orf46-48 co-cultured with TY4 was greater than with TY4-. These
              results suggest that the C55 bacteriocin produced by
              pETB-positive strains affects the proportion of each strain when
              pETB-positive and -negative strains co-exist.",
  journal  = "Microbiol. Immunol.",
  volume   =  60,
  number   =  3,
  pages    = "139--147",
  month    =  mar,
  year     =  2016,
  keywords = "Staphylococcus aureus; bacteriocin; lantibiotics; two-component
              system;Staphylococcus;Staph\_evolutionary\_history;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Stevens2017-ei,
  title    = "Draft Genome Sequence of Staphylococcus aureus 1608, a Strain
              That Caused Toxic Mastitis in Twin Cows",
  author   = "Stevens, Marc J A and Stephan, Roger and Johler, Sophia",
  abstract = "Staphylococcus aureus 1608 is a strain that caused a lethal
              mastitis in cows. Here, the draft genome sequence of the strain
              is presented.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  1,
  month    =  jan,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Milheirico2017-lu,
  title    = "{MRSA} strains carrying the novel mecC gene: full genome
              sequencing identifies in the genetic background several
              determinants that modulate the resistant phenotype",
  author   = "Milheiri{\c c}o, Catarina and de Lencastre, Herm{\'\i}nia and
              Tomasz, Alexander",
  abstract = "Most MRSA strains are resistant to beta-lactam antibiotics due to
              the presence of the mecA gene encoding an extra
              penicillin-binding protein (PBP2A) that has low affinity to
              virtually all beta-lactam antibiotics. Recently, a new resistance
              determinant - the mecC gene - was identified in S. aureus
              isolates recovered from humans and dairy cattle. Although having
              typically low MICs to beta-lactam antibiotics, MRSA strains with
              the mecC determinant are also capable of expressing high levels
              of oxacillin resistance when in an optimal genetic background. In
              order to test the impact of extensive beta-lactam selection on
              the emergence of mecC carrying strains with high levels of
              antibiotic resistance, we exposed the prototype mecC MRSA strain
              LGA251 to increasing concentrations of oxacillin. LGA251 was able
              to rapidly adapt to high concentrations of oxacillin in the
              growth medium. In such laboratory mutants with increased levels
              of oxacillin resistance, we identified mutations in genes with no
              relationship to the mecC regulatory system indicating that the
              genetic background plays an important role in the establishment
              of the levels of oxacillin resistance. Our data also indicate
              that the stringent stress response plays a critical role in the
              beta-lactam antibiotic resistant phenotype of MRSA strains
              carrying the mecC determinant.",
  journal  = "Antimicrob. Agents Chemother.",
  month    =  jan,
  year     =  2017,
  keywords = "oxacillin;Staphylococcus;antibiotics;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Kennedy2010-fe,
  title    = "Complete nucleotide sequence analysis of plasmids in strains of
              Staphylococcus aureus clone {USA300} reveals a high level of
              identity among isolates with closely related core genome
              sequences",
  author   = "Kennedy, Adam D and Porcella, Stephen F and Martens, Craig and
              Whitney, Adeline R and Braughton, Kevin R and Chen, Liang and
              Craig, Carly T and Tenover, Fred C and Kreiswirth, Barry N and
              Musser, James M and DeLeo, Frank R",
  abstract = "A community-associated methicillin-resistant Staphylococcus
              aureus (CA-MRSA) strain known as pulsed-field type USA300
              (USA300) is epidemic in the United States. Previous comparative
              whole-genome sequencing studies demonstrated that there has been
              recent clonal emergence of a subset of USA300 isolates, which
              comprise the epidemic clone. Although the core genomes of these
              isolates are closely related, the level of diversity among USA300
              plasmids was not resolved. Inasmuch as these plasmids might
              contribute to significant gene diversity among otherwise closely
              related USA300 isolates, we performed de novo sequencing of
              endogenous plasmids from 10 previously characterized USA300
              clinical isolates obtained from different geographic locations in
              the United States. All isolates tested contained small (2- to
              3-kb) and/or large (27- to 30-kb) plasmids. The large plasmids
              encoded heavy metal and/or antimicrobial resistance elements,
              including those that confer resistance to cadmium, bacitracin,
              macrolides, penicillin, kanamycin, and streptothricin, although
              all isolates were sensitive to minocycline, doxycycline,
              trimethoprim-sulfamethoxazole, vancomycin, teicoplanin, and
              linezolid. One of the USA300 isolates contained an archaic
              plasmid that encoded staphylococcal enterotoxins R, J, and P.
              Notably, the large plasmids (27 to 28 kb) from 8 USA300
              isolates--those that comprise the epidemic USA300 clone--were
              virtually identical (99\% identity) and similar to a large
              plasmid from strain USA300\_TCH1516 (a previously sequenced
              USA300 strain from Houston, TX). These plasmids are largely
              divergent from the 37-kb plasmid of FPR3757, the first sequenced
              USA300 strain. The high level of plasmid sequence identity among
              the majority of closely related USA300 isolates is consistent
              with the recent clonal emergence hypothesis for USA300.",
  journal  = "J. Clin. Microbiol.",
  volume   =  48,
  number   =  12,
  pages    = "4504--4511",
  month    =  dec,
  year     =  2010,
  keywords = "plasmid;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Lima2017-ib,
  title    = "Genomic information on multidrug-resistant livestock-associated
              methicillin-resistant Staphylococcus aureus {ST398} isolated from
              a Brazilian patient with cystic fibrosis",
  author   = "Lima, Danielle F and Cohen, Renata Wf and Rocha, G{\'e}ssica A
              and Albano, Rodolpho M and Marques, Elizabeth A and Le{\~a}o,
              Robson S",
  abstract = "Alarmingly, the isolation of methicillin-resistant Staphylococcus
              aureus (MRSA) has been increasing among patients with cystic
              fibrosis (CF). During a previous molecular characterisation of
              MRSA isolates obtained from patients with CF from Rio de Janeiro,
              Brazil, one isolate was identified as the ST398 clone, a
              livestock-associated (LA) MRSA. In this study, we report the
              draft genome sequence of an LA-MRSA ST398 clone isolated from a
              patient with CF.",
  journal  = "Mem. Inst. Oswaldo Cruz",
  volume   =  112,
  number   =  1,
  pages    = "79--80",
  month    =  jan,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Vestergaard2016-vt,
  title    = "{Genome-Wide} Identification of Antimicrobial Intrinsic
              Resistance Determinants in \textit{Staphylococcus aureus}",
  author   = "Vestergaard, Martin and Leng, Bingfeng and Haaber, Jakob and
              Bojer, Martin S and Vegge, Christina S and Ingmer, Hanne",
  abstract = "The emergence of antimicrobial resistance severely threatens our
              ability to treat bacterial infections. While acquired resistance
              has received considerable attention, relatively little is known
              of intrinsic resistance that allows bacteria to naturally
              withstand antimicrobials. Gene products that confer intrinsic
              resistance to antimicrobial agents may be explored for
              alternative antimicrobial therapies, by potentiating the efficacy
              of existing antimicrobials. In this study, we identified the
              intrinsic resistome to a broad spectrum of antimicrobials in the
              human pathogen, Staphylococcus aureus. We screened the Nebraska
              Transposon Mutant Library of 1920 single-gene inactivations in S.
              aureus strain JE2, for increased susceptibility to the
              anti-staphylococcal antimicrobials (ciprofloxacin, oxacillin,
              linezolid, fosfomycin, daptomycin, mupirocin, vancomycin, and
              gentamicin). Sixty-eight mutants were confirmed by E-test to
              display at least twofold increased susceptibility to one or more
              antimicrobial agents. The majority of the identified genes have
              not previously been associated with antimicrobial susceptibility
              in S. aureus. For example, inactivation of genes encoding for
              subunits of the ATP synthase, atpA, atpB, atpG and atpH, reduced
              the minimum inhibitory concentration (MIC) of gentamicin 16-fold.
              To elucidate the potential of the screen, we examined treatment
              efficacy in the Galleria mellonella infection model. Gentamicin
              efficacy was significantly improved, when treating larvae
              infected with the atpA mutant compared to wild type cells with
              gentamicin at a clinically relevant concentration. Our results
              demonstrate that many gene products contribute to the intrinsic
              antimicrobial resistance of S. aureus. Knowledge of these
              intrinsic resistance determinants provides alternative targets
              for compounds that may potentiate the efficacy of existing
              antimicrobial agents against this important pathogen.",
  journal  = "Front. Microbiol.",
  volume   =  7,
  pages    = "2018",
  month    =  dec,
  year     =  2016,
  keywords = "Galleria mellonella; Staphylococcus aureus; antimicrobial agents;
              intrinsic resistance; potentiator
              targets;Staphylococcus;antibiotics;confirmed\_SA-resistance-mutation;oxacillin;Staphylococcus\_aureus\_genome\_papers;Michael\_F\_papers",
  language = "en"
 }

 @ARTICLE{Capra2017-co,
  title    = "Genomic and transcriptomic comparison between Staphylococcus
              aureus strains associated with high and low within herd
              prevalence of intra-mammary infection",
  author   = "Capra, E and Cremonesi, P and Pietrelli, A and Puccio, S and
              Luini, M and Stella, A and Castiglioni, B",
  abstract = "BACKGROUND: Staphylococcus aureus (Staph. aureus) is one of the
              major pathogens causing mastitis in dairy ruminants worldwide.
              The chronic nature of Staph. aureus infection enhances the
              contagiousness risk and diffusion in herds. In order to identify
              the factors involved in intra-mammary infection (IMI) and
              diffusion in dairy cows, we investigated the molecular
              characteristics of two groups of Staph. aureus strains belonging
              to ST8 and ST398, differing in clinical properties, through
              comparison of whole genome and whole transcriptome sequencing.
              RESULTS: The two groups of strains, one originated from high IMI
              prevalence herds and the other from low IMI prevalence herds,
              present a peculiar set of genes and polymorphisms related to
              phenotypic features, such as bacterial invasion of mammary
              epithelial cells and host adaptation. Transcriptomic analysis
              supports the high propensity of ST8 strain to chronicity of
              infection and to a higher potential cytotoxicity. CONCLUSIONS:
              Our data are consistent with the invasiveness and host adaptation
              feature for the strains GTB/ST8 associated to high within-herd
              prevalence of mastitis. Variation in genes coding for surface
              exposed proteins and those associated to virulence and defence
              could constitute good targets for further research.",
  journal  = "BMC Microbiol.",
  volume   =  17,
  number   =  1,
  pages    = "21",
  month    =  jan,
  year     =  2017,
  keywords = "Genome; Mastitis; Next generation sequencing; Staphylococcus
              aureus; Transcriptome;
              Virulence;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Ledda2017-eh,
  title    = "Re-emergence of methicillin susceptibility in a resistant lineage
              of Staphylococcus aureus",
  author   = "Ledda, Alice and Price, James R and Cole, Kevin and Llewelyn,
              Martin J and Kearns, Angela M and Crook, Derrick W and Paul, John
              and Didelot, Xavier",
  abstract = "OBJECTIVES: MRSA is a leading cause of hospital-associated
              infection. Acquired resistance is encoded by the mecA gene or its
              homologue mecC, but little is known about the evolutionary
              dynamics involved in gain and loss of resistance. The objective
              of this study was to obtain an expanded understanding of
              Staphylococcus aureus methicillin resistance microevolution in
              vivo, by focusing on a single lineage. METHODS: We compared the
              whole-genome sequences of 231 isolates from a single epidemic
              lineage [clonal complex 30 (CC30) and spa-type t018] of S. aureus
              that caused an epidemic in the UK. RESULTS: We show that
              resistance to methicillin in this single lineage was gained on at
              least two separate occasions, one of which led to a clonal
              expansion around 1995 presumably caused by a selective advantage.
              Resistance was, however, subsequently lost in vivo by nine
              strains isolated between 2008 and 2012. We describe the genetic
              mechanisms involved in this loss of resistance and the imperfect
              relationship between genotypic and phenotypic resistance.
              CONCLUSIONS: The recent re-emergence of methicillin
              susceptibility in this epidemic lineage suggests a significant
              fitness cost of resistance and reduced selective advantage
              following the introduction in the mid-2000s of MRSA hospital
              control measures throughout the UK.",
  journal  = "J. Antimicrob. Chemother.",
  month    =  jan,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Uhlemann2017-db,
  title    = "Evolutionary Dynamics of Pandemic {Methicillin-Sensitive}
              Staphylococcus aureus {ST398} and Its International Spread via
              Routes of Human Migration",
  author   = "Uhlemann, Anne-Catrin and McAdam, Paul R and Sullivan, Sean B and
              Knox, Justin R and Khiabanian, Hossein and Rabadan, Raul and
              Davies, Peter R and Fitzgerald, J Ross and Lowy, Franklin D",
  abstract = "Methicillin-susceptible Staphylococcus aureus (MSSA) accounts for
              the majority of S. aureus infections globally, and yet
              surprisingly little is known about its clonal evolution. We
              applied comparative whole-genome sequencing (WGS) analyses to
              epidemiologically and geographically diverse ST398-MSSA, a
              pandemic lineage affecting both humans and livestock. Bayesian
              phylogenetic analysis predicted divergence of human-associated
              ST398-MSSA ~40 years ago. Isolates from Midwestern pigs and
              veterinarians differed substantially from those in New York City
              (NYC). Pig ST398 strains contained a large region of
              recombination representing imports from multiple sequence types
              (STs). Phylogeographic analyses supported the spread of
              ST398-MSSA along local cultural and migratory links between parts
              of the Caribbean, North America, and France, respectively.
              Applying pairwise single-nucleotide polymorphism (SNP) distances
              as a measure of genetic relatedness between isolates, we observed
              that ST398 not only clustered in households but also frequently
              extended across local social networks. Isolates collected from
              environmental surfaces reflected the full diversity of colonizing
              individuals, highlighting their potentially critical role as
              reservoirs for transmission and diversification. Strikingly, we
              observed high within-host SNP variability compared to our
              previous studies on the dominant methicillin-resistant
              Staphylococcus aureus (MRSA) clone USA300. Our data indicate that
              the dynamics of colonization, persistence, and transmission
              differ substantially between USA300-MRSA and ST398-MSSA. Taken
              together, our study reveals local and international routes of
              transmission for a major MSSA clone, indicating key impacts of
              recombination and mutation on genetic diversification and
              highlighting important ecological differences from epidemic
              USA300. Our study demonstrates extensive local and international
              routes of transmission for a major MSSA clone despite the lack of
              substantial antibiotic resistance. IMPORTANCE: Unlike
              methicillin-resistant Staphylococcus aureus (MRSA), surprisingly
              little is known about the clonal evolution of
              methicillin-susceptible S. aureus (MSSA), although these strains
              account for the majority of S. aureus infections. To better
              understand how MSSA spreads and becomes established in
              communities, we applied comparative bacterial whole-genome
              sequencing to pandemic ST398-MSSA, a clone of clinical importance
              affecting humans and livestock in different geographic regions.
              Phylogeographic analyses identified that ST398-MSSA spread along
              local cultural and migratory links between parts of the
              Caribbean, North America, and France, respectively. We observed
              high within-host SNP variability compared to our previous studies
              on the dominant MRSA clone USA300. Our data indicate that the
              dynamics of colonization, persistence, and transmission differ
              substantially between USA300 MRSA and ST398 MSSA.",
  journal  = "MBio",
  volume   =  8,
  number   =  1,
  month    =  jan,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Escobar-Perez2017-wu,
  title    = "Emergence and spread of a new community-genotype
              methicillin-resistant Staphylococcus aureus clone in Colombia",
  author   = "Escobar-Perez, Javier and Reyes, Niradiz and Marquez-Ortiz,
              Ricaurte Alejandro and Rebollo, Juan and Pinz{\'o}n, Hernando and
              Tovar, Catalina and Moreno-Casta{\~n}eda, Jaime and Corredor,
              Zayda Lorena and Castro, Betsy Esperanza and Moncada, Maria
              Victoria and Vanegas, Natasha",
  abstract = "BACKGROUND: Community-genotype methicillin-resistant
              Staphylococcus aureus (CG-MRSA) clones are a global concern due
              to their resistance and increased virulence and their ability to
              cause infections both hospitalized patients and healthy people in
              the community. Here, we characterize 32 isolates of a new CG-MRSA
              clone. These isolates were identified in four cities in Colombia,
              South America. METHODS: The isolates were recovered from four
              different epidemiological and prospective studies that were
              conducted in several regions of Colombia. Molecular
              characterizations included multilocus sequence typing;
              pulsed-field gel electrophoresis; SCCmec, agr and spa typing; and
              whole-genome sequencing. RESULTS: All isolates belonged to ST923
              (clonal complex 8), harbouring SCCmec IVa and a spa type t1635
              and lacking an arginine catabolism mobile element. The isolates
              were classified as COL923, were resistant to at least one
              non-beta-lactam antibiotic, and exhibited high frequencies
              (>60\%) of resistance to macrolides and tetracycline. Using
              whole-genome sequencing, we found that this new clone harbours
              novel prophage 3 and beta-island structures and a slightly
              different pathogenicity island 5. Moreover, isolates belonging to
              the COL923 clone are grouped in a different clade than USA300 and
              USA300-LV. CONCLUSION: Our results show the emergence and spread
              of the COL923 clone in different cities in Colombia. This clone
              is resistant to several antibiotics and possesses new structures
              in its mobile genetic elements.",
  journal  = "BMC Infect. Dis.",
  volume   =  17,
  number   =  1,
  pages    = "108",
  month    =  jan,
  year     =  2017,
  keywords = "Colombia; Community; Methicillin-resistant Staphylococcus aureus;
              New clone;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Eyre2012-xf,
  title    = "A pilot study of rapid benchtop sequencing of Staphylococcus
              aureus and Clostridium difficile for outbreak detection and
              surveillance",
  author   = "Eyre, David W and Golubchik, Tanya and Gordon, N Claire and
              Bowden, Rory and Piazza, Paolo and Batty, Elizabeth M and Ip,
              Camilla L C and Wilson, Daniel J and Didelot, Xavier and
              O'Connor, Lily and Lay, Rochelle and Buck, David and Kearns,
              Angela M and Shaw, Angela and Paul, John and Wilcox, Mark H and
              Donnelly, Peter J and Peto, Tim E A and Walker, A Sarah and
              Crook, Derrick W",
  abstract = "OBJECTIVES: To investigate the prospects of newly available
              benchtop sequencers to provide rapid whole-genome data in routine
              clinical practice. Next-generation sequencing has the potential
              to resolve uncertainties surrounding the route and timing of
              person-to-person transmission of healthcare-associated infection,
              which has been a major impediment to optimal management. DESIGN:
              The authors used Illumina MiSeq benchtop sequencing to undertake
              case studies investigating potential outbreaks of
              methicillin-resistant Staphylococcus aureus (MRSA) and
              Clostridium difficile. SETTING: Isolates were obtained from
              potential outbreaks associated with three UK hospitals.
              PARTICIPANTS: Isolates were sequenced from a cluster of eight
              MRSA carriers and an associated bacteraemia case in an intensive
              care unit, another MRSA cluster of six cases and two clusters of
              C difficile. Additionally, all C difficile isolates from cases
              over 6 weeks in a single hospital were rapidly sequenced and
              compared with local strain sequences obtained in the preceding 3
              years. MAIN OUTCOME MEASURE: Whole-genome genetic relatedness of
              the isolates within each epidemiological cluster. RESULTS:
              Twenty-six MRSA and 15 C difficile isolates were successfully
              sequenced and analysed within 5 days of culture. Both MRSA
              clusters were identified as outbreaks, with most sequences in
              each cluster indistinguishable and all within three single
              nucleotide variants (SNVs). Epidemiologically unrelated isolates
              of the same spa-type were genetically distinct ($\geq$21 SNVs).
              In both C difficile clusters, closely epidemiologically linked
              cases (in one case sharing the same strain type) were shown to be
              genetically distinct ($\geq$144 SNVs). A reconstruction applying
              rapid sequencing in C difficile surveillance provided early
              outbreak detection and identified previously undetected probable
              community transmission. CONCLUSIONS: This benchtop sequencing
              technology is widely generalisable to human bacterial pathogens.
              The findings provide several good examples of how rapid and
              precise sequencing could transform identification of transmission
              of healthcare-associated infection and therefore improve hospital
              infection control and patient outcomes in routine clinical
              practice.",
  journal  = "BMJ Open",
  volume   =  2,
  number   =  3,
  month    =  jun,
  year     =  2012,
  keywords = "Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Harrison2014-mh,
  title    = "A shared population of epidemic methicillin-resistant
              Staphylococcus aureus 15 circulates in humans and companion
              animals",
  author   = "Harrison, Ewan M and Weinert, Lucy A and Holden, Matthew T G and
              Welch, John J and Wilson, Katherine and Morgan, Fiona J E and
              Harris, Simon R and Loeffler, Anette and Boag, Amanda K and
              Peacock, Sharon J and Paterson, Gavin K and Waller, Andrew S and
              Parkhill, Julian and Holmes, Mark A",
  abstract = "UNLABELLED: Methicillin-resistant Staphylococcus aureus (MRSA) is
              a global human health problem causing infections in both
              hospitals and the community. Companion animals, such as cats,
              dogs, and horses, are also frequently colonized by MRSA and can
              become infected. We sequenced the genomes of 46 multilocus
              sequence type (ST) 22 MRSA isolates from cats and dogs in the
              United Kingdom and compared these to an extensive population
              framework of human isolates from the same lineage. Phylogenomic
              analyses showed that all companion animal isolates were
              interspersed throughout the epidemic MRSA-15 (EMRSA-15) pandemic
              clade and clustered with human isolates from the United Kingdom,
              with human isolates basal to those from companion animals,
              suggesting a human source for isolates infecting companion
              animals. A number of isolates from the same veterinary hospital
              clustered together, suggesting that as in human hospitals,
              EMRSA-15 isolates are readily transmitted in the veterinary
              hospital setting. Genome-wide association analysis did not
              identify any host-specific single nucleotide polymorphisms (SNPs)
              or virulence factors. However, isolates from companion animals
              were significantly less likely to harbor a plasmid encoding
              erythromycin resistance. When this plasmid was present in
              animal-associated isolates, it was more likely to contain
              mutations mediating resistance to clindamycin. This finding is
              consistent with the low levels of erythromycin and high levels of
              clindamycin used in veterinary medicine in the United Kingdom.
              This study furthers the ``one health'' view of infectious
              diseases that the pathogen pool of human and animal populations
              are intrinsically linked and provides evidence that antibiotic
              usage in animal medicine is shaping the population of a major
              human pathogen. IMPORTANCE: Methicillin-resistant Staphylococcus
              aureus (MRSA) is major problem in human medicine. Companion
              animals, such as cats, dogs, and horses, can also become
              colonized and infected by MRSA. Here, we demonstrate that a
              shared population of an important and globally disseminated
              lineage of MRSA can infect both humans and companion animals
              without undergoing host adaptation. This suggests that companion
              animals might act as a reservoir for human infections. We also
              show that the isolates from companion animals have differences in
              the presence of certain antibiotic resistance genes. This study
              furthers the ``one health'' view of infectious diseases by
              demonstrating that the pool of MRSA isolates in the human and
              animal populations are shared and highlights how different
              antibiotic usage patterns between human and veterinary medicine
              can shape the population of bacterial pathogens.",
  journal  = "MBio",
  volume   =  5,
  number   =  3,
  pages    = "e00985--13",
  month    =  may,
  year     =  2014,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Warne2016-sf,
  title    = "The {Ess/Type} {VII} secretion system of Staphylococcus aureus
              shows unexpected genetic diversity",
  author   = "Warne, Ben and Harkins, Catriona P and Harris, Simon R and
              Vatsiou, Alexandra and Stanley-Wall, Nicola and Parkhill, Julian
              and Peacock, Sharon J and Palmer, Tracy and Holden, Matthew T G",
  abstract = "BACKGROUND: Type VII protein secretion (T7SS) is a specialised
              system for excreting extracellular proteins across bacterial cell
              membranes and has been associated with virulence in
              Staphylococcus aureus. The genetic diversity of the ess locus,
              which encodes the T7SS, and the functions of proteins encoded
              within it are poorly understood. RESULTS: We used whole genome
              sequence data from 153 isolates representative of the diversity
              of the species to investigate the genetic variability of T7SS
              across S. aureus. The ess loci were found to comprise of four
              distinct modules based on gene content and relative conservation.
              Modules 1 and 4, comprising of the 5' and 3' modules of the ess
              locus, contained the most conserved clusters of genes across the
              species. Module 1 contained genes encoding the secreted protein
              EsxA, and the EsaAB and EssAB components of the T7SS machinery,
              and Module 4 contained two functionally uncharacterized conserved
              membrane proteins. Across the species four variants of Module 2
              were identified containing the essC gene, each of which was
              associated with a specific group of downstream genes. The most
              diverse module of the ess locus was Module 3 comprising a highly
              variable arrangement of hypothetical proteins. RNA-Seq was
              performed on representatives of the four Module 2 variants and
              demonstrated strain-specific differences in the levels of
              transcription in the conserved Module 1 components and
              transcriptional linkage Module 2, and provided evidence of the
              expression of genes the variable regions of the ess loci.
              CONCLUSIONS: The ess locus of S. aureus exhibits modularity and
              organisational variation across the species and transcriptional
              variation. In silico analysis of ess loci encoded hypothetical
              proteins identified potential novel secreted substrates for the
              T7SS. The considerable variety in operon arrangement between
              otherwise closely related isolates provides strong evidence for
              recombination at this locus. Comparison of these recombination
              regions with each other, and with the genomes of other
              Staphylococcal species, failed to identify evidence of intra- and
              inter-species recombination, however the analysis identified a
              novel T7SS in another pathogenic staphylococci, Staphylococcus
              lugdunensis.",
  journal  = "BMC Genomics",
  volume   =  17,
  pages    = "222",
  month    =  mar,
  year     =  2016,
  keywords = "Secretion; Staphylococcus aureus; Type
              VII;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Koskella2014-it,
  title    = "Bacteria-phage coevolution as a driver of ecological and
              evolutionary processes in microbial communities",
  author   = "Koskella, Britt and Brockhurst, Michael A",
  abstract = "Bacteria-phage coevolution, the reciprocal evolution between
              bacterial hosts and the phages that infect them, is an important
              driver of ecological and evolutionary processes in microbial
              communities. There is growing evidence from both laboratory and
              natural populations that coevolution can maintain phenotypic and
              genetic diversity, increase the rate of bacterial and phage
              evolution and divergence, affect community structure, and shape
              the evolution of ecologically relevant bacterial traits. Although
              the study of bacteria-phage coevolution is still in its infancy,
              with open questions regarding the specificity of the interaction,
              the gene networks of coevolving partners, and the relative
              importance of the coevolving interaction in complex communities
              and environments, there have recently been major advancements in
              the field. In this review, we sum up our current understanding of
              bacteria-phage coevolution both in the laboratory and in nature,
              discuss recent findings on both the coevolutionary process itself
              and the impact of coevolution on bacterial phenotype, diversity
              and interactions with other species (particularly their
              eukaryotic hosts), and outline future directions for the field.",
  journal  = "FEMS Microbiol. Rev.",
  volume   =  38,
  number   =  5,
  pages    = "916--931",
  month    =  sep,
  year     =  2014,
  keywords = "antagonistic; bacteriophage; host-parasite; infection;
              resistance; species
              interaction;phage;evolution;Staphylococcus;Papers\_for\_Michelle;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{McAdam2011-cn,
  title    = "Adaptive evolution of Staphylococcus aureus during chronic
              endobronchial infection of a cystic fibrosis patient",
  author   = "McAdam, Paul R and Holmes, Anne and Templeton, Kate E and
              Fitzgerald, J Ross",
  abstract = "The molecular adaptation of Staphylococcus aureus to its host
              during chronic infection is not well understood. Comparative
              genome sequencing of 3 S. aureus isolates obtained sequentially
              over 26 months from the airways of a cystic fibrosis patient,
              revealed variation in phage content, and genetic polymorphisms in
              genes which influence antibiotic resistance, and global
              regulation of virulence. The majority of polymorphisms were
              isolate-specific suggesting the existence of an heterogeneous
              infecting population that evolved from a single infecting strain
              of S. aureus. The genetic variation identified correlated with
              differences in growth rate, hemolytic activity, and antibiotic
              sensitivity, implying a profound effect on the ecology of S.
              aureus. In particular, a high frequency of mutations in loci
              associated with the alternate transcription factor SigB, were
              observed. The identification of genes under diversifying
              selection during long-term infection may inform the design of
              novel therapeutics for the control of refractory chronic
              infections.",
  journal  = "PLoS One",
  volume   =  6,
  number   =  9,
  pages    = "e24301",
  month    =  sep,
  year     =  2011,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Donker2017-te,
  title     = "Population genetic structuring of methicillin-resistant
               Staphylococcus aureus clone {EMRSA-15} within {UK} reflects
               patient referral patterns",
  author    = "Donker, Tjibbe and Reuter, Sandra and Scriberras, James and
               Reynolds, Rosy and Brown, Nicholas M and Est{\'e}e
               T{\"o}r{\"o}k, M and James, Richard and {East of England
               Microbiology Research Network} and Aanensen, David M and
               Bentley, Stephen D and Holden, Matthew T G and Parkhill, Julian
               and Spratt, Brian G and Peacock, Sharon J and Feil, Edward J and
               Grundmann, Hajo",
  abstract  = "Antibiotic resistance forms a serious threat to the health of
               hospitalised patients, rendering otherwise treatable bacterial
               infections potentially life-threatening. A thorough
               understanding of the mechanisms by which resistance spreads
               between patients in different hospitals is required in order to
               design effective control strategies. We measured the differences
               between bacterial populations of 52 hospitals in the United
               Kingdom and Ireland, using whole-genome sequences from 1085 MRSA
               clonal complex 22 isolates collected between 1998 and 2012. The
               genetic differences between bacterial populations were compared
               with the number of patients transferred between hospitals and
               their regional structure. The MRSA populations within single
               hospitals, regions and countries were genetically distinct from
               the rest of the bacterial population at each of these levels.
               Hospitals from the same patient referral regions showed more
               similar MRSA populations, as did hospitals sharing many
               patients. Furthermore, the bacterial populations from different
               time-periods within the same hospital were generally more
               similar to each other than contemporaneous bacterial populations
               from different hospitals. We conclude that, while a large part
               of the dispersal and expansion of MRSA takes place among
               patients seeking care in single hospitals, inter-hospital spread
               of resistant bacteria is by no means a rare occurrence.
               Hospitals are exposed to constant introductions of MRSA on a
               number of levels: (1) most MRSA is received from hospitals that
               directly transfer large numbers of patients, while (2) fewer
               introductions happen between regions or (3) across national
               borders, reflecting lower numbers of transferred patients. A
               joint coordinated control effort between hospitals, is therefore
               paramount for the national control of MRSA, antibiotic-resistant
               bacteria and other hospital-associated pathogens.",
  journal   = "Microbial Genomics",
  publisher = "Microbiology Society",
  month     =  jul,
  year      =  2017,
  keywords  = "hospital network; antimicrobial Resistance;
               MRSA;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language  = "en"
 }

 @ARTICLE{McMillan2017-xh,
  title    = "Draft Genome Sequences of 15 Staphylococcus aureus Isolates
              Recovered from Raw Milk and Associated Milk Filters from
              Victoria, Australia",
  author   = "McMillan, Kate and Allnutt, Theodore R and Fox, Edward M",
  abstract = "This study describes draft whole genomes of 15 Staphylococcus
              aureus isolates from dairy farms located in Victoria, Australia.
              Two novel sequence types (ST3183 and ST3184) were identified
              among these isolates.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  2,
  month    =  jan,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Franck2017-tn,
  title    = "Staphylococcal aureus Enterotoxin {C} and {Enterotoxin-Like} {L}
              Associated with Post-partum Mastitis",
  author   = "Franck, Kristina T and Gumpert, Heidi and Olesen, Bente and
              Larsen, Anders R and Petersen, Andreas and Bangsborg, Jette and
              Albertsen, Per and Westh, Henrik and Bartels, Mette D",
  abstract = "Denmark is a low prevalence country with regard to methicillin
              resistant Staphylococcus aureus (MRSA). In 2008 and 2014, two
              neonatal wards in the Copenhagen area experienced outbreaks with
              a typical community acquired MRSA belonging to the same spa type
              and sequence type (t015:ST45) and both were PVL and ACME
              negative. In outbreak 1, the isolates harbored SCCmec IVa and in
              outbreak 2 SCCmec V. The clinical presentation differed between
              the two outbreaks, as none of five MRSA positive mothers in
              outbreak 1 had mastitis vs. five of six MRSA positive mothers in
              outbreak 2 (p < 0.02). To investigate if whole-genome sequencing
              could identify virulence genes associated with mastitis,
              t015:ST45 isolates from Denmark (N = 101) were whole-genome
              sequenced. Sequence analysis confirmed two separate outbreaks
              with no sign of sustained spread into the community. Analysis of
              the accessory genome between isolates from the two outbreaks
              revealed a S. aureus pathogenicity island containing enterotoxin
              C and enterotoxin-like L only in isolates from outbreak 2.
              Enterotoxin C and enterotoxin-like L carrying S. aureus are
              associated with bovine mastitis and our findings indicate that
              these may also be important virulence factors for human mastitis.",
  journal  = "Front. Microbiol.",
  volume   =  8,
  pages    = "173",
  month    =  feb,
  year     =  2017,
  keywords = "MRSA; SaPITokyo12571; clinical presentation; enterotoxins;
              pathogenicity islands; post-partum mastitis; virulence;
              whole-genome
              sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Murray2017-uw,
  title    = "Recombination-mediated host-adaptation by avian Staphylococcus
              aureus",
  author   = "Murray, Susan and Pascoe, Ben and M{\'e}ric, Guillaume and
              Mageiros, Leonardos and Yahara, Koji and Hitchings, Matthew D and
              Friedmann, Yasmin and Wilkinson, Thomas S and Gormley, Fraser J
              and Mack, Dietrich and Bray, James E and Lamble, Sarah and
              Bowden, Rory and Jolley, Keith A and Maiden, Martin C J and
              Wendlandt, Sarah and Schwarz, Stefan and Corander, Jukka and Ross
              Fitzgerald, J and Sheppard, Samuel K",
  journal  = "Genome Biol. Evol.",
  month    =  feb,
  year     =  2017,
  keywords = "Staphylococcus;recombination;colonization;plasmid;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human"
 }

 @ARTICLE{Bakthavatchalam2017-bb,
  title    = "Draft genome sequence of reduced teicoplanin-susceptible and
              vancomycin-heteroresistant methicillin-resistant Staphylococcus
              aureus from sepsis cases",
  author   = "Bakthavatchalam, Yamuna Devi and Veeraraghavan, Balaji and
              Devanga Ragupathi, Naveen Kumar and Babu, Priyanka and Munuswamy,
              Elakkiya and David, Thambu",
  abstract = "Here we report the whole-genome shotgun sequence of six
              methicillin-resistant Staphylococcus aureus (MRSA) showing
              reduced susceptibility to both vancomycin and teicoplanin. The
              typical Indian community-acquired MRSA (CA-MRSA) clone
              ST772-MRSA-V-t657 was the most common genotype (3/6; 50\%),
              followed by ST672-MRSA-IV (2/6; 33\%) and ST22-MRSA-IV (1/6;
              17\%). All strains harboured a mutation in the tcaRAB operon,
              vraSR, graSR and/or rpoB genes, which are frequently mutated
              determinants in a heteroresistant vancomycin-intermediate S.
              aureus (hVISA) phenotype.",
  journal  = "J Glob Antimicrob Resist",
  volume   =  8,
  pages    = "169--171",
  month    =  feb,
  year     =  2017,
  keywords = "MRSA; hVISA;
              tcaA;Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Diene2017-oq,
  title    = "Prophages and adaptation of Staphylococcus aureus {ST398} to the
              human clinic",
  author   = "Diene, Seydina M and Corvaglia, Anna Rita and Fran{\c c}ois,
              Patrice and van der Mee-Marquet, Nathalie and {Regional Infection
              Control Group of the Centre Region}",
  abstract = "BACKGROUND: It has been suggested that prophages in the ST398 S.
              aureus clone are responsible for expanding ST398's spectrum of
              action and increasing its ability to cause human infections. We
              carried out the first characterization of the various prophages
              carried by 76 ST398 bloodstream infection (BSI) isolates obtained
              over 9 years of observation. RESULTS: Whole-genome sequencing of
              22 representative isolates showed (1) the presence of the
              $\varphi$3-prophage and diverse genetic features typical of
              animal-associated isolates (i.e., SCCmec XI element, Tn916
              transposon and non $\varphi$3-prophages) in a majority of BSI
              isolates, (2) one BSI isolate devoid of the $\varphi$3-prophage
              but otherwise similar to an animal-infecting isolate, (3) 35
              prophages carrying numerous genes previously associated with
              virulence or immune evasion in animal models of staphylococcal
              infections. The analysis of prophage content in all 76 BSI
              isolates showed an increasing prevalence of polylysogeny over
              time. Overall, over the course of the last 10 years, the BSI
              isolates appear to have acquired increasing numbers of genetic
              features previously shown to contribute to bacterial adaptation
              and virulence in animal models of staphylococcal infections.
              CONCLUSIONS: We hypothesize that lysogeny has played a
              significant role in increasing the ability of the ST398 clone to
              cause infections in humans. Our findings highlight the risk that
              the ST398 lineage will increase its threat to public health by
              continuing to acquire virulence and/or multiple
              antibiotic-resistance genes from hospital-associated clones of
              Staphylococcus aureus.",
  journal  = "BMC Genomics",
  volume   =  18,
  number   =  1,
  pages    = "133",
  month    =  feb,
  year     =  2017,
  keywords = "Bloodstream infections; CC398 lineage; Evolution;
              Livestock-associated; Phage content; Prophage; Staphylococcus
              aureus;
              $\varphi$3-prophage;Staphylococcus;phage;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human",
  language = "en"
 }

 @ARTICLE{Mannala2017-tj,
  title    = "Complete Genome and Plasmid Sequences of \textit{Staphylococcus
              aureus} {EDCC} 5055 ({DSM} 28763), Used To Study
              {Implant-Associated} Infections",
  author   = "Mannala, Gopala Krishna and Hain, Torsten and Spr{\"o}er, Cathrin
              and Bunk, Boyke and Overmann, J{\"o}rg and Alt, Volker and
              Domann, Eugen",
  abstract = "Staphylococcus aureus EDCC 5055 (DSM 28763) is a human clinical
              wound isolate intensively used to study implant-associated
              infections in rabbit and rat infection models. Here, we report
              its complete genome sequence (2,794,437 bp) along with that of
              one plasmid (27,437 bp). This strain belongs to sequence type 8
              and contains a mecA gene.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  8,
  month    =  feb,
  year     =  2017,
  keywords = "Staphylococcus;plasmid;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Kpeli2017-lk,
  title    = "Genomic analysis of {ST88} community-acquired methicillin
              resistant \textit{Staphylococcus aureus} in Ghana",
  author   = "Kpeli, Grace and Buultjens, Andrew H and Giulieri, Stefano and
              Owusu-Mireku, Evelyn and Aboagye, Samuel Y and Baines, Sarah L
              and Seemann, Torsten and Bulach, Dieter and Gon{\c c}alves da
              Silva, Anders and Monk, Ian R and Howden, Benjamin P and
              Pluschke, Gerd and Yeboah-Manu, Dorothy and Stinear, Timothy",
  abstract = "BACKGROUND: The emergence and evolution of community-acquired
              methicillin resistant Staphylococcus aureus (CA-MRSA) strains in
              Africa is poorly understood. However, one particular MRSA lineage
              called ST88, appears to be rapidly establishing itself as an
              ``African'' CA-MRSA clone. In this study, we employed whole
              genome sequencing to provide more information on the genetic
              background of ST88 CA-MRSA isolates from Ghana and to describe in
              detail ST88 CA-MRSA isolates in comparison with other MRSA
              lineages worldwide. METHODS: We first established a complete ST88
              reference genome (AUS0325) using PacBio SMRT sequencing. We then
              used comparative genomics to assess relatedness among 17 ST88
              CA-MRSA isolates recovered from patients attending Buruli ulcer
              treatment centres in Ghana, three non-African ST88s and 15 other
              MRSA lineages. RESULTS: We show that Ghanaian ST88 forms a
              discrete MRSA lineage (harbouring SCCmec-IV [2B]). Gene content
              analysis identified five distinct genomic regions enriched among
              ST88 isolates compared with the other S. aureus lineages. The
              Ghanaian ST88 isolates had only 658 core genome SNPs and there
              was no correlation between phylogeny and geography, suggesting
              the recent spread of this clone. The lineage was also resistant
              to multiple classes of antibiotics including $\beta$-lactams,
              tetracycline and chloramphenicol. DISCUSSION: This study reveals
              that S. aureus ST88-IV is a recently emerging and rapidly
              spreading CA-MRSA clone in Ghana. The study highlights the
              capacity of small snapshot genomic studies to provide actionable
              public health information in resource limited settings. To our
              knowledge this is the first genomic assessment of the ST88
              CA-MRSA clone.",
  journal  = "PeerJ",
  volume   =  5,
  pages    = "e3047",
  month    =  feb,
  year     =  2017,
  keywords = "CA-MRSA; Comparative genomics; MRSA; Phylogeography; ST88;
              Staphylococcus aureus; Whole genome
              sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Piso2017-yj,
  title    = "A {Cross-Sectional} Study of Colonization Rates with
              {Methicillin-Resistant} Staphylococcus aureus ({MRSA}) and
              {Extended-Spectrum} {Beta-Lactamase} ({ESBL}) and
              {Carbapenemase-Producing} Enterobacteriaceae in Four Swiss
              Refugee Centres",
  author   = "Piso, Rein Jan and K{\"a}ch, Roman and Pop, Roxana and Zillig,
              Daniela and Schibli, Urs and Bassetti, Stefano and Meinel,
              Dominik and Egli, Adrian",
  abstract = "BACKGROUND: The recent crisis of refugees seeking asylum in
              European countries challenges public health on many levels. Most
              refugees currently arrive from Syria, Afghanistan, or Eritrea.
              Data about multidrug resistant bacteria (MDR) prevalence are not
              present for these countries. However, when entering the European
              heath care systems, data about colonisation rates regarding
              highly resistant bacterial pathogens are important. METHODS: We
              performed a cross-sectional screening in four Swiss refugee
              centres to determine the colonization rates for MRSA and ESBL-
              and carbapenemase-producing Enterobacteriaceae. We used
              pharyngeal, nasal, and inguinal swabs for MRSA and rectal swabs
              and urine for ESBL and carbapenemase screening using standard
              microbiological procedures. Whole genome sequencing (WGS) was
              used to determine the relatedness of MRSA isolates with high
              resolution due to a suspected outbreak. RESULTS: 41/261(15.7\%)
              refugees were colonized with MRSA. No differences regarding the
              country of origin were observed. However, in a single centre
              significantly more were colonized, which was confirmed to be a
              recent local outbreak. 57/241 (23.7\%) refugees were colonized
              with ESBL with significantly higher colonisation in persons
              originating from the Middle East (35.1\%, p<0.001). No
              carbapenemase producers were detected. CONCLUSION: The
              colonisation rate of the refugees was about 10 times higher for
              MRSA and 2-5 times higher for ESBL compared to the Swiss
              population. Contact precaution is warranted for these persons if
              they enter medical care. In cases of infections, MRSA and
              ESBL-producing Enterobacteriaceae should be considered regarding
              antibiotic treatment choices.",
  journal  = "PLoS One",
  volume   =  12,
  number   =  1,
  pages    = "e0170251",
  month    =  jan,
  year     =  2017,
  keywords = "Staphylococcus;antibiotics;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @UNPUBLISHED{Young2017-di,
  title    = "Severe infections emerge from the microbiome by adaptive
              evolution",
  author   = "Young, Bernadette C and Wu, Chieh-Hsi and Claire Gordon, N and
              Cole, Kevin and Price, James R and Liu, Elian and Sheppard, Anna
              and Perera, Sanuki and Charlesworth, Jane and Golubchik, Tanya
              and Iqbal, Zamin and Bowden, Rory and Massey, Ruth and Paul, John
              and Crook, Derrick W and Peto, Timothy E A and Sarah Walker, A
              and Llewelyn, Martin and Wyllie, David H and Wilson, Daniel",
  abstract = "Bacteria responsible for the greatest global mortality colonize
              the human microbiome far more frequently than they cause severe
              infections. Whether mutation and selection within the microbiome
              precipitate infection is unknown. To address this question, we
              investigated de novo mutation in 1163 Staphylococcus aureus
              genomes from 105 infected patients with nose-colonization. We
              report that 72\% of the infections emerged from the microbiome,
              with infecting and nose-colonizing bacteria showing systematic
              adaptive differences. We found 3.6-fold, 2.9-fold and 2.8-fold
              enrichments of protein-altering variants in genes responding to
              rsp, which regulates surface antigens and toxicity; agr, which
              regulates quorum-sensing, toxicity and abscess formation; and
              host-derived antimicrobial peptides, respectively. These adaptive
              signatures were not observed in healthy carriers and differed
              from prevailing species-level signals of selection, suggesting
              disease-associated, short-term, within-host selection pressures.
              Our results show that infection, like a cancer of the microbiome,
              emerges through spontaneous adaptive evolution, raising new
              possibilities for diagnosis and treatment.",
  journal  = "bioRxiv",
  pages    = "116681",
  month    =  mar,
  year     =  2017,
  keywords = "microbiome;Staphylococcus;evolution;systems\_biology;confirmed\_SA-resistance-mutation;within-host-evolution;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Murray2017-if,
  title    = "Recombination-mediated host-adaptation by avian Staphylococcus
              aureus",
  author   = "Murray, Susan and Pascoe, Ben and M{\'e}ric, Guillaume and
              Mageiros, Leonardos and Yahara, Koji and Hitchings, Matthew D and
              Friedmann, Yasmin and Wilkinson, Thomas S and Gormley, Fraser J
              and Mack, Dietrich and Bray, James E and Lamble, Sarah and
              Bowden, Rory and Jolley, Keith A and Maiden, Martin C J and
              Wendlandt, Sarah and Schwarz, Stefan and Corander, Jukka and Ross
              Fitzgerald, J and Sheppard, Samuel K",
  abstract = "Staphylococcus aureus are globally disseminated among farmed
              chickens causing skeletal muscle infections, dermatitis and
              septicaemia. The emergence of poultry-associated lineages has
              involved zoonotic transmission from humans to chickens but
              questions remain about the specific adaptations that promote
              proliferation of chicken pathogens. We characterised genetic
              variation in a population of genome-sequenced S. aureus isolates
              of poultry and human origin. Genealogical analysis identified a
              dominant poultry-associated sequence cluster within the CC5
              clonal complex. Poultry and human CC5 isolates were significantly
              distinct from each other and more recombination events were
              detected in the poultry isolates. We identified forty-four
              recombination events in 33 genes along the branch extending to
              the poultry-specific CC5 cluster, and 47 genes were found more
              often in CC5 poultry isolates compared to those from humans. Many
              of these gene sequences were common in chicken isolates from
              other clonal complexes suggesting horizontal gene transfer among
              poultry associated lineages. Consistent with functional
              predictions for putative poultry-associated genes, poultry
              isolates showed enhanced growth at 42oC and greater erythrocyte
              lysis on chicken blood agar in comparison with human isolates. By
              combining phenotype information with evolutionary analysis of
              staphylococcal genomes, we provide evidence of adaptation,
              following a human-to-poultry host transition. This has important
              implications for the emergence and dissemination of new
              pathogenic clones associated with modern agriculture.",
  journal  = "Genome Biol. Evol.",
  month    =  feb,
  year     =  2017,
  keywords = "Evolution; Genomics; Poultry infection; Recombination;
              Staphylococcus;Staphylococcus;recombination;colonization;plasmid;Staphylococcus\_aureus\_genome\_papers;Staph-animal-human",
  language = "en"
 }

 % The entry below contains non-ASCII chars that could not be converted
 % to a LaTeX equivalent.
 @ARTICLE{Bayliss2017-kb,
  title    = "The use of Oxford Nanopore native barcoding for complete genome
              assembly",
  author   = "Bayliss, Sion C and Hunt, Vicky L and Yokoyama, Maho and Thorpe,
              Harry A and Feil, Edward J",
  abstract = "Background: The Oxford Nanopore Technologies MinION(TM) is a
              mobile DNA sequencer that can produce long read sequences with a
              short turn-around time. Here we report the first demonstration of
              single contig genome assembly using Oxford Nanopore native
              barcoding when applied to a multiplexed library of 12 samples and
              combined with existing Illumina short-read data. This paves the
              way for the closure of multiple bacterial genomes from a single
              MinION(TM) sequencing run, given the availability of existing
              short-read data. The strain we used, MHO\_001, represents the
              important community-acquired methicillin resistant Staphylococcus
              aureus lineage USA300. Findings: Using a hybrid assembly of
              existing short read and barcoded long read sequences from
              multiplexed data, we completed a genome of the S. aureus USA300
              strain MHO\_001. The long-read data represented only ∼5-10\% of
              an average MinION(TM) run (∼7x genomic coverage), but, using
              standard tools, this was sufficient to complete the circular
              chromosome of S. aureus strain MHO\_001 (2.86 Mb) and two
              complete plasmids (27 Kb and 3 Kb). Minor differences were noted
              when compared to USA300 reference genome, USA300\_FPR3757,
              including the translocation, loss and gain of mobile genetic
              elements. Conclusion: Here we demonstrate that MinION(TM) reads,
              multiplexed using native barcoding, can be used in combination
              with short-read data, to fully complete a bacterial genome. The
              ability to complete multiple genomes, for which short-read data
              is already available, from a single MinION(TM) run is set to
              impact on our understanding of accessory genome content, plasmid
              diversity and genome rearrangements.",
  journal  = "Gigascience",
  month    =  feb,
  year     =  2017,
  keywords = "MinION; Staphylococcus aureus; Whole genome sequencing; bacterial
              genomics; hybrid assembly; long read; multiplexing; native
              barcoding;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Hau2017-cu,
  title    = "Draft Genome Sequences of 14 \textit{Staphylococcus aureus}
              Sequence Type 5 Isolates from California, {USA}",
  author   = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and
              Nicholson, Tracy L",
  abstract = "Staphylococcus aureus is part of the human epithelial microbiota;
              however, it is also a pathogen. The acquisition of mobile genetic
              elements plays a role in the virulence of S. aureus isolates and
              contributes to treatment failures. This report details the draft
              genome sequences of 14 clinical S. aureus isolates.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  13,
  month    =  mar,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Hau2017-yd,
  title    = "Complete Genome Sequences of Two \textit{Staphylococcus aureus}
              Sequence Type 5 Isolates from California, {USA}",
  author   = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and
              Nicholson, Tracy L",
  abstract = "Staphylococcus aureus causes a variety of human diseases ranging
              in severity. The pathogenicity of S. aureus can be partially
              attributed to the acquisition of mobile genetic elements. In this
              report, we provide two complete genome sequences from human
              clinical S. aureus isolates.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  13,
  month    =  mar,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Balachandran2017-ld,
  title    = "Complete Genome Sequence of \textit{Staphylococcus aureus} Strain
              Wood 46",
  author   = "Balachandran, Manasi and Riley, Matthew C and Bemis, David A and
              Kania, Stephen A",
  abstract = "Here, we report the first complete genome sequence of the
              Staphylococcus aureus strain Wood 46. Wood 46 has played an
              important role in understanding the virulence and pathogenesis of
              S. aureus infections. This report will assist efforts in vaccine
              development against methicillin-resistant S. aureus (MRSA)
              infections.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  13,
  month    =  mar,
  year     =  2017,
  keywords = "Staphylococcus;phage;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Lin2017-aq,
  title    = "Nucleotide Sequence Variations in Autolysis Genes of {ST} 59
              {Methicillin-Resistant} Staphylococcus aureus Isolates",
  author   = "Lin, Lee-Chung and Shu, Jwu-Ching and Chang, Shih-Cheng and Ge,
              Mao-Cheng and Liu, Tsui-Ping and Chen, Chien-Wei and Lu, Jang-Jih",
  abstract = "Biofilm formation is a virulence factor of bacteria. The goal of
              this study was to understand the mechanisms of biofilm formation
              by methicillin-resistant Staphylococcus aureus (MRSA).
              Whole-genome sequencing of eight MRSA strains was performed to
              identify sequence variations in genes related to biofilm
              formation. Thirty-one genes involved in MRSA biofilm formation
              were analyzed and 11 amino acid sequence variations in four genes
              related to autolysis were found. These variations include E121D
              and H387 N in ArlS; Q117K, T424S, K428T, A509S, V752E, A754V, and
              T771A in Atl; T184K in CidC; and D251N in CidR. Among the 26
              clinical MRSA isolates studied, 13 isolates were nonbiofilm
              producers and were found to harbor these mutations. Furthermore,
              all of these 13 isolates belonged to ST59. Ten of these 13 ST59
              isolates became able to produce biofilms when they were incubated
              with extracellular DNA from MRSA N315. Results of this study
              suggest that sequence variations in arlS, atl, cidC, and cidR
              genes may render MRSA unable to produce biofilms. Further
              investigations are needed to correlate these sequence variations
              with the biofilm-forming ability of MRSA isolates.",
  journal  = "Microb. Drug Resist.",
  month    =  mar,
  year     =  2017,
  keywords = "MRSA; ST59; biofilm;
              eDNA;Staphylococcus;phage;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Tosas_Auguet2016-co,
  title    = "Evidence for Community Transmission of {Community-Associated} but
              Not {Health-Care-Associated} {Methicillin-Resistant}
              Staphylococcus Aureus Strains Linked to Social and Material
              Deprivation: Spatial Analysis of Cross-sectional Data",
  author   = "Tosas Auguet, Olga and Betley, Jason R and Stabler, Richard A and
              Patel, Amita and Ioannou, Avgousta and Marbach, Helene and Hearn,
              Pasco and Aryee, Anna and Goldenberg, Simon D and Otter, Jonathan
              A and Desai, Nergish and Karadag, Tacim and Grundy, Chris and
              Gaunt, Michael W and Cooper, Ben S and Edgeworth, Jonathan D and
              Kypraios, Theodore",
  abstract = "BACKGROUND: Identifying and tackling the social determinants of
              infectious diseases has become a public health priority following
              the recognition that individuals with lower socioeconomic status
              are disproportionately affected by infectious diseases. In many
              parts of the world, epidemiologically and genotypically defined
              community-associated (CA) methicillin-resistant Staphylococcus
              aureus (MRSA) strains have emerged to become frequent causes of
              hospital infection. The aim of this study was to use spatial
              models with adjustment for area-level hospital attendance to
              determine the transmission niche of genotypically defined CA- and
              health-care-associated (HA)-MRSA strains across a diverse region
              of South East London and to explore a potential link between MRSA
              carriage and markers of social and material deprivation. METHODS
              AND FINDINGS: This study involved spatial analysis of
              cross-sectional data linked with all MRSA isolates identified by
              three National Health Service (NHS) microbiology laboratories
              between 1 November 2011 and 29 February 2012. The cohort of
              hospital-based NHS microbiology diagnostic services serves
              867,254 usual residents in the Lambeth, Southwark, and Lewisham
              boroughs in South East London, United Kingdom (UK). Isolates were
              classified as HA- or CA-MRSA based on whole genome sequencing.
              All MRSA cases identified over 4 mo within the three-borough
              catchment area (n = 471) were mapped to small geographies and
              linked to area-level aggregated socioeconomic and demographic
              data. Disease mapping and ecological regression models were used
              to infer the most likely transmission niches for each MRSA
              genetic classification and to describe the spatial epidemiology
              of MRSA in relation to social determinants. Specifically, we
              aimed to identify demographic and socioeconomic population traits
              that explain cross-area extra variation in HA- and CA-MRSA
              relative risks following adjustment for hospital attendance data.
              We explored the potential for associations with the English
              Indices of Deprivation 2010 (including the Index of Multiple
              Deprivation and several deprivation domains and subdomains) and
              the 2011 England and Wales census demographic and socioeconomic
              indicators (including numbers of households by deprivation
              dimension) and indicators of population health. Both CA-and
              HA-MRSA were associated with household deprivation (CA-MRSA
              relative risk [RR]: 1.72 [1.03-2.94]; HA-MRSA RR: 1.57
              [1.06-2.33]), which was correlated with hospital attendance
              (Pearson correlation coefficient [PCC] = 0.76). HA-MRSA was also
              associated with poor health (RR: 1.10 [1.01-1.19]) and residence
              in communal care homes (RR: 1.24 [1.12-1.37]), whereas CA-MRSA
              was linked with household overcrowding (RR: 1.58 [1.04-2.41]) and
              wider barriers, which represent a combined score for household
              overcrowding, low income, and homelessness (RR: 1.76
              [1.16-2.70]). CA-MRSA was also associated with recent immigration
              to the UK (RR: 1.77 [1.19-2.66]). For the area-level variation in
              RR for CA-MRSA, 28.67\% was attributable to the spatial
              arrangement of target geographies, compared with only 0.09\% for
              HA-MRSA. An advantage to our study is that it provided a
              representative sample of usual residents receiving care in the
              catchment areas. A limitation is that relationships apparent in
              aggregated data analyses cannot be assumed to operate at the
              individual level. CONCLUSIONS: There was no evidence of community
              transmission of HA-MRSA strains, implying that HA-MRSA cases
              identified in the community originate from the hospital reservoir
              and are maintained by frequent attendance at health care
              facilities. In contrast, there was a high risk of CA-MRSA in
              deprived areas linked with overcrowding, homelessness, low
              income, and recent immigration to the UK, which was not
              explainable by health care exposure. Furthermore, areas adjacent
              to these deprived areas were themselves at greater risk of
              CA-MRSA, indicating community transmission of CA-MRSA. This
              ongoing community transmission could lead to CA-MRSA becoming the
              dominant strain types carried by patients admitted to hospital,
              particularly if successful hospital-based MRSA infection control
              programmes are maintained. These results suggest that community
              infection control programmes targeting transmission of CA-MRSA
              will be required to control MRSA in both the community and
              hospital. These epidemiological changes will also have
              implications for effectiveness of risk-factor-based hospital
              admission MRSA screening programmes.",
  journal  = "PLoS Med.",
  volume   =  13,
  number   =  1,
  pages    = "e1001944",
  month    =  jan,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @UNPUBLISHED{Kanjilal2017-av,
  title    = "Increasing Antibiotic Susceptibility In Staphylococcus aureus In
              Boston, Massachusetts, 2000-2014: An Observational Study",
  author   = "Kanjilal, Sanjat and Sater, Mohamad and Thayer, Maile and
              Lagoudas, Georgia and Kim, Soohong and Blainey, Paul and Grad,
              Yonatan",
  abstract = "Background: Methicillin resistant S. aureus (MRSA) has been
              declining over the past decade, but changes in S. aureus overall
              and the implications for trends in antibiotic resistance remain
              unclear. Objective: To determine whether the decline in rates of
              infection by MRSA has been accompanied by changes in rates of
              infection by methicillin susceptible, penicillin resistant S.
              aureus (MSSA) and penicillin susceptible S. aureus (PSSA). We
              test if these dynamics are associated with specific genetic
              lineages and evaluate gains and losses of resistance at the
              strain level. Methods: We conducted a 15 year retrospective
              observational study at two tertiary care institutions in Boston,
              MA of 31,589 adult inpatients with S. aureus infections.
              Surveillance swabs and duplicate specimens were excluded. We also
              sequenced a sample of contemporary isolates (n = 180) obtained
              between January 2016 and July 2016. We determined changes in the
              annual rates of infection per 1,000 inpatient admissions by S.
              aureus subtype and in the annual mean antibiotic resistance by
              subtype. We performed phylogenetic analysis to generate a
              population structure and infer gain and loss of the genetic
              determinants of resistance. Results: Of the 43,954 S. aureus
              infections over the study period, 21,779 were MRSA, 17,565 MSSA
              and 4,610 PSSA. After multivariate adjustment, annual rates of
              infection by S. aureus declined from 2003 to 2014 by 2.9\% (95\%
              CI, 1.6\%-4.3\%), attributable to an annual decline in MRSA of
              9.1\% (95\% CI, 6.3\%-11.9\%) and in MSSA by 2.2\% (95\% CI,
              0.4\%-4.0\%). PSSA increased over this time period by 4.6\% (95\%
              CI, 3.0\%-6.3\%) annually. Resistance in S. aureus decreased from
              2000 to 2014 by 0.86 antibiotics (95\% CI, 0.81-0.91). By
              phylogenetic inference, 5/35 MSSA and 2/20 PSSA isolates in the
              common MRSA lineages ST5/USA100 and ST8/USA300 arose from the
              loss of genes conferring resistance. Conclusions and relevance:
              At two large tertiary care centers in Boston, MA, S. aureus
              infections have decreased in rate and have become more
              susceptible to antibiotics, with a rise in PSSA making penicillin
              an increasingly viable and important treatment option.",
  journal  = "bioRxiv",
  pages    = "125369",
  month    =  apr,
  year     =  2017,
  keywords = "Staphylococcus;antibiotics;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{De_Carvalho2017-rz,
  title    = "Draft Genome Sequences of Two Clinical {Methicillin-Resistant}
              \textit{Staphylococcus aureus} Strains Isolated from Healthy
              Children in Brazil",
  author   = "de Carvalho, Suzi P and de Almeida, J{\'e}ssica B and de Freitas,
              Leandro M and Guimaraes, Ana Marcia S and do Nascimento,
              Na{\'\i}la C and Dos Santos, Andrea P and Messick, Joanne B and
              Timenetsky, Jorge and Marques, Lucas M",
  abstract = "We report here the draft genome sequences of two
              community-associated methicillin-resistant Staphylococcus aureus
              (CA-MRSA) strains, C18 and C80, isolated from healthy children
              from day care centers. To our knowledge, these are the first
              draft genome sequences of CA-MRSA ST398/CC398/SccmecV and CA-MRSA
              ST5/CC5/SccmecIVa isolated from healthy children in Brazil.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  15,
  month    =  apr,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Earls2017-dk,
  title    = "The recent emergence in hospitals of multidrug-resistant
              community-associated sequence type 1 and spa type t127
              methicillin-resistant Staphylococcus aureus investigated by
              whole-genome sequencing: Implications for screening",
  author   = "Earls, Megan R and Kinnevey, Peter M and Brennan, Gr{\'a}inne I
              and Lazaris, Alexandros and Skally, Mairead and O'Connell, Brian
              and Humphreys, Hilary and Shore, Anna C and Coleman, David C",
  abstract = "Community-associated spa type t127/t922 methicillin-resistant
              Staphylococcus aureus (MRSA) prevalence increased from 1\%-7\% in
              Ireland between 2010-2015. This study tracked the spread of 89
              such isolates from June 2013-June 2016. These included 78
              healthcare-associated and 11 community associated-MRSA isolates
              from a prolonged hospital outbreak (H1) (n = 46), 16 other
              hospitals (n = 28), four other healthcare facilities (n = 4) and
              community-associated sources (n = 11). Isolates underwent
              antimicrobial susceptibility testing, DNA microarray profiling
              and whole-genome sequencing. Minimum spanning trees were
              generated following core-genome multilocus sequence typing and
              pairwise single nucleotide variation (SNV) analysis was
              performed. All isolates were sequence type 1 MRSA staphylococcal
              cassette chromosome mec type IV (ST1-MRSA-IV) and 76/89 were
              multidrug-resistant. Fifty isolates, including 40/46 from H1,
              were high-level mupirocin-resistant, carrying a conjugative 39 kb
              iles2-encoding plasmid. Two closely related ST1-MRSA-IV strains
              (I and II) and multiple sporadic strains were identified. Strain
              I isolates (57/89), including 43/46 H1 and all high-level
              mupirocin-resistant isolates, exhibited $\leq$80 SNVs. Two strain
              I isolates from separate H1 healthcare workers differed from
              other H1/strain I isolates by 7-47 and 12-53 SNVs, respectively,
              indicating healthcare worker involvement in this outbreak. Strain
              II isolates (19/89), including the remaining H1 isolates,
              exhibited $\leq$127 SNVs. For each strain, the pairwise SNVs
              exhibited by healthcare-associated and community-associated
              isolates indicated recent transmission of ST1-MRSA-IV within and
              between multiple hospitals, healthcare facilities and communities
              in Ireland. Given the interchange between healthcare-associated
              and community-associated isolates in hospitals, the risk factors
              that inform screening for MRSA require revision.",
  journal  = "PLoS One",
  volume   =  12,
  number   =  4,
  pages    = "e0175542",
  month    =  apr,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Rolo2017-tl,
  title    = "Evidence for the evolutionary steps leading to mecA-mediated
              $\beta$-lactam resistance in staphylococci",
  author   = "Rolo, Joana and Worning, Peder and Boye Nielsen, Jesper and
              Sobral, Rita and Bowden, Rory and Bouchami, Ons and Damborg,
              Peter and Guardabassi, Luca and Perreten, Vincent and Westh,
              Henrik and Tomasz, Alexander and de Lencastre, Herm{\'\i}nia and
              Miragaia, Maria",
  abstract = "The epidemiologically most important mechanism of antibiotic
              resistance in Staphylococcus aureus is associated with mecA-an
              acquired gene encoding an extra penicillin-binding protein
              (PBP2a) with low affinity to virtually all $\beta$-lactams. The
              introduction of mecA into the S. aureus chromosome has led to the
              emergence of methicillin-resistant S. aureus (MRSA) pandemics,
              responsible for high rates of mortality worldwide. Nonetheless,
              little is known regarding the origin and evolution of mecA.
              Different mecA homologues have been identified in species
              belonging to the Staphylococcus sciuri group representing the
              most primitive staphylococci. In this study we aimed to identify
              evolutionary steps linking these mecA precursors to the
              $\beta$-lactam resistance gene mecA and the resistance phenotype.
              We sequenced genomes of 106 S. sciuri, S. vitulinus and S.
              fleurettii strains and determined their oxacillin susceptibility
              profiles. Single-nucleotide polymorphism (SNP) analysis of the
              core genome was performed to assess the genetic relatedness of
              the isolates. Phylogenetic analysis of the mecA gene homologues
              and promoters was achieved through nucleotide/amino acid sequence
              alignments and mutation rates were estimated using a Bayesian
              analysis. Furthermore, the predicted structure of mecA
              homologue-encoded PBPs of oxacillin-susceptible and -resistant
              strains were compared. We showed for the first time that
              oxacillin resistance in the S. sciuri group has emerged multiple
              times and by a variety of different mechanisms. Development of
              resistance occurred through several steps including structural
              diversification of the non-binding domain of native PBPs; changes
              in the promoters of mecA homologues; acquisition of SCCmec and
              adaptation of the bacterial genetic background. Moreover, our
              results suggest that it was exposure to $\beta$-lactams in
              human-created environments that has driven evolution of native
              PBPs towards a resistance determinant. The evolution of
              $\beta$-lactam resistance in staphylococci highlights the
              numerous resources available to bacteria to adapt to the
              selective pressure of antibiotics.",
  journal  = "PLoS Genet.",
  volume   =  13,
  number   =  4,
  pages    = "e1006674",
  month    =  apr,
  year     =  2017,
  keywords = "Staphylococcus;evolution;antibiotics;oxacillin;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{De_Almeida2017-qf,
  title    = "Draft Genome Sequence of {Methicillin-Resistant}
              \textit{Staphylococcus aureus} Strain {LC33} Isolated from Human
              Breast Milk",
  author   = "de Almeida, J{\'e}ssica B and de Carvalho, Suzi P and de Freitas,
              Leandro M and Guimar{\~a}es, Ana Marcia S and do Nascimento,
              Na{\'\i}la C and Dos Santos, Andrea P and Messick, Joanne B and
              Timenetsky, Jorge and Marques, Lucas M",
  abstract = "Here, we report the draft genome sequence of Staphylococcus
              aureus strain LC33, isolated from human breast milk in Brazil.
              This microorganism has been typed as ST1/t127/sccmecV. To our
              knowledge, this is the first draft genome sequence of a
              methicillin-resistant S. aureus strain isolated from human breast
              milk.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  15,
  month    =  apr,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Cunningham2017-vi,
  title    = "Comparison of Two {Whole-Genome} Sequencing Methods for Analysis
              of Three {Methicillin-Resistant} \textit{Staphylococcus aureus}
              Outbreaks",
  author   = "Cunningham, Scott A and Chia, Nicholas and Jeraldo, Patricio R
              and Quest, Daniel J and Johnson, Julie A and Boxrud, Dave J and
              Taylor, Angela J and Chen, Jun and Jenkins, Gregory D and
              Drucker, Travis M and Nelson, Heidi and Patel, Robin",
  abstract = "Whole genome sequencing (WGS) can provide excellent resolution in
              global and local epidemiological investigations of Staphylococcus
              aureus outbreaks. A variety of sequencing approaches and
              analytical tools have been used; it is not clear which is ideal.
              We compared two WGS strategies and two analytical approaches to
              the standard method of SmaI restriction digestion pulsed-field
              gel electrophoresis (PFGE) for typing S. aureus Forty-two S.
              aureus isolates from three outbreaks and 12 reference isolates
              were studied. Near-complete genomes, assembled de novo with
              paired-end and long mate pair (8 Kb) libraries were first
              assembled and analyzed utilizing an in-house assembly and
              analytical informatics pipeline. In addition, paired-end data was
              assembled and analyzed using a commercial software package.
              Single nucleotide variant (SNP) analysis was performed using the
              in-house pipeline. Two assembly strategies were used to generate
              core genome multi-locus sequence typing (cgMLST) data. First, the
              near-complete genome data generated with the in-house pipeline
              was imported into the commercial software and used to perform
              cgMLST analysis. Second, the commercial software was used to
              assemble paired-end data and resolved assemblies were used to
              perform cgMLST. Similar isolate clustering was observed using SNP
              calling and cgMLST, regardless of data assembly strategy. All
              methods provided more discrimination between outbreaks than did
              PFGE. Overall, all of the evaluated WGS strategies yielded
              statistically similar results for S. aureus typing.",
  journal  = "J. Clin. Microbiol.",
  month    =  apr,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Millar2017-sn,
  title    = "Genomic Characterization of {USA300} {MRSA} to Evaluate
              Intraclass Transmission and Recurrence of {SSTI} among High Risk
              Military Trainees",
  author   = "Millar, Eugene V and Rice, Gregory K and Elassal, Emad M and
              Schlett, Carey D and Bennett, Jason W and Redden, Cassie L and
              Mor, Deepika and Law, Natasha N and Tribble, David R and
              Hamilton, Theron and Ellis, Michael W and Bishop-Lilly, Kimberly
              A",
  abstract = "Background.: Military trainees are at increased risk for
              methicillin-resistant Staphylococcus aureus (MRSA) skin and soft
              tissue infection (SSTI). Whole genome sequencing (WGS) can refine
              our understanding of MRSA transmission and microevolution in
              congregate settings. Methods.: We conducted a prospective
              case-control study of SSTI among US Army Infantry trainees at
              Fort Benning, GA from July 2012-December 2014. We identified
              clusters of USA300 MRSA SSTI within select training classes and
              performed WGS on clinical isolates. We then linked genomic,
              phylogenetic data, epidemiologic, and clinical data in order to
              evaluate intra- and interclass disease transmission. Furthermore,
              among cases of recurrent MRSA SSTI, we evaluated the intrahost
              relatedness of infecting strains. Results.: Nine training classes
              with $\geq$5 cases of USA300 MRSA SSTI were selected. Eighty
              USA300 MRSA clinical isolates from 74 trainees, six (8.1\%) of
              whom had recurrent infection, were subjected to WGS. We
              identified 2719 single nucleotide variants (SNV). The overall
              median (range) SNV difference between isolates was 173 (1-339).
              Intraclass median SNV differences ranged from 23 to 245. Two
              phylogenetic clusters were suggestive of interclass MRSA
              transmission. One of these clusters stemmed from two classes that
              were separated by a 13-month period but housed in the same
              barracks. Among trainees with recurrent MRSA SSTI, the intrahost
              median SNV difference was 7.5 (1-48). Conclusions.: Application
              of WGS revealed intra- and interclass transmission of MRSA among
              military trainees. An interclass cluster between two
              non-contemporaneous classes suggests a long-term reservoir for
              MRSA in this setting.",
  journal  = "Clin. Infect. Dis.",
  month    =  apr,
  year     =  2017,
  keywords = "Methicillin-resistant Staphylococcus aureus (MRSA); genomic
              epidemiology; military; skin and soft tissue infection; whole
              genome
              sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Moon2016-be,
  title    = "Draft Genome Sequences of a Unique {t324-ST541-V}
              {Methicillin-Resistant} Staphylococcus aureus Strain from a Pig",
  author   = "Moon, Dong Chan and Kim, Byung-Yong and Nam, Hyang-Mi and Jang,
              Geum-Chan and Jung, Suk-Chan and Lee, Hee-Soo and Park, Yong-Ho
              and Lim, Suk-Kyung",
  abstract = "Methicillin-resistant Staphylococcus aureus (MRSA), the major
              causative agent of nosocomial infection, has also been reported
              from non-human sources. A sequence type (ST) 541 MRSA isolate
              designated K12PJN53 was isolated from a healthy pig in 2012. The
              genome of K12PJN53 consists of 44 contiguous sequences (contigs),
              totalling 2,880,108 bases with 32.88\% GC content. Among the
              annotated contigs, 14, 17, and 18 contained genes related to
              antimicrobial resistance, adherence, and toxin genes,
              respectively. The genomic distance of strain K12PJN53 was close
              to the ST398 strains. This is the first report of the draft
              genome sequence of a novel livestock-associated MRSA ST541
              strain.",
  journal  = "J. Microbiol. Biotechnol.",
  volume   =  26,
  number   =  4,
  pages    = "799--805",
  month    =  apr,
  year     =  2016,
  keywords = "Genomics; MRSA;
              Pig;Staphylococcus;antibiotics;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Gordon2017-um,
  title    = "Whole Genome Sequencing reveals the contribution of long-term
              carriers in Staphylococcus aureus outbreak investigation",
  author   = "Gordon, N C and Pichon, B and Golubchik, T and Wilson, D J and
              Paul, J and Blanc, D S and Cole, K and Collins, J and Cortes, N
              and Cubbon, M and Gould, F K and Jenks, P J and Llewelyn, M and
              Nash, J Q and Orendi, J M and Paranthaman, K and Price, J and
              Senn, L and Thomas, H L and Wyllie, S and Crook, D W and Peto, T
              E A and Walker, A S and Kearns, A M",
  abstract = "Whole genome sequencing (WGS) makes it possible to determine the
              relatedness of bacterial isolates at high resolution, helping to
              characterise outbreaks. However, for Staphylococcus aureus,
              accumulation of within-host diversity during carriage might limit
              interpretation of sequencing data.In this study, we hypothesised
              the converse: that within-host diversity can in fact be exploited
              to reveal the involvement of long-term carriers (LTCs) in
              outbreaks. We analysed WGS data from 20 historical outbreaks, and
              applied phylogenetic methods to assess genetic relatedness and
              estimate time to most recent common ancestor (TMRCA). Findings
              were compared with the routine investigation results and
              epidemiological evidence.Outbreaks with epidemiological evidence
              for an LTC source had a mean estimated TMRCA (adjusted for
              outbreak duration) of 243 days (95\% CI 143-343), compared with
              55 days (28-81) for outbreaks lacking epidemiological evidence
              for an LTC (p=0.004). A threshold of 156 days predicted LTC
              involvement with a sensitivity of 0.875 and a specificity of 1.We
              also found 6/20 outbreaks included isolates with differing
              antimicrobial susceptibility profiles, however, these had only
              modestly increased pairwise diversity (mean 17.5 single
              nucleotide variants (SNVs) (95\% CI 17.3-17.8) vs 12.7 SNVs
              (12.5-12.8)) compared with isolates with identical antibiograms
              (p<0.0001). Additionally, for 2 outbreaks, WGS identified 1 or
              more isolates which were genetically distinct despite having the
              outbreak PFGE pulsotype.Duration-adjusted TMRCA allowed the
              involvement of LTCs in outbreaks to be identified and could be
              used to decide whether screening for long-term carriage (e.g. in
              healthcare workers) is warranted. Requiring identical
              antibiograms to trigger investigation could miss important
              contributors to outbreaks.",
  journal  = "J. Clin. Microbiol.",
  month    =  may,
  year     =  2017,
  keywords = "Staphylococcus;transmission-epidemiology;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Ankrum2017-pp,
  title    = "Population dynamics of \textit{Staphylococcus aureus} in Cystic
              Fibrosis patients to determine transmission events utilizing
              {WGS}",
  author   = "Ankrum, Andrea and Hall, Barry G",
  abstract = "Strict infection control practices have been implemented for
              healthcare visits by Cystic Fibrosis patients in an attempt to
              prevent transmission of important pathogens. This study used
              whole genome sequencing (WGS) to determine strain relatedness and
              assess population dynamics of Staphylococcus aureus isolates from
              a cohort of CF patients as assessed by strain relatedness. 311 S.
              aureus isolates were collected from respiratory cultures of 115
              CF patients during a 22 month study period. Whole genome
              sequencing was performed and using SNP analysis, phylogenetic
              trees were assembled to determine relatedness between isolates.
              MRSA phenotypes were predicted using PPFS2 and compared to the
              observed phenotype. The accumulation of SNPs in multiple isolates
              obtained over time from the same patient was examined to
              determine if a genomic molecular clock could be calculated.Pairs
              of isolates with $\leq$ 71 SNP differences were considered to be
              the ``same'' strain. All of the ``same'' strain isolates were
              either from the same patient or siblings pairs. There were 47
              examples of patients being superinfected with an unrelated
              strain. Predicted MRSA phenotype was accurate in all but three
              isolates. Mutation rates were unable to be determined because the
              branching order in the phylogenetic tree was inconsistent with
              the order of isolation.The observation that transmissions were
              identified between sibling patients shows that WGS is an
              effective tool for determining transmission between patients. The
              observation that transmission only occurred between siblings
              suggests that Staphylococcus aureus acquisition in our CF
              population occurred outside the hospital environment and
              indicates that current infection prevention efforts appear
              effective.",
  journal  = "J. Clin. Microbiol.",
  month    =  apr,
  year     =  2017,
  keywords = "bacerial\_genetics;Staphylococcus;bacterial comparative
              genomics;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Mekonnen2017-oe,
  title    = "Signatures of cytoplasmic proteins in the exoproteome distinguish
              community- and hospital-associated methicillin-resistant
              Staphylococcus aureus {USA300} lineages",
  author   = "Mekonnen, Solomon A and Palma Medina, Laura M and Glasner,
              Corinna and Tsompanidou, Eleni and de Jong, Anne and Grasso,
              Stefano and Schaffer, Marc and M{\"a}der, Ulrike and Larsen,
              Anders R and Gumpert, Heidi and Westh, Henrik and V{\"o}lker, Uwe
              and Otto, Andreas and Becher, D{\"o}rte and van Dijl, Jan Maarten",
  abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) is the common
              name for a heterogeneous group of highly drug-resistant
              staphylococci. Two major MRSA classes are distinguished based on
              epidemiology, namely community-associated (CA) and
              hospital-associated (HA) MRSA. Notably, the distinction of CA-
              and HA-MRSA based on molecular traits remains difficult due to
              the high genomic plasticity of S. aureus. Here we sought to
              pinpoint global distinguishing features of CA- and HA-MRSA
              through a comparative genome and proteome analysis of the
              notorious MRSA lineage USA300. We show for the first time that
              CA- and HA-MRSA isolates can be distinguished by two distinct
              extracellular protein abundance clusters that are predictive not
              only for epidemiologic behavior, but also for their growth and
              survival within epithelial cells. This 'exoproteome profiling'
              also groups more distantly related HA-MRSA isolates into the HA
              exoproteome cluster. Comparative genome analysis suggests that
              these distinctive features of CA- and HA-MRSA isolates relate
              predominantly to the accessory genome. Intriguingly, the
              identified exoproteome clusters differ in the relative abundance
              of typical cytoplasmic proteins, suggesting that signatures of
              cytoplasmic proteins in the exoproteome represent a new
              distinguishing feature of CA- and HA-MRSA. Our comparative genome
              and proteome analysis focuses attention on potentially
              distinctive roles of 'liberated' cytoplasmic proteins in the
              epidemiology and intracellular survival of CA- and HA-MRSA
              isolates. Such extracellular cytoplasmic proteins were recently
              invoked in staphylococcal virulence, but their implication in the
              epidemiology of MRSA is unprecedented.",
  journal  = "Virulence",
  pages    = "0",
  month    =  may,
  year     =  2017,
  keywords = "MRSA; Staphylococcus; USA300; community; epithelial cells;
              exoproteome; hospital; moonlighting; protein secretion; virulence
              factor;Staphylococcus;controversial;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Makarova2017-yd,
  title    = "Complete Genome Sequence of the {Livestock-Associated}
              {Methicillin-Resistant} Strain \textit{Staphylococcus aureus}
              subsp. \textit{aureus} {08S00974} (Sequence Type 398)",
  author   = "Makarova, Olga and Johnston, Paul and Walther, Birgit and Rolff,
              Jens and Roesler, Uwe",
  abstract = "We report here the complete genome sequence of the
              livestock-associated methicillin-resistant Staphylococcus aureus
              strain 08S00974 from sequence type 398 (ST398 LA-MRSA) isolated
              from a fatting pig at a farm in Germany.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  19,
  month    =  may,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Makarova2017-tq,
  title    = "Complete Genome Sequence of the Disinfectant Susceptibility
              Testing Reference Strain \textit{Staphylococcus aureus} subsp.
              \textit{aureus} {ATCC} 6538",
  author   = "Makarova, Olga and Johnston, Paul and Walther, Birgit and Rolff,
              Jens and Roesler, Uwe",
  abstract = "We report here the complete genome sequence of the
              methicillin-sensitive Staphylococcus aureus subsp. aureus strain
              ATCC 6538 (FDA 209, DSM 799, WDCM 00032, and NCTC 10788).",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  19,
  month    =  may,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Tewhey2012-yx,
  title    = "Genetic structure of community acquired methicillin-resistant
              Staphylococcus aureus {USA300}",
  author   = "Tewhey, Ryan and Cannavino, Christopher R and Leake, John A D and
              Bansal, Vikas and Topol, Eric J and Torkamani, Ali and Bradley,
              John S and Schork, Nicholas J",
  abstract = "BACKGROUND: Community-associated methicillin-resistant
              Staphylococcus aureus (CA-MRSA) is a significant bacterial
              pathogen that poses considerable clinical and public health
              challenges. The majority of the CA-MRSA disease burden consists
              of skin and soft tissue infections (SSTI) not associated with
              significant morbidity; however, CA-MRSA also causes severe,
              invasive infections resulting in significant morbidity and
              mortality. The broad range of disease severity may be influenced
              by bacterial genetic variation. RESULTS: We sequenced the
              complete genomes of 36 CA-MRSA clinical isolates from the
              predominant North American community acquired clonal type USA300
              (18 SSTI and 18 severe infection-associated isolates). While all
              36 isolates shared remarkable genetic similarity, we found
              greater overall time-dependent sequence diversity among SSTI
              isolates. In addition, pathway analysis of non-synonymous
              variations revealed increased sequence diversity in the putative
              virulence genes of SSTI isolates. CONCLUSIONS: Here we report the
              first whole genome survey of diverse clinical isolates of the
              USA300 lineage and describe the evolution of the pathogen over
              time within a defined geographic area. The results demonstrate
              the close relatedness of clinically independent CA-MRSA isolates,
              which carry implications for understanding CA-MRSA epidemiology
              and combating its spread.",
  journal  = "BMC Genomics",
  volume   =  13,
  pages    = "508",
  month    =  sep,
  year     =  2012,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Larsen2017-ln,
  title    = "Emergence of livestock-associated methicillin-resistant
              Staphylococcus aureus bloodstream infections in Denmark",
  author   = "Larsen, Jesper and Petersen, Andreas and Larsen, Anders R and
              Sieber, Raphael N and Stegger, Marc and Koch, Anders and
              Aarestrup, Frank M and Price, Lance B and Skov, Robert L",
  abstract = "Livestock-associated methicillin-resistant Staphylococcus aureus
              clonal complex 398 (LA-MRSA CC398) is causing an increasing
              number of skin and soft tissue infections (SSTIs) in Denmark and
              other European countries with industrial pig production. Yet, its
              impact on MRSA bloodstream infections (BSIs) has not been well
              studied.We investigated the clinical epidemiology of all human
              cases of LA-MRSA CC398 BSI during 2010--2015. Cases of LA-MRSA
              CC398 BSI were compared to cases of BSI caused by other types of
              MRSA and cases of SSTI caused by LA-MRSA CC398. Whole-genome
              sequence analysis was used to assess the phylogenetic
              relationship among LA-MRSA CC398 isolates from Danish pigs and
              cases of BSI and SSTI.The number of LA-MRSA CC398 BSIs and SSTIs
              increased over the years, peaking in 2014, where LA-MRSA CC398
              accounted for 16\% (7/44) and 21\% (211/985) of all MRSA BSIs and
              SSTIs, corresponding to 1.2 and 37.4 cases of BSI and SSTI per
              1,000,000 person-years, respectively. Most patients with LA-MRSA
              CC398 BSI had no contact to livestock, although they tended to
              live in rural areas. LA-MRSA CC398 caused 24.3 BSIs per 1,000
              SSTIs among people with no livestock contact, which is similar to
              the ratio observed for other types of MRSA. Whole-genome sequence
              analysis showed that most of the BSI and SSTI isolates were
              closely related to Danish pig isolates.This study demonstrates
              that the increasing number of LA-MRSA CC398 BSIs occurred in
              parallel with a much larger wave of LA-MRSA CC398 SSTIs and an
              expanding pig reservoir.",
  journal  = "Clin. Infect. Dis.",
  month    =  may,
  year     =  2017,
  keywords = "denmark; methicillin-resistant staphylococcus aureus; skin and
              soft tissue infections; animals, farm; bloodstream infection;
              genome; sequence analysis; family suidae;
              epidemiology;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Park2017-ym,
  title    = "Molecular epidemiology of Staphylococcus aureus bacteremia in a
              single large Minnesota medical center in 2015 as assessed using
              {MLST}, core genome {MLST} and spa typing",
  author   = "Park, Kyung-Hwa and Greenwood-Quaintance, Kerryl E and Uhl, James
              R and Cunningham, Scott A and Chia, Nicholas and Jeraldo,
              Patricio R and Sampathkumar, Priya and Nelson, Heidi and Patel,
              Robin",
  abstract = "Staphylococcus aureus is a leading cause of bacteremia in
              hospitalized patients. Whether or not S. aureus bacteremia (SAB)
              is associated with clonality, implicating potential nosocomial
              transmission, has not, however, been investigated. Herein, we
              examined the epidemiology of SAB using whole genome sequencing
              (WGS). 152 SAB isolates collected over the course of 2015 at a
              single large Minnesota medical center were studied.
              Staphylococcus protein A (spa) typing was performed by PCR/Sanger
              sequencing; multilocus sequence typing (MLST) and core genome
              MLST (cgMLST) were determined by WGS. Forty-eight isolates (32\%)
              were methicillin-resistant S. aureus (MRSA). The isolates
              encompassed 66 spa types, clustered into 11 spa clonal complexes
              (CCs) and 10 singleton types. 88\% of 48 MRSA isolates belonged
              to spa CC-002 or -008. Methicillin-susceptible S. aureus (MSSA)
              isolates were more genotypically diverse, with 61\% distributed
              across four spa CCs (CC-002, CC-012, CC-008 and CC-084). By MLST,
              there was 31 sequence types (STs), including 18 divided into 6
              CCs and 13 singleton STs. Amongst MSSA isolates, the common MLST
              clones were CC5 (23\%), CC30 (19\%), CC8 (15\%) and CC15 (11\%).
              Common MRSA clones were CC5 (67\%) and CC8 (25\%); there were no
              MRSA isolates in CC45 or CC30. By cgMLST analysis, there were 9
              allelic differences between two isolates, with the remaining 150
              isolates differing from each other by over 40 alleles. The two
              isolates were retroactively epidemiologically linked by medical
              record review. Overall, cgMLST analysis resulted in higher
              resolution epidemiological typing than did multilocus sequence or
              spa typing.",
  journal  = "PLoS One",
  volume   =  12,
  number   =  6,
  pages    = "e0179003",
  month    =  jun,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{McClure2017-cr,
  title    = "Complete Genome Sequence of a {Community-Associated}
              {Methicillin-Resistant} Staphylococcus aureus Hypervirulent
              Strain, {USA300-C2406}, Isolated from a Patient with a Lethal
              Case of Necrotizing Pneumonia",
  author   = "McClure, Jo-Ann and Zhang, Kunyan",
  abstract = "USA300 is a predominant community-associated
              methicillin-resistant Staphylococcus aureus strain causing
              significant morbidity and mortality. We present here the full
              annotated genome of a USA300 hypervirulent clinical strain,
              USA300-C2406, isolated from a patient with a lethal case of
              necrotizing pneumonia, to gain a better understanding of USA300
              hypervirulence.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  22,
  month    =  jun,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Sabrina_Pankey2017-cu,
  title     = "Host-selected mutations converging on a global regulator drive
               an adaptive leap towards symbiosis in bacteria",
  author    = "Sabrina Pankey, M and Foxall, Randi L and Ster, Ian M and Perry,
               Lauren A and Schuster, Brian M and Donner, Rachel A and Coyle,
               Matthew and Cooper, Vaughn S and Whistler, Cheryl A",
  abstract  = "Most bacteria that associate with animals do not cause harm, and
               many are essential to health or provide other benefits. An
               animal's immune system must permit these beneficial associations
               and at the same time block harmful microbes. This ultimately
               means that even beneficial bacteria must adapt to the immune
               barriers that they encounter. Different species that live in a
               close relationship with each other are known as symbionts. A
               species of bacteria called Vibrio fischeri can form a mutually
               beneficial symbiotic relationship with squid. The squid provide
               food for the bacteria, but only the bacteria that successfully
               navigate immune barriers and reach the squid's ``light organ''
               are fed. In return, the bacteria produce bioluminescence, making
               the nocturnal squid appear like moonlight in the water. As the
               bacteria reproduce, some individuals randomly acquire genetic
               mutations, some of which might improve the bacteria's chances of
               survival. Which mutations and associated traits allow bacteria
               to beat out the competition and evolve to become animal
               symbionts? To investigate, Pankey, Foxall et al. grew V.
               fischeri bacteria from several ancestors that were poor at
               colonizing squid. Groups of newly hatched squid selected
               potential symbionts from the resulting mix of bacteria. The
               selected symbionts were allowed to reproduce within the squid to
               form a new population of bacteria and were later vented out for
               a new batch of squid to sort through. This was repeated to
               ultimately form a final group of bacteria that had passed
               through 15 squid in turn. Unexpectedly, the bacteria in the
               final group all found the same solution to help them adapt to
               symbiotic life with the squid: mutations to the gene that
               encodes a signaling protein called BinK. Eight distinct
               mutations arose that dramatically changed how the bacteria
               interacted with squid. The evolved bacteria created a coating
               that hid them from squid immune cells and protected them from
               chemicals that squid use to kill invaders. The mutations also
               altered how the bacteria communicated with each other. This
               adjusted the intensity of light that they produced for their
               host to a more natural level, and improved their ability to grow
               on squid-provided food. Overall, the results presented by
               Pankey, Foxall et al. demonstrate that small genetic mutations
               can transform non-symbionts into symbionts, enabling them to
               evolve rapidly to form a symbiosis with a new host. This
               demonstrates that these bacteria already had the ability to
               coordinate the complex behaviors necessary to overcome the
               multiple barriers provided to them by the squid immune system.
               Other beneficial animal--bacteria associations are likely to
               work on similar principles; the study exemplifies the utility of
               experimental evolution systems and lays a foundation for further
               work to investigate these principles in more detail.",
  journal   = "eLife Sciences",
  publisher = "eLife Sciences Publications Limited",
  volume    =  6,
  pages     = "e24414",
  month     =  apr,
  year      =  2017,
  keywords  = "Vibrio fischeri; Euprymna scolopes; experimental
               evolution;evolution;Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
  language  = "en"
 }

 @ARTICLE{Tabuchi2017-hq,
  title    = "D-cycloserine increases the effectiveness of vancomycin against
              vancomycin-highly resistant Staphylococcus aureus",
  author   = "Tabuchi, Fumiaki and Matsumoto, Yasuhiko and Ishii, Masaki and
              Tatsuno, Keita and Okazaki, Mitsuhiro and Sato, Tomoaki and
              Moriya, Kyoji and Sekimizu, Kazuhisa",
  abstract = "Vancomycin is a widely used clinical drug to treat for infection
              by methicillin-resistant Staphylococcus aureus. Some patients
              show a weak response to vancomycin treatment. We previously
              reported that $\beta$-lactams increase the susceptibility to
              vancomycin by vancomycin-highly resistant S. aureus (VRSA)
              strains obtained following repeated in vitro mutagenesis and
              vancomycin selection. Here we found that the susceptibility of
              the VRSA strains to vancomycin was remarkably increased by
              combined treatment with D-cycloserine. On the other hand, VRSA
              did not show increased susceptibility to vancomycin in
              combination with bacitracin, fosfomycin, erythromycin,
              lincomycin, gentamicin, levofloxacin or nisin. Furthermore, in an
              in vivo infection model with silkworms, combined treatment with
              vancomycin and D-cycloserine exhibited therapeutic effects,
              whereas treatment with each compound alone did not. These
              findings suggest that combined treatment with vancomycin and
              D-cycloserine could be therapeutically effective against
              infectious diseases caused by VRSA.The Journal of Antibiotics
              advance online publication, 7 June 2017; doi:10.1038/ja.2017.56.",
  journal  = "J. Antibiot.",
  month    =  jun,
  year     =  2017,
  keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Ronco2017-yo,
  title    = "Draft Genome Sequence of a Sequence Type 398
              {Methicillin-Resistant} \textit{Staphylococcus aureus} Isolate
              from a Danish Dairy Cow with Mastitis",
  author   = "Ronco, Troels and Stegger, Marc and Pedersen, Karl",
  abstract = "Livestock-associated (LA) methicillin-resistant Staphylococcus
              aureus (MRSA) strains of sequence type 398 (ST398) colonize both
              humans and various livestock species. In 2016, an ST398 LA-MRSA
              isolate (Sa52) was collected from a Danish dairy cow with
              mastitis, and here, we report the draft genome sequence of strain
              Sa52.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  23,
  month    =  jun,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{McClure2017-aj,
  title    = "Complete Genome Sequences of Five Representative
              \textit{Staphylococcus aureus} {ST398} Strains from Five Major
              Sequence Heterogeneity Groups of a Diverse Isolate Collection",
  author   = "McClure, Jo-Ann and Zhang, Kunyan",
  abstract = "Staphylococcus aureus sequence type 398 (ST398) is a rapidly
              emerging livestock-associated strain causing zoonotic disease in
              humans. The course of pathogen evolution remains unclear,
              prompting whole-genome comparative studies in attempts to
              elucidate this issue. We present the full, annotated genomes of
              five newly isolated representative ST398 strains from five major
              sequence heterogeneity groups of our diverse isolate collection.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  23,
  month    =  jun,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Panthee2017-vo,
  title    = "Draft Genome Sequence of the {Vancomycin-Resistant} Clinical
              Isolate \textit{Staphylococcus aureus} {VRS3b}",
  author   = "Panthee, Suresh and Paudel, Atmika and Hamamoto, Hiroshi and
              Sekimizu, Kazuhisa",
  abstract = "We report here the draft genome sequence of the
              vancomycin-resistant strain Staphylococcus aureus VRS3b. The
              2.8-Mb genome, assembled into 46 contigs, harbored 2,915 putative
              coding sequences. The G+C content of the genome was 32.7\%.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  22,
  month    =  jun,
  year     =  2017,
  keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{McClure2017-aw,
  title    = "Complete Genome Sequence of the {Methicillin-Resistant}
              \textit{Staphylococcus aureus} Colonizing Strain {M92}",
  author   = "McClure, Jo-Ann and Zhang, Kunyan",
  abstract = "M92 is a methicillin-resistant Staphylococcus aureus (MRSA)
              colonizing strain belonging to ST239-MRSA-III. It frequently
              shows local nasal colonization in our hospital staff, but has
              never been associated with infection. We sequenced the complete
              genome of M92, in order to compare it to highly virulent MRSA
              strains to gain insight into MRSA virulence factors.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  23,
  month    =  jun,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Basco2017-pi,
  title    = "Draft Genome Sequences of Two \textit{Staphylococcus aureus}
              Strains Isolated in Succession from a Case of Bacteremia",
  author   = "Basco, M D S and Revollo, J R and McKinzie, P B and Agnihothram,
              S and Kothari, A and Saccente, M and Hart, M E",
  abstract = "Staphylococcus aureus strains MEH1 and MEH7 were successively
              isolated from the blood of a patient with recurrent bacteremia.
              The submitted draft genomes of strains MEH1 and MEH7 are
              2,914,972 and 2,911,704 bp, respectively.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  23,
  month    =  jun,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Larsen2017-yf,
  title    = "Emergence of livestock-associated methicillin-resistant
              Staphylococcus aureus bloodstream infections in Denmark",
  author   = "Larsen, Jesper and Petersen, Andreas and Larsen, Anders R and
              Sieber, Raphael N and Stegger, Marc and Koch, Anders and
              Aarestrup, Frank M and Price, Lance B and Skov, Robert L and
              {Danish MRSA Study Group}",
  abstract = "Background: Livestock-associated methicillin-resistant
              Staphylococcus aureus clonal complex 398 (LA-MRSA CC398) is
              causing an increasing number of skin and soft tissue infections
              (SSTIs) in Denmark and other European countries with industrial
              pig production. Yet, its impact on MRSA bloodstream infections
              (BSIs) has not been well studied. Methods: We investigated the
              clinical epidemiology of all human cases of LA-MRSA CC398 BSI
              during 2010-2015. Cases of LA-MRSA CC398 BSI were compared to
              cases of BSI caused by other types of MRSA and cases of SSTI
              caused by LA-MRSA CC398. Whole-genome sequence analysis was used
              to assess the phylogenetic relationship among LA-MRSA CC398
              isolates from Danish pigs and cases of BSI and SSTI. Results: The
              number of LA-MRSA CC398 BSIs and SSTIs increased over the years,
              peaking in 2014, where LA-MRSA CC398 accounted for 16\% (7/44)
              and 21\% (211/985) of all MRSA BSIs and SSTIs, corresponding to
              1.2 and 37.4 cases of BSI and SSTI per 1,000,000 person-years,
              respectively. Most patients with LA-MRSA CC398 BSI had no contact
              to livestock, although they tended to live in rural areas.
              LA-MRSA CC398 caused 24.3 BSIs per 1,000 SSTIs among people with
              no livestock contact, which is similar to the ratio observed for
              other types of MRSA. Whole-genome sequence analysis showed that
              most of the BSI and SSTI isolates were closely related to Danish
              pig isolates. Conclusions: This study demonstrates that the
              increasing number of LA-MRSA CC398 BSIs occurred in parallel with
              a much larger wave of LA-MRSA CC398 SSTIs and an expanding pig
              reservoir.",
  journal  = "Clin. Infect. Dis.",
  month    =  may,
  year     =  2017,
  keywords = "MRSA; bacteremia.; humans; livestock;
              zoonosis;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Larsen2017-yf,
  title    = "Emergence of livestock-associated methicillin-resistant
              Staphylococcus aureus bloodstream infections in Denmark",
  author   = "Larsen, Jesper and Petersen, Andreas and Larsen, Anders R and
              Sieber, Raphael N and Stegger, Marc and Koch, Anders and
              Aarestrup, Frank M and Price, Lance B and Skov, Robert L and
              {Danish MRSA Study Group}",
  abstract = "Background: Livestock-associated methicillin-resistant
              Staphylococcus aureus clonal complex 398 (LA-MRSA CC398) is
              causing an increasing number of skin and soft tissue infections
              (SSTIs) in Denmark and other European countries with industrial
              pig production. Yet, its impact on MRSA bloodstream infections
              (BSIs) has not been well studied. Methods: We investigated the
              clinical epidemiology of all human cases of LA-MRSA CC398 BSI
              during 2010-2015. Cases of LA-MRSA CC398 BSI were compared to
              cases of BSI caused by other types of MRSA and cases of SSTI
              caused by LA-MRSA CC398. Whole-genome sequence analysis was used
              to assess the phylogenetic relationship among LA-MRSA CC398
              isolates from Danish pigs and cases of BSI and SSTI. Results: The
              number of LA-MRSA CC398 BSIs and SSTIs increased over the years,
              peaking in 2014, where LA-MRSA CC398 accounted for 16\% (7/44)
              and 21\% (211/985) of all MRSA BSIs and SSTIs, corresponding to
              1.2 and 37.4 cases of BSI and SSTI per 1,000,000 person-years,
              respectively. Most patients with LA-MRSA CC398 BSI had no contact
              to livestock, although they tended to live in rural areas.
              LA-MRSA CC398 caused 24.3 BSIs per 1,000 SSTIs among people with
              no livestock contact, which is similar to the ratio observed for
              other types of MRSA. Whole-genome sequence analysis showed that
              most of the BSI and SSTI isolates were closely related to Danish
              pig isolates. Conclusions: This study demonstrates that the
              increasing number of LA-MRSA CC398 BSIs occurred in parallel with
              a much larger wave of LA-MRSA CC398 SSTIs and an expanding pig
              reservoir.",
  journal  = "Clin. Infect. Dis.",
  month    =  may,
  year     =  2017,
  keywords = "denmark; methicillin-resistant staphylococcus aureus; skin and
              soft tissue infections; animals, farm; bloodstream infection;
              genome; sequence analysis; family suidae;
              epidemiology;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Feng2017-gr,
  title    = "Genome comparisons of two Taiwanese community-associated
              methicillin-resistant Staphylococcus aureus {ST59} clones support
              the multi-origin theory of {CA-MRSA}",
  author   = "Feng, Ye and Chen, Hsiu-Ling and Chen, Chih-Jung and Chen,
              Chyi-Liang and Chiu, Cheng-Hsun",
  abstract = "Sequence type (ST) 59 is an epidemic lineage of
              community-associated methicillin-resistant Staphylococcus aureus
              (CA-MRSA) in Asia. Two ST59 clones are prevalent in Taiwan: the
              Taiwan clone (TW) causes severe infections, whereas the
              Asian-Pacific clone (AP) is usually commensal. In this study, we
              sequenced the genome and transcriptome of the representative
              strains of these two clones and found their differences to focus
              on three mobile genetic elements: TW carries SCCmec Type VT,
              Panton-Valentine leucocidin (PVL)-encoding prophage $\Phi$Sa2,
              whereas AP carries SCCmec Type IV and staphylokinase
              (SAK)-encoding prophage $\Phi$Sa3. The anti-virulent role of SAK
              was confirmed using murine skin and bloodstream infection models.
              $\Phi$Sa3 usually integrates into the hlb gene, but in AP was
              found to be integrated at the genomic island $\nu$Sa$\beta$. The
              mutation of the attB site ``TGTATCCAAACTGG'' to
              ``TGTATCCGAATTGG'' led to a failure in the integration of
              $\Phi$Sa3 in hlb, prompting atypical integration at other sites.
              The sak gene possessed remarkably different patterns of
              distribution among the different STs of S. aureus. We conclude
              that the atypical integration of $\Phi$Sa3 may help S. aureus
              adapt to the human host habitat and that the subsequent loss of
              $\Phi$Sa3 contributes toward the development of a virulent
              CA-MRSA lineage for wider horizontal transmission.",
  journal  = "Infect. Genet. Evol.",
  volume   =  54,
  pages    = "60--65",
  month    =  jun,
  year     =  2017,
  keywords = "Anti-virulence factor; Bacteriophage; CA-MRSA; Clone;
              Staphylokinase;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Edslev2017-oi,
  title    = "Identification of a {PVL-negative} {SCCmec-IVa} sub-lineage of
              the methicillin-resistant Staphylococcus aureus {CC80} lineage:
              Understanding the clonal origin of {CA-MRSA}",
  author   = "Edslev, Sofie Marie and Westh, Henrik Torkil and Andersen, Paal
              Skytt and Skov, Robert and Kobayashi, Nobumichi and Bartels,
              Mette Damkj{\ae}r and Vandenesh, Francois and Petersen, Andreas
              and Worning, Peder and Larsen, Anders Rhod and Stegger, Marc",
  abstract = "OBJECTIVES: Community-acquired MRSA (CA-MRSA) isolates belonging
              to clonal complex 80 (CC80) are recognized as the European
              CA-MRSA. The prevailing European CA-MRSA clone carries a type IVc
              staphylococcal cassette chromosome mec (SCCmec) and expresses
              Panton-Valentine leukocidin (PVL). Recently, a significant
              increase of PVL-negative CC80 MRSA has been observed in Denmark.
              The aim of this study was to examine the genetics and the
              epidemiology of these, and to compare them to the European
              CA-MRSA clone in order to understand the emergence of
              PVL-negative CC80 MRSA. METHODS: Phylogenetic analysis of the
              CC80 S. aureus lineage was conducted from whole-genome sequences
              of 217 isolates (23 MSSA and 194 MRSA) from 22 countries. All
              isolates were further genetically characterized in regard to
              resistance determinants and PVL carriage, and epidemiological
              data was obtained for selected isolates. RESULTS: The
              phylogenetic analysis revealed the existence of three distinct
              clades of the CC80 lineage: i) an MSSA clade encompassing
              Sub-Saharan African isolates (n=13); ii) a derived clade
              encompassing the European CA-MRSA SCCmec-IVc clone (n=185); and
              iii) a novel and genetically distinct clade encompassing MRSA
              SCCmec-IVa isolates (n=19). All isolates in the novel clade were
              PVL negative, but carried remnant parts (8 -12 kb) of the
              PVL-encoding prophage $\Phi$Sa2, and were susceptible to fusidic
              acid and kanamycin/amikacin. Geospatial mapping could link these
              isolates to regions in the Middle East, Asia and South Pacific.
              CONCLUSIONS: This study reports the emergence of a novel CC80
              CA-MRSA sub-lineage, showing that the CC80 lineage is more
              diverse than previously assumed.",
  journal  = "Clin. Microbiol. Infect.",
  month    =  jun,
  year     =  2017,
  keywords = "Antibiotic resistance; CA-MRSA; Epidemiology; Evolution;
              Genetics; Phylogeny;
              SCCmec;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Byrd2017-yt,
  title     = "Staphylococcus aureus and Staphylococcus epidermidis strain
               diversity underlying pediatric atopic dermatitis",
  author    = "Byrd, Allyson L and Deming, Clay and Cassidy, Sara K B and
               Harrison, Oliver J and Ng, Weng-Ian and Conlan, Sean and
               Program, Nisc Comparative Sequencing and Belkaid, Yasmine and
               Segre, Julia A and Kong, Heidi H",
  abstract  = "The heterogeneous course, severity, and treatment responses
               among patients with atopic dermatitis (AD; eczema) highlight the
               complexity of this multifactorial disease. Prior studies have
               used traditional typing methods on cultivated isolates or
               sequenced a bacterial marker gene to study the skin microbial
               communities of AD patients. Shotgun metagenomic sequence
               analysis provides much greater resolution, elucidating multiple
               levels of microbial community assembly ranging from kingdom to
               species and strain-level diversification. We analyzed microbial
               temporal dynamics from a cohort of pediatric AD patients sampled
               throughout the disease course. Species-level investigation of AD
               flares showed greater Staphylococcus aureus predominance in
               patients with more severe disease and Staphylococcus epidermidis
               predominance in patients with less severe disease. At the strain
               level, metagenomic sequencing analyses demonstrated clonal S.
               aureus strains in more severe patients and heterogeneous S.
               epidermidis strain communities in all patients. To investigate
               strain-level biological effects of S. aureus, we topically
               colonized mice with human strains isolated from AD patients and
               controls. This cutaneous colonization model demonstrated S.
               aureus strain--specific differences in eliciting skin
               inflammation and immune signatures characteristic of AD
               patients. Specifically, S. aureus isolates from AD patients with
               more severe flares induced epidermal thickening and expansion of
               cutaneous T helper 2 (TH2) and TH17 cells. Integrating
               high-resolution sequencing, culturing, and animal models
               demonstrated how functional differences of staphylococcal
               strains may contribute to the complexity of AD disease.",
  journal   = "Sci. Transl. Med.",
  publisher = "American Association for the Advancement of Science",
  volume    =  9,
  number    =  397,
  pages     = "eaal4651",
  month     =  jul,
  year      =  2017,
  keywords  = "Staphylococcus;immunology-immunogenomics;fungus;grants;Staphylococcus\_aureus\_genome\_papers;skin\_shotgun\_microbiome",
  language  = "en"
 }

 @ARTICLE{Moradigaravand2017-mi,
  title    = "Evolution of the \textit{Staphylococcus argenteus} {ST2250} Clone
              in Northeastern Thailand Is Linked with the Acquisition of
              {Livestock-Associated} Staphylococcal Genes",
  author   = "Moradigaravand, Danesh and Jamrozy, Dorota and Mostowy, Rafal and
              Anderson, Annaliesa and Nickerson, Emma K and Thaipadungpanit,
              Janjira and Wuthiekanun, Vanaporn and Limmathurotsakul, Direk and
              Tandhavanant, Sarunporn and Wikraiphat, Chanthiwa and Wongsuvan,
              Gumphol and Teerawattanasook, Nittaya and Jutrakul, Yaowaruk and
              Srisurat, Nuttiya and Chaimanee, Prajuab and Eoin West, T and
              Blane, Beth and Parkhill, Julian and Chantratita, Narisara and
              Peacock, Sharon J",
  abstract = "Staphylococcus argenteus is a newly named species previously
              described as a divergent lineage of Staphylococcus aureus that
              has recently been shown to have a global distribution. Despite
              growing evidence of the clinical importance of this species,
              knowledge about its population epidemiology and genomic
              architecture is limited. We used whole-genome sequencing to
              evaluate and compare S. aureus (n = 251) and S. argenteus (n =
              68) isolates from adults with staphylococcal sepsis at several
              hospitals in northeastern Thailand between 2006 and 2013. The
              majority (82\%) of the S. argenteus isolates were of multilocus
              sequence type 2250 (ST2250). S. aureus was more diverse, although
              43\% of the isolates belonged to ST121. Bayesian analysis
              suggested an S. argenteus ST2250 substitution rate of 4.66 (95\%
              confidence interval [CI], 3.12 to 6.38) mutations per genome per
              year, which was comparable to the S. aureus ST121 substitution
              rate of 4.07 (95\% CI, 2.61 to 5.55). S. argenteus ST2250 emerged
              in Thailand an estimated 15 years ago, which contrasts with the
              S. aureus ST1, ST88, and ST121 clades that emerged around 100 to
              150 years ago. Comparison of S. argenteus ST2250 genomes from
              Thailand and a global collection indicated a single introduction
              into Thailand, followed by transmission to local and more distant
              countries in Southeast Asia and further afield. S. argenteus and
              S. aureus shared around half of their core gene repertoire,
              indicating a high level of divergence and providing strong
              support for their classification as separate species. Several
              gene clusters were present in ST2250 isolates but absent from the
              other S. argenteus and S. aureus study isolates. These included
              multiple exotoxins and antibiotic resistance genes that have been
              linked previously with livestock-associated S. aureus, consistent
              with a livestock reservoir for S. argenteus These genes appeared
              to be associated with plasmids and mobile genetic elements and
              may have contributed to the biological success of
              ST2250.IMPORTANCE In this study, we used whole-genome sequencing
              to understand the genome evolution and population structure of a
              systematic collection of ST2250 S. argenteus isolates. A newly
              identified ancestral species of S. aureus, S. argenteus has
              become increasingly known as a clinically important species that
              has been reported recently across various countries. Our results
              indicate that S. argenteus has spread at a relatively rapid pace
              over the past 2 decades across northeastern Thailand and acquired
              multiple exotoxin and antibiotic resistance genes that have been
              linked previously with livestock-associated S. aureus Our
              findings highlight the clinical importance and potential
              pathogenicity of S. argenteus as a recently emerging pathogen.",
  journal  = "MBio",
  volume   =  8,
  number   =  4,
  month    =  jul,
  year     =  2017,
  keywords = "Staphylococcus argenteus; Staphylococcus aureus; antibiotic
              resistance; genomic
              epidemiology;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Weterings2017-wc,
  title    = "Next-generation sequence analysis reveals methicillin-resistance
              transfer to a methicillin-susceptible \textit{Staphylococcus
              aureus} ({MSSA}) strain that subsequently caused a
              methicillin-resistant \textit{Staphylococcus aureus} ({MRSA})
              outbreak: a descriptive study",
  author   = "Weterings, Veronica and Bosch, Thijs and Witteveen, Sandra and
              Landman, Fabian and Schouls, Leo and Kluytmans, Jan",
  abstract = "Resistance to methicillin in Staphylococcus aureus is primarily
              caused by the mecA gene, which is carried on a mobile genetic
              element: the staphylococcal cassette chromosome mec (SCCmec).
              Horizontal transfer of this element is supposed to play an
              important factor in the emergence of new clones of
              methicillin-resistant Staphylococcus aureus (MRSA), but has been
              rarely observed in real-time.In 2012, an outbreak occurred
              involving a healthcare worker (HCW) and three patients all
              carrying a fusidic-acid resistant MRSA strain. The husband of the
              HCW was screened for MRSA carriage, but only a
              methicillin-susceptible S. aureus (MSSA) was detected, which was
              also resistant for fusidic acid. Multiple Locus Variable-number
              Tandem Repeat Analysis (MLVA)-typing showed that both the MSSA
              and the MRSA isolates were MT4053-MC0005. This finding led to the
              hypothesis that the MSSA strain acquired the SCCmec and
              subsequently caused an outbreak. To support this hypothesis,
              next-generation sequencing of the MSSA and MRSA isolates was
              performed.This study showed that the MSSA isolate clustered
              closely with the outbreak isolates based on whole-genome
              multilocus sequence typing (wgMLST) and the single nucleotide
              polymorphism (SNP) analysis, with a distance of 17 genes and 44
              SNPs, respectively. Remarkably, there were relatively large
              differences in mobile genetic elements in strains within and
              between individuals.The limited genetic distance between the MSSA
              and the MRSA isolates in combination with a clear epidemiologic
              link, support the hypothesis that the MSSA isolate acquired a
              SCCmec and that the resulting MRSA strain caused an
              outbreak.IMPORTANCE This report shows that acquisition of the
              staphylococcal cassette chromosome mec (SCCmec) by a
              methicillin-susceptible S. aureus does occur. In this case it
              concerned a healthcare worker (HCW) and this subsequently caused
              an outbreak in a vulnerable group of patients. The whole genome
              sequence based analysis further showed that considerable genetic
              variability occurred in a relatively short time span. These
              findings are important to reconsider the exclusion of HCW with
              regard to control measures for methicillin-resistant S. aureus
              Also the genetic variation in related microorganisms is likely to
              be larger than currently assumed.",
  journal  = "J. Clin. Microbiol.",
  month    =  jul,
  year     =  2017,
  keywords = "Staphylococcus;antibiotics;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{DeFrancesco2017-dv,
  title    = "Genome-wide screen for genes involved in {eDNA} release during
              biofilm formation by \textit{Staphylococcus aureus}",
  author   = "DeFrancesco, Alicia S and Masloboeva, Nadezda and Syed, Adnan K
              and DeLoughery, Aaron and Bradshaw, Niels and Li, Gene-Wei and
              Gilmore, Michael S and Walker, Suzanne and Losick, Richard",
  abstract = "Staphylococcus aureus is a leading cause of both nosocomial and
              community-acquired infection. Biofilm formation at the site of
              infection reduces antimicrobial susceptibility and can lead to
              chronic infection. During biofilm formation, a subset of cells
              liberate cytoplasmic proteins and DNA, which are repurposed to
              form the extracellular matrix that binds the remaining cells
              together in large clusters. Using a strain that forms robust
              biofilms in vitro during growth under glucose supplementation, we
              carried out a genome-wide screen for genes involved in the
              release of extracellular DNA (eDNA). A high-density transposon
              insertion library was grown under biofilm-inducing conditions,
              and the relative frequency of insertions was compared between
              genomic DNA (gDNA) collected from cells in the biofilm and eDNA
              from the matrix. Transposon insertions into genes encoding
              functions necessary for eDNA release were identified by reduced
              representation in the eDNA. On direct testing, mutants of some of
              these genes exhibited markedly reduced levels of eDNA and a
              concomitant reduction in cell clustering. Among the genes with
              robust mutant phenotypes were gdpP, which encodes a
              phosphodiesterase that degrades the second messenger
              cyclic-di-AMP, and xdrA, the gene for a transcription factor
              that, as revealed by RNA-sequencing analysis, influences the
              expression of multiple genes, including many involved in cell
              wall homeostasis. Finally, we report that growth in
              biofilm-inducing medium lowers cyclic-di-AMP levels and does so
              in a manner that depends on the gdpP phosphodiesterase gene.",
  journal  = "Proc. Natl. Acad. Sci. U. S. A.",
  month    =  jul,
  year     =  2017,
  keywords = "Staphylococcus aureus; biofilm; cyclic-di-AMP;
              eDNA;Staphylococcus;tn-seq;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Putonti2017-qz,
  title    = "Draft Genome Sequences of Two {ATCC} \textit{Staphylococcus
              aureus} subsp. \textit{aureus} Strains",
  author   = "Putonti, Catherine and Kalesinskas, Laurynas and Cudone, Evan and
              Engelbrecht, Kathleen C and Koenig, David W and Wolfe, Alan J",
  abstract = "Draft genome sequences for Staphylococcus aureus subsp. aureus
              Rosenbach ATCC 14458 and ATCC 27217 strains were investigated.
              The genome sizes were 2,880,761 bp and 2,759,100 bp,
              respectively. Strain ATCC 14458 was assembled into 39 contigs,
              including 3 plasmids, and strain ATCC 27217 was assembled into 25
              contigs, including 2 plasmids.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  27,
  month    =  jul,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Sahibzada2017-gl,
  title    = "Transmission of highly virulent community-associated {MRSA}
              {ST93} and livestock-associated {MRSA} {ST398} between humans and
              pigs in Australia",
  author   = "Sahibzada, S and Abraham, S and Coombs, G W and Pang, S and
              Hern{\'a}ndez-Jover, M and Jordan, D and Heller, J",
  abstract = "Pigs have been recognised as a reservoir of livestock associated
              methicillin-resistant Staphylococcus aureus (LA-MRSA) in Europe,
              Asia and North America. However, little is known about the
              presence and distribution of MRSA in the Australian pig
              population and pig industry. This study describes the presence,
              distribution and molecular characteristics of the human adapted
              Australian CA-MRSA ST93 isolated from pigs, people, and the
              environment within a piggery. Isolates were subjected to
              antibiotic susceptibility testing, DNA microarray, whole genome
              sequencing, multi locus sequence typing, virulence and resistance
              gene characterization and phylogenetic analysis. MRSA were
              isolated from 60\% (n = 52) of farm workers where 84\% of
              isolates returned ST93 and the rest ST398. Of the thirty-one pig
              isolates tested further, an equal number of ST398 and ST93 (15
              each) and one as ST30-V were identified. Four of six
              environmental isolates were identified as ST93 and two as ST398.
              This study has identified for the first time in Australia the
              occurrence of CA-MRSA ST93 and LA-MRSA ST398 amongst farm
              workers, pigs, and the farm environment. Comparative genome
              analysis indicates that ST398 is likely to have been introduced
              into Australia from Europe or North America. This study also
              reports the first linezolid resistant MRSA isolated in Australia.",
  journal  = "Sci. Rep.",
  volume   =  7,
  number   =  1,
  pages    = "5273",
  month    =  jul,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Ward2016-el,
  title    = "Identification of source and sink populations for the emergence
              and global spread of the {East-Asia} clone of
              community-associated {MRSA}",
  author   = "Ward, Melissa J and Goncheva, Mariya and Richardson, Emily and
              McAdam, Paul R and Raftis, Emma and Kearns, Angela and Daum,
              Robert S and David, Michael Z and Lauderdale, Tsai Ling and
              Edwards, Giles F and Nimmo, Graeme R and Coombs, Geoffrey W and
              Huijsdens, Xander and Woolhouse, Mark E J and Fitzgerald, J Ross",
  abstract = "BACKGROUND: Our understanding of the factors influencing the
              emergence, dissemination and global distribution of epidemic
              clones of bacteria is limited. ST59 is a major epidemic clone of
              community-associated MRSA in East Asia, responsible for extensive
              morbidity and mortality, but has a much lower prevalence in other
              parts of the world. The geographic origin of ST59 and its
              international routes of dissemination are unclear and disputed in
              the literature. RESULTS: To investigate the origin and spread of
              the ST59 clone, we obtained whole genome sequences of isolates
              from four continents, sampled over more than a decade, and
              carried out a time-scaled phylogeographic analysis. We discover
              that two distinct ST59 clades emerged concurrently, in East Asia
              and the USA, but underwent clonal expansion at different times.
              The East Asia clade was strongly enriched for gene determinants
              associated with antibiotic resistance, consistent with regional
              differences in antibiotic usage. Both clones spread independently
              to Australia and Europe, and we found evidence of the persistence
              of multi-drug resistance following export from East Asia. Direct
              transfer of strains between Taiwan and the USA was not observed
              in either direction, consistent with geographic niche exclusion.
              CONCLUSIONS: Our results resolve a longstanding controversy
              regarding the origin of the ST59 clone, revealing the major
              global source and sink populations and routes for the spread of
              multi-drug resistant clones. Additionally, our findings indicate
              that diversification of the accessory genome of epidemic clones
              partly reflects region-specific patterns of antibiotic usage,
              which may influence bacterial fitness after transmission to
              different geographic locations.",
  journal  = "Genome Biol.",
  volume   =  17,
  number   =  1,
  pages    = "160",
  month    =  jul,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Hayden2016-uc,
  title    = "Chlorhexidine and Mupirocin Susceptibility of
              {Methicillin-Resistant} Staphylococcus aureus Isolates in the
              {REDUCE-MRSA} Trial",
  author   = "Hayden, Mary K and Lolans, Karen and Haffenreffer, Katherine and
              Avery, Taliser R and Kleinman, Ken and Li, Haiying and Kaganov,
              Rebecca E and Lankiewicz, Julie and Moody, Julia and Septimus,
              Edward and Weinstein, Robert A and Hickok, Jason and Jernigan,
              John and Perlin, Jonathan B and Platt, Richard and Huang, Susan S",
  abstract = "Whether targeted or universal decolonization strategies for the
              control of methicillin-resistant Staphylococcus aureus (MRSA)
              select for resistance to decolonizing agents is unresolved. The
              REDUCE-MRSA trial (ClinicalTrials registration no. NCT00980980)
              provided an opportunity to investigate this question. REDUCE-MRSA
              was a 3-arm, cluster-randomized trial of either screening and
              isolation without decolonization, targeted decolonization with
              chlorhexidine and mupirocin, or universal decolonization without
              screening to prevent MRSA infection in intensive-care unit (ICU)
              patients. Isolates from the baseline and intervention periods
              were collected and tested for susceptibility to chlorhexidine
              gluconate (CHG) by microtiter dilution; mupirocin susceptibility
              was tested by Etest. The presence of the qacA or qacB gene was
              determined by PCR and DNA sequence analysis. A total of 3,173
              isolates were analyzed; 2 were nonsusceptible to CHG (MICs, 8
              $\mu$g/ml), and 5/814 (0.6\%) carried qacA or qacB At baseline,
              7.1\% of MRSA isolates expressed low-level mupirocin resistance,
              and 7.5\% expressed high-level mupirocin resistance. In a
              mixed-effects generalized logistic regression model, the odds of
              mupirocin resistance among clinical MRSA isolates or MRSA
              isolates acquired in an ICU in intervention versus baseline
              periods did not differ across arms, although estimates were
              imprecise due to small numbers. Reduced susceptibility to
              chlorhexidine and carriage of qacA or qacB were rare among MRSA
              isolates in the REDUCE-MRSA trial. The odds of mupirocin
              resistance were no different in the intervention versus baseline
              periods across arms, but the confidence limits were broad, and
              the results should be interpreted with caution.",
  journal  = "J. Clin. Microbiol.",
  volume   =  54,
  number   =  11,
  pages    = "2735--2742",
  month    =  nov,
  year     =  2016,
  keywords = "Staphylococcus;chlorhexidine;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Sun2017-ib,
  title    = "Characterization of a {PVL-negative} community-acquired
              methicillin-resistant Staphylococcus aureus strain of sequence
              type 88 in China",
  author   = "Sun, Lu and Wu, Dandan and Chen, Yan and Wang, Qian and Wang,
              Haiping and Yu, Yunsong",
  abstract = "Sequence type 88 community-acquired methicillin-resistant
              Staphylococcus aureus (CA-MRSA) strain SR434, isolated from an
              outpatient with skin and soft tissue infection, was subjected to
              whole genome sequencing, antimicrobial susceptibility testing,
              mouse skin infection model and hemolysis analysis to identify its
              virulence and resistance determinants. MRSA strain SR434 is
              resistant to clindamycin, erythromycin and fosfomycin. Four
              plasmids with resistance genes were identified in this strain,
              including a 20,658bp blaZ-carrying plasmid, a 2473bp
              ermC-carrying plasmid, a 2622bp fosB7-carrying plasmid (86\%
              identity with plasmid in a ST2590 MRSA strain) and a 4817bp
              lnuA-carrying plasmid (99\% identity with pLNU4 from bovine
              coagulase-nagetive Staphylococci). This strain contains
              staphylococcal cassette chromosome mec type IV and does not
              contain arginine catabolic mobile element or
              Panton-Valentine-Leukocidin. SR434 harbors genomic islands
              $\nu$Sa$\alpha$, $\nu$Sa$\beta$, $\nu$Sa$\gamma$ and $\Phi$Sa3
              and pathogenicity islands $\nu$Sa2 that carries genes encoding
              toxic shock syndrome toxin 1, superantigen enterotoxin C and
              superantigen enterotoxin L. Mouse skin infection model results
              show that SR434 had similar virulence potential causing invasive
              skin infection as a PVL-negative epidemic Korea clone HL1 (ST72).
              CA-MRSA strain of ST88 lineage might be a great concern for its
              high virulence. PVL has limited contribution to virulence
              phenotype among this lineage.",
  journal  = "Int. J. Med. Microbiol.",
  month    =  jul,
  year     =  2017,
  keywords = "CA-MRSA; Genome; High virulence;
              ST88;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Harkins2017-uw,
  title    = "Methicillin-resistant Staphylococcus aureus emerged long before
              the introduction of methicillin into clinical practice",
  author   = "Harkins, Catriona P and Pichon, Bruno and Doumith, Michel and
              Parkhill, Julian and Westh, Henrik and Tomasz, Alexander and de
              Lencastre, Herminia and Bentley, Stephen D and Kearns, Angela M
              and Holden, Matthew T G",
  abstract = "BACKGROUND: The spread of drug-resistant bacterial pathogens
              poses a major threat to global health. It is widely recognised
              that the widespread use of antibiotics has generated selective
              pressures that have driven the emergence of resistant strains.
              Methicillin-resistant Staphylococcus aureus (MRSA) was first
              observed in 1960, less than one year after the introduction of
              this second generation beta-lactam antibiotic into clinical
              practice. Epidemiological evidence has always suggested that
              resistance arose around this period, when the mecA gene encoding
              methicillin resistance carried on an SCCmec element, was
              horizontally transferred to an intrinsically sensitive strain of
              S. aureus. RESULTS: Whole genome sequencing a collection of the
              first MRSA isolates allows us to reconstruct the evolutionary
              history of the archetypal MRSA. We apply Bayesian phylogenetic
              reconstruction to infer the time point at which this early MRSA
              lineage arose and when SCCmec was acquired. MRSA emerged in the
              mid-1940s, following the acquisition of an ancestral type I
              SCCmec element, some 14 years before the first therapeutic use of
              methicillin. CONCLUSIONS: Methicillin use was not the original
              driving factor in the evolution of MRSA as previously thought.
              Rather it was the widespread use of first generation beta-lactams
              such as penicillin in the years prior to the introduction of
              methicillin, which selected for S. aureus strains carrying the
              mecA determinant. Crucially this highlights how new drugs,
              introduced to circumvent known resistance mechanisms, can be
              rendered ineffective by unrecognised adaptations in the bacterial
              population due to the historic selective landscape created by the
              widespread use of other antibiotics.",
  journal  = "Genome Biol.",
  volume   =  18,
  number   =  1,
  pages    = "130",
  month    =  jul,
  year     =  2017,
  keywords = "Antibiotic resistance; MRSA; Staphylococcus
              aureus;Staphylococcus;antibiotics;transmission-epidemiology;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Arias2017-iu,
  title    = "Molecular Epidemiology and Phylogenomics of
              \textit{Staphylococcus aureus} Bacteremia in {Latin-America}: A
              Prospective Cohort Multicenter Study in Nine Countries",
  author   = "Arias, Cesar A and Reyes, Jinnethe and Carvajal, Lina Paola and
              Rincon, Sandra and Diaz, Lorena and Panesso, Diana and Ibarra,
              Gabriel and Rios, Rafael and Munita, Jose M and Salles, Mauro J
              and Alvarez-Moreno, Carlos and Labarca, Jaime and Garcia,
              Coralith and Luna, Carlos M and Mejia-Villatoro, Carlos and
              Zurita, Jeannete and Guzman-Blanco, Manuel and Rodriguez-Noriega,
              Eduardo and Narechania, Apurva and Rojas, Laura J and Planet,
              Paul J and Weinstock, George M and Gotuzzo, Eduardo and Seas,
              Carlos",
  abstract = "Staphylococcus aureus are important pathogens causing a spectrum
              of diseases ranging from mild skin and soft tissue infections to
              life-threatening conditions. Bloodstream infections are
              particularly important and the treatment approach is complicated
              by the presence of methicillin resistance among S. aureus
              isolates (MRSA). Emergence of new genetic lineages of MRSA has
              occurred in Latin America (LA) with the rise and dissemination of
              the community-associated USA300 Latin American Variant
              (USA300-LV). Here, we prospectively characterized bloodstream
              MRSA recovered from selected hospitals in 9 Latin American
              countries. All isolates were typed by pulsed field gel
              electrophoresis (PFGE) and subjected to antibiotic susceptibility
              testing. Whole genome sequencing was performed in 96 MRSA
              representatives. MRSA represented 45\% of all isolates (out of
              1,185 S. aureus). The majority of MRSA isolates belonged to
              clonal cluster (CC) 5. In Colombia and Ecuador, most isolates
              ($\geq$ 72\%) belonged to the USA300-LV lineage (CC8).
              Phylogenetic reconstructions indicated that MRSA isolates from
              participating hospitals belonged to three major clades. Clade A
              grouped isolates with ST5, ST105, and ST1011 (mostly SCCmec I and
              II). Clade B included ST8, ST88, ST97, and ST72 strains (SCCmec
              IV, subtypes a, b, and c/E) and clade C grouped mostly
              Argentinian MRSA belonging to ST30. In summary, CC5 MRSA was
              prevalent in bloodstream infections in LA with the exception of
              Colombia and Ecuador where USA300-LV is now the dominant lineage.
              Clonal replacement appears to be a common phenomenon and
              continuous surveillance is crucial to identify changes in the
              molecular epidemiology of MRSA.",
  journal  = "Antimicrob. Agents Chemother.",
  month    =  jul,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Hung2016-fz,
  title    = "Molecular Evolutionary Pathways toward Two Successful
              {Community-Associated} but {Multidrug-Resistant} {ST59}
              {Methicillin-Resistant} Staphylococcus aureus Lineages in Taiwan:
              Dynamic Modes of Mobile Genetic Element Salvages",
  author   = "Hung, Wei-Chun and Wan, Tsai-Wen and Kuo, Yu-Chia and Yamamoto,
              Tatsuo and Tsai, Jui-Chang and Lin, Yu-Tzu and Hsueh, Po-Ren and
              Teng, Lee-Jene",
  abstract = "Clonal complex 59 (CC59) Staphylococcus aureus in Taiwan includes
              both methicillin-susceptible S. aureus (MSSA) and
              methicillin-resistant S. aureus (MRSA). As the most prominent
              community-associated MRSA (CA-MRSA) in Taiwan, CC59 has two major
              clones characterized as PVL-negative SCCmec IV (carrying the
              staphylococcal cassette chromosome mec IV but Panton-Valentine
              leukocidin-negative) and PVL-positive SCCmec V (5C2\&5). We
              investigated the drug resistance, phylogeny and the distribution
              and sequence variation of SCCmec, staphylococcal bacteriophage
              $\varphi$SA3, genomic island $\nu$Sa$\beta$ and MES (an
              enterococcal mobile genetic element conferring multidrug
              resistance) in 195 CC59 S. aureus. Sequencing and PCR mapping
              revealed that all of the CC59/SCCmec V (5C2\&5) MRSA strains had
              acquired MESPM1 or its segregants, and obtained a
              $\varphi$SA3-related fragment in $\nu$Sa$\beta$. In contrast,
              MES6272-2 and MES4578, which showed gentamicin resistance that
              was not encoded by MESPM1, were dominant in SCCmec IVg MRSA.
              Translocation of a whole $\varphi$SA3 into $\nu$Sa$\beta$ instead
              of only a $\varphi$SA3-related fragment was common in SCCmec IVg
              MRSA. However, the non-subtype-g SCCmec IV MRSA (SCCmec IVa is
              the major) still carried MES and $\nu$Sa$\beta$ structures
              similar to those in SCCmec V (5C2\&5) MRSA. A minimum spanning
              tree constructed by multiple-locus variable-number tandem repeat
              analysis revealed that SCCmec IVg MRSA and SCCmec V (5C2\&5) MRSA
              grouped respectively in two major clades. The CC59 MSSA was
              equally distributed among the two clades, while the non-subtype-g
              SCCmec IV MRSA mostly clustered with SCCmec V (5C2\&5) MRSA. Our
              findings strongly suggest that CC59 MSSA acquired divergent
              mobile genetic elements and evolved to SCCmec IVg MRSA and SCCmec
              V (5C2\&5) MRSA/non-subtype-g SCCmec IV MRSA independently. The
              evolutionary history of CC59 S. aureus explains how mobile
              genetic elements increase the antimicrobial resistance and
              virulence and contribute to the success of CA-MRSA in Taiwan.",
  journal  = "PLoS One",
  volume   =  11,
  number   =  9,
  pages    = "e0162526",
  month    =  sep,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Werth2017-wu,
  title    = "Emergence of dalbavancin non-susceptible, vancomycin-intermediate
              Staphylococcus aureus ({VISA}) after treatment of {MRSA} central
              line-associated bloodstream infection with a dalbavancin- and
              vancomycin-containing regimen",
  author   = "Werth, Brian J and Jain, Rupali and Hahn, Andrew and Cummings,
              Lisa and Weaver, Tatiana and Waalkes, Adam and Sengupta, Dhruba
              and Salipante, Stephen J and Rakita, Robert M and Butler-Wu,
              Susan M",
  abstract = "OBJECTIVES: Dalbavancin is a long-acting lipoglycopeptide with
              activity against Gram-positives, including methicillin-resistant
              Staphylococcus aureus(MRSA). The potential for lipoglycopeptides,
              with half-lives greater than one-week, to select for resistance
              is unknown. Here we explore a case of MRSA central
              line-associated blood stream infection in which dalbavancin and
              vancomycin non-susceptibility emerged in a urine isolate
              collected after the patient was treated with vancomycin and
              dalbavancin sequentially. METHODS: Isolates from blood and urine
              underwent susceptibility testing, and whole genome sequencing
              (WGS). The blood isolate was subjected to successive passage in
              vitro in the presence of escalating dalbavancin concentrations
              and the emergent isolate was subjected to repeat susceptibility
              testing and WGS. RESULTS: The blood isolate was fully susceptible
              to vancomycin, however, MICs of the urine isolate to dalbavancin,
              vancomycin, telavancin and daptomycin were $\geq$4-fold higher
              than the blood-derived strain. Both strains were
              indistinguishable by spa and variable number tandem repeat (VNTR)
              typing, and WGS revealed only 7 variants, indicating clonality.
              Four variants affected genes, including a non-synonymous change
              in yvqF, which has been implicated in glycopeptide resistance.
              Vancomycin and dalbavancin non-susceptibility emerged in the
              blood isolate after successive passage in vitro in the presence
              of dalbavancin, and WGS identified a single non-synonymous
              variant in yvqF. CONCLUSIONS: This is the first case in which
              VISA has emerged in the context of a dalbavancin-containing
              regimen. The selection for cross-resistance to vancomycin in
              vitro by dalbavancin exposure alone is troubling. Clinicians
              should be aware of the possibility for emergence of dalbavancin
              non-susceptibility and glycopeptide cross-resistance arising
              following therapy.",
  journal  = "Clin. Microbiol. Infect.",
  month    =  aug,
  year     =  2017,
  keywords = "CLABSI; cross-resistance; glycopeptide resistance;
              lipoglycopeptide;Staphylococcus;confirmed\_SA-resistance-mutation;Papers\_for\_Michelle;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Hau2017-ag,
  title    = "Complete Genome Sequence of {Livestock-Associated}
              {Methicillin-Resistant} \textit{Staphylococcus aureus} Sequence
              Type 398 Isolated from Swine in the United States",
  author   = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and Frana,
              Timothy S and Nicholson, Tracy L",
  abstract = "Methicillin-resistant Staphylococcus aureus (MRSA) colonizes and
              causes disease in many animal species. Livestock-associated MRSA
              (LA-MRSA) isolates are represented by isolates of the sequence
              type 398 (ST398). These isolates are considered to be livestock
              adapted. This report provides the complete genome sequence of one
              swine-associated LA-MRSA ST398 isolate from the United States.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  32,
  month    =  aug,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Hau2017-vj,
  title    = "Complete Genome Sequence of a {Livestock-Associated}
              {Methicillin-Resistant} \textit{Staphylococcus aureus} Sequence
              Type 5 Isolate from the United States",
  author   = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and Frana,
              Timothy S and Nicholson, Tracy L",
  abstract = "Livestock-associated methicillin-resistant Staphylococcus aureus
              (LA-MRSA) may be the largest MRSA reservoir outside the hospital
              setting. One concern with LA-MRSA is the acquisition of novel
              mobile genetic elements by these isolates. Here, we report the
              complete genome sequence of a swine LA-MRSA sequence type 5
              isolate from the United States.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  32,
  month    =  aug,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Harrison2017-fy,
  title    = "Genomic surveillance reveals low prevalence of
              livestock-associated methicillin-resistant Staphylococcus aureus
              in the East of England",
  author   = "Harrison, Ewan M and Coll, Francesc and Toleman, Michelle S and
              Blane, Beth and Brown, Nicholas M and T{\"o}r{\"o}k, M Estee and
              Parkhill, Julian and Peacock, Sharon J",
  abstract = "Livestock-associated methicillin-resistant Staphylococcus aureus
              (LA-MRSA) is an emerging problem in many parts of the world.
              LA-MRSA has been isolated previously from animals and humans in
              the United Kingdom (UK), but the prevalence is unknown. The aim
              of this study was to determine the prevalence and to describe the
              molecular epidemiology of LA-MRSA isolated in the East of England
              (broadly Cambridge and the surrounding area). We accessed whole
              genome sequence data for 2,283 MRSA isolates from 1,465 people
              identified during a 12-month prospective study between 2012 and
              2013 conducted in the East of England, United Kingdom. This
              laboratory serves four hospitals and 75 general practices. We
              screened the collection for multilocus sequence types (STs) and
              for host specific resistance and virulence factors previously
              associated with LA-MRSA. We identified 13 putative LA-MRSA
              isolates from 12 individuals, giving an estimated prevalence of
              0.82\% (95\% CI 0.47\% to 1.43\%). Twelve isolates were mecC-MRSA
              (ten CC130, one ST425 and one ST1943) and single isolate was
              ST398. Our data demonstrate a low burden of LA-MRSA in the East
              of England, but the detection of mecC-MRSA and ST398 indicates
              the need for vigilance. Genomic surveillance provides a mechanism
              to detect and track the emergence and spread of MRSA clones of
              human importance.",
  journal  = "Sci. Rep.",
  volume   =  7,
  number   =  1,
  pages    = "7406",
  month    =  aug,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Caldelari2017-tn,
  title    = "Complete Genome Sequence and Annotation of the
              \textit{Staphylococcus aureus} Strain {HG001}",
  author   = "Caldelari, Isabelle and Chane-Woon-Ming, B{\'e}atrice and Noirot,
              C{\'e}line and Moreau, Karen and Romby, Pascale and Gaspin,
              Christine and Marzi, Stefano",
  abstract = "Staphylococcus aureus is an opportunistic Gram-positive pathogen
              responsible for a wide range of infections from minor skin
              abscesses to life-threatening diseases. Here, we report the draft
              genome assembly and current annotation of the HG001 strain, a
              derivative of the RN1 (NCT8325) strain with restored rbsU (a
              positive activator of SigB).",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  32,
  month    =  aug,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Grinberg2017-ax,
  title    = "Genomic epidemiology of methicillin-susceptible Staphylococcus
              aureus across colonisation and skin and soft tissue infection",
  author   = "Grinberg, Alex and Biggs, Patrick J and Zhang, Ji and Ritchie,
              Stephen and Oneroa, Zachary and O'Neil, Charlotte and Karkaba,
              Ali and Velathanthiri, Niluka S and Coombs, Geoffrey W",
  abstract = "OBJECTIVES: Staphylococcus aureus skin and soft tissue infection
              (Sa-SSTI) places a significant burden on healthcare systems. New
              Zealand has a high incidence of Sa-SSTI, and here most morbidity
              is caused by a polyclonal methicillin-susceptible (MSSA)
              population. However, MSSA also colonise asymptomatically the
              cornified epithelia of approximately 20\% of the population, and
              their divide between commensalism and pathogenicity is poorly
              understood. We aimed to see whether MSSA is genetically
              differentiated across asymptomatic colonisation and SSTI; and
              given the close interactions between people and pets, whether
              strains isolated from pets differ from human strains. METHODS: We
              compared the genomes of contemporaneous asymptomatic colonisation
              and clinical MSSA isolates obtained in New Zealand from humans
              and pets. RESULTS: Core and accessory genome comparisons revealed
              a homogeneous bacterial population across colonisation, disease,
              humans, and pets. The rate of MSSA colonisation in dogs was
              comparatively low (5.4\%). CONCLUSIONS: In New Zealand, most
              Sa-SSTI morbidity is caused by a random sample of the colonising
              MSSA population, consistent with the opportunistic infection
              paradigm rather than a model distinguishing pathogenic from
              innocuous strains. Thus, studies of host factors determining
              colonisation and immune-escape may be more beneficial than
              comparative virulence studies. Contact with house-hold pets may
              pose low zoonotic risk.",
  journal  = "J. Infect.",
  month    =  aug,
  year     =  2017,
  keywords = "SSTI; Skin and soft tissue infection; Staphylococcus aureus;
              Whole genome sequencing;
              Zoonoses;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Recker2017-lp,
  title    = "Clonal differences in Staphylococcus aureus
              bacteraemia-associated mortality",
  author   = "Recker, Mario and Laabei, Maisem and Toleman, Michelle S and
              Reuter, Sandra and Saunderson, Rebecca B and Blane, Beth and
              T{\"o}r{\"o}k, M Estee and Ouadi, Khadija and Stevens, Emily and
              Yokoyama, Maho and Steventon, Joseph and Thompson, Luke and
              Milne, Gregory and Bayliss, Sion and Bacon, Leann and Peacock,
              Sharon J and Massey, Ruth C",
  abstract = "The bacterium Staphylococcus aureus is a major human pathogen for
              which the emergence of antibiotic resistance is a global public
              health concern. Infection severity, and in particular
              bacteraemia-associated mortality, has been attributed to several
              host-related factors, such as age and the presence of
              comorbidities. The role of the bacterium in infection severity is
              less well understood, as it is complicated by the multifaceted
              nature of bacterial virulence, which has so far prevented a
              robust mapping between genotype, phenotype and infection outcome.
              To investigate the role of bacterial factors in contributing to
              bacteraemia-associated mortality, we phenotyped a collection of
              sequenced clinical S. aureus isolates from patients with
              bloodstream infections, representing two globally important
              clonal types, CC22 and CC30. By adopting a genome-wide
              association study approach we identified and functionally
              verified several genetic loci that affect the expression of
              cytolytic toxicity and biofilm formation. By analysing the pooled
              data comprising bacterial genotype and phenotype together with
              clinical metadata within a machine-learning framework, we found
              significant clonal differences in the determinants most
              predictive of poor infection outcome. Whereas elevated cytolytic
              toxicity in combination with low levels of biofilm formation was
              predictive of an increased risk of mortality in infections by
              strains of a CC22 background, these virulence-specific factors
              had little influence on mortality rates associated with CC30
              infections. Our results therefore suggest that different clones
              may have adopted different strategies to overcome host responses
              and cause severe pathology. Our study further demonstrates the
              use of a combined genomics and data analytic approach to enhance
              our understanding of bacterial pathogenesis at the individual
              level, which will be an important step towards personalized
              medicine and infectious disease management.A genome-wide
              association approach identifies differential biofilm and
              virulence attributes associated with mortality in two
              Staphylococcus aureus clonal complexes.",
  journal  = "Nat Microbiol",
  month    =  aug,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Kleinert2017-cf,
  title    = "Influence of {IS\textit{256}} on genome variability and formation
              of {SCV} in \textit{Staphylococcus aureus}",
  author   = "Kleinert, Franziska and Kallies, Ren{\'e} and Hort, Michael and
              Zweynert, Annegret and Szekat, Christiane and Nagel, Michael and
              Bierbaum, Gabriele",
  abstract = "Staphylococcus aureus has acquired resistance to nearly all
              antibiotics used in clinical practice. Whereas some resistance
              mechanisms are conferred by uptake of resistance genes, others
              evolve by mutation. Here, the insertion sequence 256 (IS256) has
              been shown to play a role, e. g. in S. aureus strains displaying
              intermediate resistance to vancomycin (VISA).To characterize the
              IS256 insertion sites in the genomes of two closely related
              sequence type (ST) 247 VISA strains, all insertions were mapped
              in both VISA and a susceptible control strain. The results showed
              that the three ST247 strains contained the highest number so far
              of IS256 insertions of all sequenced S. aureus strains.
              Furthermore, in contrast to the other IS elements in these
              genomes, the IS256 insertion sites were not identical in the
              closely related strains, indicating a high transposition
              frequency of IS256 When IS256 was introduced into a laboratory
              strain which was then cultured in the presence of antibiotics, it
              was possible to isolate small colony variants (SCV) that
              possessed IS256 insertions in guaA and hemY that displayed
              increased resistance to vancomycin and aminoglycosides,
              respectively. For these clones, a very rapid reversion to the
              wild type was observed, that resembled the fast reversion of
              clinical SCV. The reversion was caused by excision of IS256 in a
              small number of fast growing clones that quickly outcompeted the
              SCVs in broth cultures. In conclusion, the presence of IS256
              confers a strong genomic plasticity that is useful for adaptation
              to antibiotic stress.",
  journal  = "Antimicrob. Agents Chemother.",
  month    =  jun,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Panthee2017-to,
  title    = "Genomic analysis of vancomycin-resistant Staphylococcus aureus
              {VRS3b} and its comparison with other {VRSA} isolates",
  author   = "Panthee, Suresh and Hamamoto, Hiroshi and Paudel, Atmika and
              Sekimizu, Kazuhisa",
  abstract = "High-level vancomycin resistance among Staphylococcus aureus
              poses a grave threat to global health as the treatment options
              for this pathogen are very limited. A detailed evaluation of the
              genetic background of vancomycin-resistant S. aureus (VRSA) is
              expected to facilitate the understanding of its origin and
              pathogenicity. In this study, we performed the genetic analysis
              of the clinical VRSA isolates and identified the genetic basis of
              resistance to multiple antibiotics among these strains, based on
              the available draft genome sequences. In addition, we generated
              the draft genome of the strain VRS3b, which was considered to be
              same as VRS3a based on its isolation from the same patient. We
              found that strain VRS3b did not harbor the genes responsible for
              tetracycline and gentamicin, which was further confirmed by the
              sensitivity towards these antibiotics. Our results suggest that
              the strains VRS3a and VRS3b are different from the view of
              antibiotic resistance and highlight the possibility of generation
              of two distinct VRSA strains from the same patient.",
  journal  = "Drug Discov. Ther.",
  month    =  apr,
  year     =  2017,
  keywords = "Staphylococcus aureus; genomics; methicillin; resistance;
              vancomycin;Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Chow2017-ed,
  title    = "{MRSA} Transmission Dynamics Among Interconnected Acute,
              {Intermediate-Term}, and {Long-Term} Healthcare Facilities in
              Singapore",
  author   = "Chow, Angela and Lim, Vanessa W and Khan, Ateeb and Pettigrew,
              Kerry and Lye, David C B and Kanagasabai, Kala and Phua, Kelvin
              and Krishnan, Prabha and Ang, Brenda and Marimuthu, Kalisvar and
              Hon, Pei-Yun and Koh, Jocelyn and Leong, Ian and Parkhill, Julian
              and Hsu, Li-Yang and Holden, Matthew T G",
  abstract = "Background: Methicillin-resistant Staphylococcus aureus (MRSA) is
              the most common healthcare-associated multidrug-resistant
              organism. Despite the interconnectedness between acute care
              hospitals (ACHs) and intermediate- and long-term care facilities
              (ILTCFs), the transmission dynamics of MRSA between healthcare
              settings is not well understood. Methods: We conducted a
              cross-sectional study in a network comprising an ACH and 5
              closely affiliated ILTCFs in Singapore. A total of 1700
              inpatients were screened for MRSA over a 6-week period in 2014.
              MRSA isolates underwent whole-genome sequencing, with a pairwise
              single-nucleotide polymorphism (Hamming distance) cutoff of 60
              core genome single-nucleotide polymorphisms used to define recent
              transmission clusters (clades) for the 3 major clones. Results:
              MRSA prevalence was significantly higher in intermediate-term
              (29.9\%) and long-term (20.4\%) care facilities than in the ACH
              (11.8\%) (P < .001). The predominant clones were sequence type
              [ST] 22 (n = 183; 47.8\%), ST45 (n = 129; 33.7\%), and ST239 (n =
              26; 6.8\%), with greater diversity of STs in ILTCFs relative to
              the ACH. A large proportion of the clades in ST22 (14 of 21
              clades; 67\%) and ST45 (7 of 13; 54\%) included inpatients from
              the ACH and ILTCFs. The most frequent source of the interfacility
              transmissions was the ACH (n = 28 transmission events; 36.4\%).
              Conclusions: MRSA transmission dynamics between the ACH and
              ILTCFs were complex. The greater diversity of STs in ILTCFs
              suggests that the ecosystem in such settings might be more
              conducive for intrafacility transmission events. ST22 and ST45
              have successfully established themselves in ILTCFs. The
              importance of interconnected infection prevention and control
              measures and strategies cannot be overemphasized.",
  journal  = "Clin. Infect. Dis.",
  volume   =  64,
  number   = "suppl\_2",
  pages    = "S76--S81",
  month    =  may,
  year     =  2017,
  keywords = "MRSA; intermediate-care facilities; long-term care facilities.;
              transmission; whole-genome
              sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Canovas2016-ts,
  title    = "{Cross-Talk} between Staphylococcus aureus and Other
              Staphylococcal Species via the agr Quorum Sensing System",
  author   = "Canovas, Jaime and Baldry, Mara and Bojer, Martin S and Andersen,
              Paal S and Grzeskowiak, Piotr K and Stegger, Marc and Damborg,
              Peter and Olsen, Christian A and Ingmer, Hanne",
  abstract = "Staphylococci are associated with both humans and animals. While
              most are non-pathogenic colonizers, Staphylococcus aureus is an
              opportunistic pathogen capable of causing severe infections. S.
              aureus virulence is controlled by the agr quorum sensing system
              responding to secreted auto-inducing peptides (AIPs) sensed by
              AgrC, a two component histidine kinase. agr loci are found also
              in other staphylococcal species and for Staphylococcus
              epidermidis, the encoded AIP represses expression of agr
              regulated virulence genes in S. aureus. In this study we aimed to
              better understand the interaction between staphylococci and S.
              aureus, and show that this interaction may eventually lead to the
              identification of new anti-virulence candidates to target S.
              aureus infections. Here we show that culture supernatants of 37
              out of 52 staphylococcal isolates representing 17 different
              species inhibit S. aureus agr. The dog pathogen, Staphylococcus
              schleiferi, expressed the most potent inhibitory activity and was
              active against all four agr classes found in S. aureus. By
              employing a S. aureus strain encoding a constitutively active AIP
              receptor we show that the activity is mediated via agr.
              Subsequent cloning and heterologous expression of the S.
              schleiferi AIP in S. aureus demonstrated that this molecule was
              likely responsible for the inhibitory activity, and further proof
              was provided when pure synthetic S. schleiferi AIP was able to
              completely abolish agr induction of an S. aureus reporter strain.
              To assess impact on S. aureus virulence, we co-inoculated S.
              aureus and S. schleiferi in vivo in the Galleria mellonella wax
              moth larva, and found that expression of key S. aureus virulence
              factors was abrogated. Our data show that the S. aureus agr locus
              is highly responsive to other staphylococcal species suggesting
              that agr is an inter-species communication system. Based on these
              results we speculate that interactions between S. aureus and
              other colonizing staphylococci will significantly influence the
              ability of S. aureus to cause infection, and we propose that
              other staphylococci are potential sources of compounds that can
              be applied as anti-virulence therapy for combating S. aureus
              infections.",
  journal  = "Front. Microbiol.",
  volume   =  7,
  pages    = "1733",
  month    =  nov,
  year     =  2016,
  keywords = "Staphylococcus aureus; Staphylococcus schleiferi; agr;
              anti-virulence therapy; auto-inducing peptide; cross-talk; quorum
              sensing; quorum sensing
              inhibition;Staphylococcus;Papers\_for\_Michelle;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Roe2016-uc,
  title    = "Whole genome {SNP} typing to investigate methicillin-resistant
              \textit{Staphylococcus aureus} carriage in a health-care provider
              as the source of multiple surgical site infections",
  author   = "Roe, Chandler C and Horn, Kimberly S and Driebe, Elizabeth M and
              Bowers, Jolene and Terriquez, Joel A and Keim, Paul and
              Engelthaler, David M",
  abstract = "BACKGROUND: Prevention of nosocomial transmission of infections
              is a central responsibility in the healthcare environment, and
              accurate identification of transmission events presents the first
              challenge. Phylogenetic analysis based on whole genome sequencing
              provides a high-resolution approach for accurately relating
              isolates to one another, allowing precise identification or
              exclusion of transmission events and sources for nearly all
              cases. We sequenced 24 methicillin-resistant Staphylococcus
              aureus (MRSA) genomes to retrospectively investigate a suspected
              point source of three surgical site infections (SSIs) that
              occurred over a one-year period. The source of transmission was
              believed to be a surgical team member colonized with MRSA,
              involved in all surgeries preceding the SSI cases, who was
              subsequently decolonized. Genetic relatedness among isolates was
              determined using whole genome single nucleotide polymorphism
              (SNP) data. RESULTS: Whole genome SNP typing (WGST) revealed 283
              informative SNPs between the surgical team member's isolate and
              the closest SSI isolate. The second isolate was 286 and the third
              was thousands of SNPs different, indicating the nasal carriage
              strain from the surgical team member was not the source of the
              SSIs. Given the mutation rates estimated for S. aureus, none of
              the SSI isolates share a common ancestor within the past 16
              years, further discounting any common point source for these
              infections. The decolonization procedures and resources spent on
              the point source infection control could have been prevented if
              WGST was performed at the time of the suspected transmission,
              instead of retrospectively. CONCLUSIONS: Whole genome sequence
              analysis is an ideal method to exclude isolates involved in
              transmission events and nosocomial outbreaks, and coupling this
              method with epidemiological data can determine if a transmission
              event occurred. These methods promise to direct infection control
              resources more appropriately.",
  journal  = "Hereditas",
  volume   =  153,
  pages    = "11",
  month    =  nov,
  year     =  2016,
  keywords = "MRSA; Nasal carriage; Surgical site infections; Transmission;
              Whole genome
              sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Post2016-tm,
  title    = "Characterisation of nasal methicillin-resistant Staphylococcus
              aureus isolated from international human and veterinary surgeons",
  author   = "Post, Virginia and Harris, Llinos and Morgenstern, Mario and
              Richards, R Geoff and Sheppard, Samuel K and Moriarty, Fintan",
  abstract = "Nasal colonization with methicillin-resistant Staphylococcus
              aureus is poorly described for surgeons, despite the increased
              exposure to nosocomial pathogens and at-risk patients. This study
              investigated the molecular epidemiology and antimicrobial
              resistance of 26 MRSA isolates cultured from the nares of an
              international cross-sectional study of 1,166 human and 60
              veterinary surgeons. All isolates were subjected to agr-, spa-
              and MLST typing and the presence of 22 virulence factors were
              screened for by PCR. Additionally, biofilm-forming ability,
              haemolytic activity, staphyloxanthin production and antibiotic
              resistance were determined. The genome of a rifampicin resistant
              MRSA was sequenced. Approximately half of the isolates belonged
              to well-described clonal lineages, ST1, ST5, ST8, ST45 and ST59,
              that have been previously associated with severe infections and
              increased patient mortality. Two of the 3 veterinarian MRSA
              belonged to epidemic livestock-associated MRSA clonal lineages
              (ST398 and ST8) previously associated with high transmission
              potential between animals and humans. The isolates did not
              display any consistent virulence gene pattern, and 35\% of the
              isolates carried at least one of: the Panton-Valentine leukocidin
              lukFS-PV; the exfoliative toxin eta; or the toxic shock syndrome
              tst genes. Resistance to rifampicin was detected in one
              veterinarian isolate, and was found to be due to 3 mutations in
              the rpoB gene. Surgeons occupy a critical position in the
              healthcare profession due to their close contact with patients.
              In this study, surgeons were found to be colonized with MRSA at
              low rates that are similar to the general population, and the
              colonising strains were often common clonal lineages.",
  journal  = "J. Med. Microbiol.",
  month    =  dec,
  year     =  2016,
  keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Costa2013-dt,
  title     = "Complete genome sequence of a variant of the
               methicillin-resistant Staphylococcus aureus {ST239} lineage,
               strain {BMB9393}, displaying superior ability to accumulate
               ica-independent biofilm",
  author    = "Costa, Maiana Oliveira Cerqueira and Beltrame, Cristiana
               Ossaille and Ferreira, Fabienne Antunes and Botelho, Ana Maria
               Nunes and Lima, Nicholas Costa Barroso and Souza, Rangel Celso
               and de Almeida, Luiz Gonzaga Paula and Vasconcelos, Ana Tereza
               Ribeiro and Nicol{\'a}s, Marisa Fabiana and Figueiredo, Agnes
               Marie S{\'a}",
  abstract  = "ABSTRACT Biofilm is considered an important virulence factor in
               nosocomial infections. Herein, we report the complete genome
               sequence of a variant of methicillin-resistant Staphylococcus
               aureus, strain BMB9393, which is highly disseminated in Brazil.
               This ...",
  journal   = "Genome Announc.",
  publisher = "Am Soc Microbiol",
  volume    =  1,
  number    =  4,
  pages     = "e00576--13",
  year      =  2013,
  keywords  = "Staphylococcus;experimental\_design;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Lee2017-xz,
  title    = "Emerging multidrug resistance in community-associated
              Staphylococcus aureus involved in skin and soft tissue infections
              and nasal colonization",
  author   = "Lee, Grace C and Dallas, Steven D and Wang, Yufeng and Olsen,
              Randall J and Lawson, Kenneth A and Wilson, James and Frei,
              Christopher R",
  abstract = "Background:Staphylococcus aureus is a major pathogen causing
              significant morbidity and mortality worldwide. The emergence of
              MDR S. aureus strains in the community setting has major
              implications in disease management. However, data regarding the
              occurrence and patterns of MDR community-associated S. aureus
              sub-clones is limited.Objectives: To use whole-genome sequences
              to describe the diversity and distribution of resistance
              mechanisms among community-associated S. aureus
              isolates.Methods:S. aureus isolates from skin and soft tissue
              infections (SSTIs) and nasal colonization were collected from
              patients within 10 primary care clinics from 2007 to 2015. The
              Illumina Miseq platform was used to determine the genome
              sequences for 144 S. aureus isolates. Phylogenetic and
              bioinformatics analyses were performed using in silico tools. The
              resistome was assembled and compared with the phenotypically
              derived antibiogram.Results: Approximately one-third of S. aureus
              isolates in the South Texas primary care setting were MDR. A
              higher proportion of SSTI isolates were MDR in comparison with
              nasal colonization isolates. Individuals with MDR S. aureus SSTIs
              were more likely to be African American and obese. Furthermore,
              S. aureus populations are able to acquire and lose antimicrobial
              resistance genes. USA300 strains were differentiated by a stable
              chromosomal mutation in gyrA conferring quinolone resistance. The
              resistomes were highly predictive of antimicrobial resistance
              phenotypes.Conclusions: These findings highlight the high
              prevalence and epidemiological factors associated with MDR S.
              aureus strains in the community setting and demonstrate the
              utility of next-generation sequencing to potentially quicken
              antimicrobial resistance detection and surveillance for targeted
              interventions.",
  journal  = "J. Antimicrob. Chemother.",
  month    =  jul,
  year     =  2017,
  keywords = "staphylococcus aureus; drug resistance, microbial; nose; skin and
              soft tissue infections; microbial colonization; community; drug
              resistance, multiple; phenotype; genome; genes; mutation; clone
              cells; african american; chromosomes; obesity; primary health
              care; disease management; surveillance, medical;
              antibiogram;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Bayer2016-hc,
  title    = "Dysregulation of mprF and {dltABCD} expression among
              daptomycin-non-susceptible {MRSA} clinical isolates",
  author   = "Bayer, Arnold S and Mishra, Nagendra N and Cheung, Ambrose L and
              Rubio, Aileen and Yang, Soo-Jin",
  abstract = "BACKGROUND: In small series or individual reports, SNPs within
              the mprF ORF and dysregulation of its expression in
              Staphylococcus aureus have been linked to daptomycin resistance
              (DAP-R) via a proposed gain-in-function mechanism. Similarly,
              dysregulation of dltABCD has also been associated with DAP-R.
              METHODS: Using 22 well-characterized, isogenic
              daptomycin-susceptible (DAP-S)/DAP-R clinical MRSA strain pairs,
              we assessed potential relationships of the DAP-R phenotype with:
              (i) regulation of mprF transcription; (ii) regulation of dltABCD
              transcription; (iii) expression of the two-component regulatory
              system, graRS (upstream regulator for both mprF and dltABCD
              transcription); (iv) SNPs within the graRS promoter or its ORF;
              and (v) altered mprF transcription and lysyl-phosphatidylglycerol
              (L-PG) synthesis. RESULTS: Enhanced expression of mprF occurred
              with SNPs in highly distinct and well-chronicled MprF domain 'hot
              spots' and rarely occurred without such mutations. Increased
              expression and/or dysregulation of mprF and dltABCD were not
              uncommon in DAP-R strains, occurring in 27\% of strains for each
              gene. In these latter strains, neither graRS expression profiles
              nor polymorphic sequences within the graRS promoter or ORF could
              be significantly linked to altered transcription of mprF or dlt.
              CONCLUSIONS: Although graRS can co-regulate mprF and dltABCD
              expression, loci outside of this regulon appear to be involved in
              dysregulation of these latter two genes and the DAP-R phenotype.
              Finally, DAP-R strains exhibiting significantly altered mprF
              transcription profiles produced significantly increased levels of
              L-PG.",
  journal  = "J. Antimicrob. Chemother.",
  volume   =  71,
  number   =  8,
  pages    = "2100--2104",
  month    =  aug,
  year     =  2016,
  keywords = "confirmed\_SA-resistance-mutation;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Stevens2017-ff,
  title    = "Draft Genome Sequence of \textit{Staphylococcus aureus} S681, a
              {Tetracycline-Sensitive} {Livestock-Associated}
              {Methicillin-Resistant} Clonal Complex 398 Strain",
  author   = "Stevens, Marc J A and Stephan, Roger and Johler, Sophia",
  abstract = "We present the draft genome sequence of an atypical
              tetracycline-susceptible livestock-associated
              methicillin-resistant Staphylococcus aureus (MRSA) strain. It
              contains 2,817,340 bp and 2,858 coding sequences, including 6
              rRNA operons, 56 tRNAs, and 4 noncoding RNA (ncRNA) genes. The
              strain harbors a tet(M) gene, but 15 point mutations in amino
              acids are present that likely impair the functionality of TetM.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  33,
  month    =  aug,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Ugolotti2017-fa,
  title    = "Genomic characterization of a paediatric {MRSA} outbreak by Next
              Generation Sequencing",
  author   = "Ugolotti, Elisabetta and Di Marco, Eddi and Bandettini, Roberto
              and Biassoni, Roberto",
  abstract = "INTRODUCTION: Twelve strains of meticillin-resistant
              Staphylococcus aureus (MRSA) isolated during a suspected outbreak
              in a Paediatric Intensive Care Unit were analyzed by Whole Genome
              Sequence (WGS). AIM: To define the clonality of MRSA strains to a
              high discriminative power and to evaluate the presence of genetic
              determinants responsible for antibiotic resistance and for
              virulence. RESULTS: Ten out of 12 strains belonged to the MLST
              ST2625, while the other two were ST8. Among the ST2625 strains,
              analysis based on 1126 genes showed that they were clonal sharing
              more than 98.3\% of allelic identities and one of them was
              isolated from a health care worker. All the ST2625 strains were
              characterized by a SCC-Mec cassette IVa and the Resistoma
              analysis indicated a correspondence between phenotypic and
              genotypic characteristics. The study of 63 genes associated with
              the virulence was correlated to the pattern of clonality shown.
              CONCLUSION: This analysis confirmed the occurrence of an
              outbreak, which allowed us to strictly enforce standard infection
              control measures that promptly terminated the outbreak.",
  journal  = "J. Hosp. Infect.",
  month    =  aug,
  year     =  2017,
  keywords = "MRSA; Paediatric Nosocomial Infections; Resistoma; Staphylococcus
              aureus; Toxoma; Whole-genome
              sequencing;Staphylococcus;transmission-epidemiology;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Satoo2017-ue,
  title    = "Complete Sequence of a \textit{Staphylococcus aureus} Clonal
              Complex 81 Strain, the Dominant Lineage in Food Poisoning
              Outbreaks in Japan",
  author   = "Sato'o, Yusuke and Hisatsune, Junzo and Hirakawa, Hideki and Ono,
              Hisaya K and Omoe, Katsuhiko and Sugai, Motoyuki",
  abstract = "Staphylococcus aureus No. 10 is an isolate from a staphylococcal
              food poisoning outbreak in Japan, classified as clonal complex 81
              subtype 1. It preferentially produces larger quantities of
              staphylococcal enterotoxin A (SEA) and staphylococcal enterotoxin
              H (SEH) in foods and media. Here, we report the complete
              annotated genome sequence of the chromosome and a plasmid.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  34,
  month    =  aug,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Sivaraman2017-uf,
  title    = "Draft Genome Sequence of a {Methicillin-Resistant}
              \textit{Staphylococcus aureus} Isolate (Sequence Type 1) from
              Seafood",
  author   = "Sivaraman, G K and Vanik, Deesha and Visnuvinayagam, S and
              Prasad, M M and Ravishankar, C N",
  abstract = "The draft genome sequence of a methicillin-resistant
              Staphylococcus aureus (MRSA) isolate (sequence type 1 [ST 1])
              from the salted dried ribbonfish from Gujarat, India, is reported
              here. Staphylococcus genus-specific genes were present in this
              MRSA isolate. The whole-genome sequence of this strain contains
              2,797 protein-coding genes and 80 RNAs within the 2.85-Mb genome.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  34,
  month    =  aug,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Lee2017-lr,
  title    = "Emerging multidrug resistance in community-associated
              Staphylococcus aureus involved in skin and soft tissue infections
              and nasal colonization",
  author   = "Lee, Grace C and Dallas, Steven D and Wang, Yufeng and Olsen,
              Randall J and Lawson, Kenneth A and Wilson, James and Frei,
              Christopher R",
  abstract = "Background: Staphylococcus aureus is a major pathogen causing
              significant morbidity and mortality worldwide. The emergence of
              MDR S. aureus strains in the community setting has major
              implications in disease management. However, data regarding the
              occurrence and patterns of MDR community-associated S. aureus
              sub-clones is limited. Objectives: To use whole-genome sequences
              to describe the diversity and distribution of resistance
              mechanisms among community-associated S. aureus isolates.
              Methods: S. aureus isolates from skin and soft tissue infections
              (SSTIs) and nasal colonization were collected from patients
              within 10 primary care clinics from 2007 to 2015. The Illumina
              Miseq platform was used to determine the genome sequences for 144
              S. aureus isolates. Phylogenetic and bioinformatics analyses were
              performed using in silico tools. The resistome was assembled and
              compared with the phenotypically derived antibiogram. Results:
              Approximately one-third of S. aureus isolates in the South Texas
              primary care setting were MDR. A higher proportion of SSTI
              isolates were MDR in comparison with nasal colonization isolates.
              Individuals with MDR S. aureus SSTIs were more likely to be
              African American and obese. Furthermore, S. aureus populations
              are able to acquire and lose antimicrobial resistance genes.
              USA300 strains were differentiated by a stable chromosomal
              mutation in gyrA conferring quinolone resistance. The resistomes
              were highly predictive of antimicrobial resistance phenotypes.
              Conclusions: These findings highlight the high prevalence and
              epidemiological factors associated with MDR S. aureus strains in
              the community setting and demonstrate the utility of
              next-generation sequencing to potentially quicken antimicrobial
              resistance detection and surveillance for targeted interventions.",
  journal  = "J. Antimicrob. Chemother.",
  volume   =  72,
  number   =  9,
  pages    = "2461--2468",
  month    =  sep,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Hansen2017-hf,
  title    = "Whole Genome Sequencing of Danish \textit{Staphylococcus
              argenteus} Reveals a Genetically Diverse Collection with Clear
              Separation from \textit{Staphylococcus aureus}",
  author   = "Hansen, Thomas A and Bartels, Mette D and H{\o}gh, Silje V and
              Dons, Lone E and Pedersen, Michael and Jensen, Th{\o}ger G and
              Kemp, Michael and Skov, Marianne N and Gumpert, Heidi and
              Worning, Peder and Westh, Henrik",
  abstract = "Staphylococcus argenteus (S. argenteus) is a newly identified
              Staphylococcus species that has been misidentified as
              Staphylococcus aureus (S. aureus) and is clinically relevant. We
              identified 25 S. argenteus genomes in our collection of whole
              genome sequenced S. aureus. These genomes were compared to
              publicly available genomes and a phylogeny revealed seven
              clusters corresponding to seven clonal complexes. The genome of
              S. argenteus was found to be different from the genome of S.
              aureus and a core genome analysis showed that ~33\% of the total
              gene pool was shared between the two species, at 90\% homology
              level. An assessment of mobile elements shows flow of SCCmec
              cassettes, plasmids, phages, and pathogenicity islands, between
              S. argenteus and S. aureus. This dataset emphasizes that S.
              argenteus and S. aureus are two separate species that share
              genetic material.",
  journal  = "Front. Microbiol.",
  volume   =  8,
  pages    = "1512",
  month    =  aug,
  year     =  2017,
  keywords = "S. argenteus; S. aureus; SargPI; SargPID7903; Staphylococcus;
              phage;
              plasmid;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Jo2016-qi,
  title    = "Phenotypic and genotypic characterisation of multiple
              antibiotic-resistant Staphylococcus aureus exposed to
              subinhibitory levels of oxacillin and levofloxacin",
  author   = "Jo, Ara and Ahn, Juhee",
  abstract = "BACKGROUND: The emergence and spread of multidrug resistant
              methicillin-resistant Staphylococcus aureus (MDR-MRSA) has
              serious health consequences in the presence of sub-MIC
              antibiotics. Therefore, this study was designed to evaluate
              $\beta$-lactamase activity, efflux activity, biofilm formation,
              and gene expression pattern in Staphylococcus aureus KACC 10778,
              S. aureus ATCC 15564, and S. aureus CCARM 3080 exposed to
              sublethal concentrations of levofloxacin and oxacillin. RESULTS:
              The decreased MICs were observed in S. aureus KACC and S. aureus
              ATCC when exposed to levofloxacin and oxacillin, while and S.
              aureus CCARM remained resistance to streptomycin (512 $\mu$g/mL)
              in the presence of levofloxacin and imipenem (>512 $\mu$g/mL) in
              the presence of oxacillin. The considerable increase in
              extracellular and membrane-bound $\beta$-lactamase activities was
              observed in S. aureus ATCC exposed to oxacillin (>26
              $\mu$mol/min/mL). The antibiotic susceptibility of all strains
              exposed to EPIs (CCCP and PA$\beta$N) varied depending on the
              classes of antibiotics. The relative expression levels of
              adhesion-related genes (clfA, clfB, fnbA, fnnB, and icaD),
              efflux-related genes (norB, norC, and qacA/B), and enterotoxin
              gene (sec) were increased more than 5-fold in S. aureus CCARM.
              The eno and qacA/B genes were highly overexpressed by more than
              12- and 9-folds, respectively, in S. aureus CCARM exposed to
              levofloxacin. The antibiotic susceptibility, lactamase activity,
              biofilm-forming ability, efflux activity, and gene expression
              pattern varied with the intrinsic antibiotic resistance of S.
              aureus KACC, S. aureus ATCC, and S. aureus CCARM exposed to
              levofloxacin and oxacillin. CONCLUSIONS: This study would provide
              useful information for better understating of combination therapy
              related to antibiotic resistance mechanisms and open the door for
              designing effective antibiotic treatment protocols to prevent
              excessive use of antibiotics in clinical practice.",
  journal  = "BMC Microbiol.",
  volume   =  16,
  number   =  1,
  pages    = "170",
  month    =  jul,
  year     =  2016,
  keywords = "Antibiotic resistance; Biofilm; Efflux pump; Gene expression;
              Lactamase; Levofloxacin; Oxacillin; Staphylococcus
              aureus;Staphylococcus;antibiotics;oxacillin;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Hisatsune2017-ce,
  title    = "Complete Genome Sequence of Systemically Disseminated Sequence
              Type 8 Staphylococcal Cassette Chromosome \textit{mec} Type {IVl}
              {Community-Acquired} {Methicillin-Resistant}
              \textit{Staphylococcus aureus}",
  author   = "Hisatsune, Junzo and Hagiya, Hideharu and Shiota, Sumiko and
              Sugai, Motoyuki",
  abstract = "Staphylococcus aureus JH4899, a community-acquired
              methicillin-resistant Staphylococcus aureus (CA-MRSA) isolate
              collected from a patient with systematically disseminated
              infection, is classified as sequence type 8 and carries the
              staphylococcal cassette chromosome mec type IVl (SCCmecIVl). It
              produces TSST-1, SEC, a newly discovered enterotoxin (SE1), and
              epidermal cell differentiation inhibitor A (EDIN-A). Here, we
              present the complete genome sequence of the chromosome and a
              plasmid harboring the se1 and ednA genes.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  35,
  month    =  aug,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Zhang2017-bb,
  title    = "Genome Sequence of \textit{Staphylococcus aureus} {PX03}, an
              {Acetoin-Producing} Strain with a {Small-Sized} Genome",
  author   = "Zhang, Ge and Wang, Qian and Su, Yulong and Li, Shugui and Liu,
              Haobao",
  abstract = "Staphylococcus aureus PX03 can produce acetoin efficiently. Here,
              we present a 2.38-Mb assembly of its genome sequence, which might
              provide further insights into the molecular mechanism of its
              acetoin biosynthesis to further improve its biotechnological
              applications.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  37,
  month    =  sep,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Lebughe2017-qk,
  title    = "The Impact of the \textit{Staphylococcus aureus} Virulome on
              Infection in a Developing Country: A Cohort Study",
  author   = "Lebughe, Marthe and Phaku, Patrick and Niemann, Silke and Mumba,
              Dieudonn{\'e} and Peters, Georg and Muyembe-Tamfum, Jean-Jacques
              and Mellmann, Alexander and Strau{\ss}, Lena and Schaumburg,
              Frieder",
  abstract = "We performed a cohort study to analyze the virulome of
              Staphylococcus aureus from the Democratic Republic of the Congo
              using whole genome sequencing and to assess its impact on the
              course of S. aureus infections. Community-associated S. aureus
              from nasal colonization (n = 100) and infection (n = 86) were
              prospectively collected. Phenotypic susceptibility testing and
              WGS was done for each isolate. WGS data were used to screen for
              79 different virulence factors and for genotyping purposes (spa
              typing, multilocus sequence typing). The majority of the 79
              virulence factors were equally distributed among isolates from
              colonization and infection. Panton-Valentine leukocidin (PVL) and
              the non-truncated hemolysin $\beta$ were associated with skin and
              soft tissue infection (SSTI) and recurrence of disease but did
              not influence the course of infection (i.e., mortality, surgical
              intervention). For the first time, we show that not only PVL but
              also hemolysin $\beta$ could contribute to the development of
              SSTI in PVL-endemic areas such as Africa.",
  journal  = "Front. Microbiol.",
  volume   =  8,
  pages    = "1662",
  month    =  aug,
  year     =  2017,
  keywords = "Africa; Staphylococcus aureus; infection; virulome; whole genome
              sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Sassi2017-mx,
  title    = "An outbreak in intravenous drug users due to {USA300}
              {Latin-American} variant community-acquired methicillin-resistant
              Staphylococcus aureus in France as early as 2007",
  author   = "Sassi, M and Felden, B and Revest, M and Tattevin, P and
              Augagneur, Y and Donnio, P-Y",
  abstract = "Intravenous drug users are at increased risk of Staphylococcus
              aureus infections. Most cases are related to clones prevalent in
              the community. We report an outbreak of community-acquired
              methicillin-resistant Staphylococcus aureus infections that
              occurred from 2007 to 2009 in intravenous drug users and their
              close contacts in Northwestern France. Clinical and molecular
              investigations suggested that the clones were more similar than
              those usually isolated in the American continent although none of
              the patients traveled abroad or had contact with individuals who
              had traveled to the Americas. Then, a retrospective whole genome
              sequencing and phylogenetic analyses demonstrated that the
              strains isolated from the first case belong to the USA300
              Latin-American variant clone, based on the absence of arginine
              catabolic mobile element (ACME), and the presence of copper and
              mercury resistance mobile element (COMER), a distinctive feature
              of the South American variant. Our study shows genetic evidence
              for introduction of this clone as early as 2007 in France. This
              report also illustrates the importance of genome sequencing to
              finely characterize and monitor the emergence of unexpected S.
              aureus clones among high-risk populations, especially when living
              in promiscuity.",
  journal  = "Eur. J. Clin. Microbiol. Infect. Dis.",
  month    =  sep,
  year     =  2017,
  keywords = "Staphylococcus;transmission-epidemiology;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Katayama2017-uq,
  title    = "Prevalence of Slow-growth Vancomycin Non-susceptibility In
              Methicillin-resistant Staphylococcus aureus",
  author   = "Katayama, Yuki and Azechi, Takuya and Miyazaki, Motoyasu and
              Takata, Tohru and Sekine, Miwa and Matsui, Hidehito and Hanaki,
              Hideaki and Yahara, Koji and Sasano, Hiroshi and Asakura, Kota
              and Takaku, Tomoiku and Ochiai, Tomonori and Komatsu, Norio and
              Chambers, Henry F",
  abstract = "We have previsously reported a novel phenotype of
              vancomycin-intermediate Staphylococcus aureus (VISA) strains,
              ``slow-VISA,'' in which colonies appear only after 72 h of
              incubation. Slow-VISA strains can be difficult to detect because
              prolonged incubation is required and the phenotype is unstable.
              To develop a method for detection of slow-VISA isolates, we
              studied 23 slow-VISA isolates derived from heteroVISA clinical
              strain Mu3. We identified single nucleotide polymorphisms (SNP)
              in genes involved in various pathways such as purine/pyrimidine
              synthesis, cell metabolism, and cell-wall peptidoglycan
              synthesis, which have been implicated in the stringent response.
              We found that mupirocin, which also induces a stringent response,
              caused stable expression of vancomycin resistance. On the basis
              of these results, we developed a method for detection of
              slow-VISA using mupirocin 0.032 $\mu$g/ml (Patent Application No.
              PCT/JP2017/008975filed on March 7, 2017). Using this method, we
              detected 53 (15.6\%) slow-VISA isolates among clinical
              methicillin-resistant S.aureus (MRSA) isolates. In contrast, the
              VISA phenotype was detected in fewer than 1\% of isolates.
              Deep-sequencing analysis showed that slow-VISA clones are present
              in small numbers among hVISA isolates, and proliferate in the
              presence of vancomycin. This slow-VISA subpopulation could
              account in part for the recurrence and persistence of MRSA
              infection.",
  journal  = "Antimicrob. Agents Chemother.",
  month    =  aug,
  year     =  2017,
  keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Stanczak-Mrozek2015-ds,
  title    = "Within-host diversity of {MRSA} antimicrobial resistances",
  author   = "Stanczak-Mrozek, Kinga I and Manne, Anusha and Knight, Gwenan M
              and Gould, Katherine and Witney, Adam A and Lindsay, Jodi A",
  abstract = "OBJECTIVES: MRSA is a major antimicrobial resistance (AMR)
              pathogen. The reservoir of infecting isolates is colonization,
              which is the site of evolutionary selection. The aim was to
              identify if AMRs in colonizing MRSA populations diversified and
              potential mechanisms of resistance gene transfer in vivo.
              METHODS: Nasal swabs from 38 MRSA carriers admitted to hospital
              were plated and 20 individual colonies from each patient tested
              for phenotypic antibiotic susceptibility and genetically for
              lineage, carriage of four prophages and three plasmid families.
              Free bacteriophages were detected in swabs as well as their
              capacity for transducing resistance genes. RESULTS: Nine (24\%)
              patients carried phenotypic AMR variants and 24 (63\%) carried
              prophage and plasmid variants. If a single colony was selected
              for testing, the probability of detecting all AMR in that patient
              was 87\%. Sixty-four different AMR and mobile genetic element
              (MGE) profiles were detected, mostly in the MRSA CC22 background
              (where CC stands for clonal complex), with up to 8 profiles per
              patient. Nearly half of the patients carried detectable free
              bacteriophages and phages successfully transduced resistance
              genes between laboratory and patient isolates in vitro. WGS
              showed MRSA core genomes were stable, while AMR and MGEs varied.
              CONCLUSIONS: 'Clouds' of MRSA variants that have acquired or lost
              AMR and MGEs are common in nasal colonizing populations and
              bacteriophages may play an important role in gene transfer.
              Accurate estimation of AMR and genetic variability has
              implications for diagnostics, epidemiology, antimicrobial
              stewardship and understanding the evolutionary selection of AMR
              in colonizing populations.",
  journal  = "J. Antimicrob. Chemother.",
  volume   =  70,
  number   =  8,
  pages    = "2191--2198",
  month    =  aug,
  year     =  2015,
  keywords = "horizontal gene transfer; mobile genetic elements; transduction;
              whole-genome
              sequencing;Staphylococcus;bacerial\_genetics;colonization;phage;Staph\_evolutionary\_history;Staph\_evolutionary\_history/staph
              microbial
              interactions;antibiotcs-evolution-fitness;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Aanensen2016-lz,
  title    = "{Whole-Genome} Sequencing for Routine Pathogen Surveillance in
              Public Health: a Population Snapshot of Invasive Staphylococcus
              aureus in Europe",
  author   = "Aanensen, David M and Feil, Edward J and Holden, Matthew T G and
              Dordel, Janina and Yeats, Corin A and Fedosejev, Artemij and
              Goater, Richard and Castillo-Ram{\'\i}rez, Santiago and Corander,
              Jukka and Colijn, Caroline and Chlebowicz, Monika A and Schouls,
              Leo and Heck, Max and Pluister, Gerlinde and Ruimy, Raymond and
              Kahlmeter, Gunnar and {\AA}hman, Jenny and Matuschek, Erika and
              Friedrich, Alexander W and Parkhill, Julian and Bentley, Stephen
              D and Spratt, Brian G and Grundmann, Hajo and {European SRL
              Working Group}",
  abstract = "UNLABELLED: The implementation of routine whole-genome sequencing
              (WGS) promises to transform our ability to monitor the emergence
              and spread of bacterial pathogens. Here we combined WGS data from
              308 invasive Staphylococcus aureus isolates corresponding to a
              pan-European population snapshot, with epidemiological and
              resistance data. Geospatial visualization of the data is made
              possible by a generic software tool designed for public health
              purposes that is available at the project URL
              (http://www.microreact.org/project/EkUvg9uY?tt=rc). Our analysis
              demonstrates that high-risk clones can be identified on the basis
              of population level properties such as clonal relatedness,
              abundance, and spatial structuring and by inferring virulence and
              resistance properties on the basis of gene content. We also show
              that in silico predictions of antibiotic resistance profiles are
              at least as reliable as phenotypic testing. We argue that this
              work provides a comprehensive road map illustrating the three
              vital components for future molecular epidemiological
              surveillance: (i) large-scale structured surveys, (ii) WGS, and
              (iii) community-oriented database infrastructure and analysis
              tools. IMPORTANCE: The spread of antibiotic-resistant bacteria is
              a public health emergency of global concern, threatening medical
              intervention at every level of health care delivery. Several
              recent studies have demonstrated the promise of routine
              whole-genome sequencing (WGS) of bacterial pathogens for
              epidemiological surveillance, outbreak detection, and infection
              control. However, as this technology becomes more widely adopted,
              the key challenges of generating representative national and
              international data sets and the development of bioinformatic
              tools to manage and interpret the data become increasingly
              pertinent. This study provides a road map for the integration of
              WGS data into routine pathogen surveillance. We emphasize the
              importance of large-scale routine surveys to provide the
              population context for more targeted or localized investigation
              and the development of open-access bioinformatic tools to provide
              the means to combine and compare independently generated data
              with publicly available data sets.",
  journal  = "MBio",
  volume   =  7,
  number   =  3,
  month    =  may,
  year     =  2016,
  keywords = "cloning;Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Reuter2016-yp,
  title    = "Building a genomic framework for prospective {MRSA} surveillance
              in the United Kingdom and the Republic of Ireland",
  author   = "Reuter, Sandra and T{\"o}r{\"o}k, M Est{\'e}e and Holden, Matthew
              T G and Reynolds, Rosy and Raven, Kathy E and Blane, Beth and
              Donker, Tjibbe and Bentley, Stephen D and Aanensen, David M and
              Grundmann, Hajo and Feil, Edward J and Spratt, Brian G and
              Parkhill, Julian and Peacock, Sharon J",
  abstract = "The correct interpretation of microbial sequencing data applied
              to surveillance and outbreak investigation depends on accessible
              genomic databases to provide vital genetic context. Our aim was
              to construct and describe a United Kingdom MRSA database
              containing over 1000 methicillin-resistant Staphylococcus aureus
              (MRSA) genomes drawn from England, Northern Ireland, Wales,
              Scotland, and the Republic of Ireland over a decade. We sequenced
              1013 MRSA submitted to the British Society for Antimicrobial
              Chemotherapy by 46 laboratories between 2001 and 2010. Each
              isolate was assigned to a regional healthcare referral network in
              England and was otherwise grouped based on country of origin.
              Phylogenetic reconstructions were used to contextualize MRSA
              outbreak investigations and to detect the spread of resistance.
              The majority of isolates (n = 783, 77\%) belonged to CC22, which
              contains the dominant United Kingdom epidemic clone (EMRSA-15).
              There was marked geographic structuring of EMRSA-15, consistent
              with widespread dissemination prior to the sampling decade
              followed by local diversification. The addition of MRSA genomes
              from two outbreaks and one pseudo-outbreak demonstrated the
              certainty with which outbreaks could be confirmed or refuted. We
              identified local and regional differences in antibiotic
              resistance profiles, with examples of local expansion, as well as
              widespread circulation of mobile genetic elements across the
              bacterial population. We have generated a resource for the future
              surveillance and outbreak investigation of MRSA in the United
              Kingdom and Ireland and have shown the value of this during
              outbreak investigation and tracking of antimicrobial resistance.",
  journal  = "Genome Res.",
  volume   =  26,
  number   =  2,
  pages    = "263--270",
  month    =  feb,
  year     =  2016,
  keywords = "Staphylococcus;Staph\_evolutionary\_history/staph microbial
              interactions;Read-lab-shared;Staphylococcus\_aureus\_genome\_papers;Staph\_evolution\_toxins",
  language = "en"
 }

 @ARTICLE{Dekker2016-rk,
  title    = "{Next-Generation} Epidemiology: Using {Real-Time} Core Genome
              Multilocus Sequence Typing To Support Infection Control Policy",
  author   = "Dekker, John P and Frank, Karen M",
  abstract = "Multidrug-resistant bacteria are responsible for substantial
              morbidity and mortality worldwide. Tracking the nosocomial spread
              of resistant bacteria is critical to infection control. Mellmann
              et al. (J. Clin. Microbiol. 54:2874-2881, 2016,
              http://dx.doi.org/10.1128/JCM.00790-16) have described
              prospective whole-genome sequencing with core genome multilocus
              sequencing typing (cgMLST) analysis for real-time surveillance
              and have addressed the practical aspects of implementing this
              type of operation in the hospital setting.",
  journal  = "J. Clin. Microbiol.",
  volume   =  54,
  number   =  12,
  pages    = "2850--2853",
  month    =  dec,
  year     =  2016,
  keywords = "Staphylococcus;clinical-diagnosis-genomics;Staphylococcus\_aureus\_genome\_papers;Anti-infectives\_course",
  language = "en"
 }

 @ARTICLE{Hau2017-rx,
  title    = "Draft Genome Sequences of Nine {Livestock-Associated}
              {Methicillin-Resistant} \textit{Staphylococcus aureus} Sequence
              Type 5 Isolates Obtained from Humans after {Short-Term} Swine
              Contact",
  author   = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and Frana,
              Timothy S and Nicholson, Tracy L",
  abstract = "Livestock-associated methicillin-resistant Staphylococcus aureus
              (LA-MRSA) sequence type 5 (ST5) has raised concerns surrounding
              the potential for these isolates to colonize or cause disease in
              humans with swine contact. Here, we report draft genome sequences
              for nine LA-MRSA ST5 isolates obtained from humans after short
              term swine contact.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  41,
  month    =  oct,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Donker2017-qu,
  title    = "Population genetic structuring of methicillin-resistant
              \textit{Staphylococcus aureus} clone {EMRSA-15} within {UK}
              reflects patient referral patterns",
  author   = "Donker, Tjibbe and Reuter, Sandra and Scriberras, James and
              Reynolds, Rosy and Brown, Nicholas M and T{\"o}r{\"o}k, M
              Est{\'e}e and James, Richard and Network, East Of England
              Microbiology Research and Aanensen, David M and Bentley, Stephen
              D and Holden, Matthew T G and Parkhill, Julian and Spratt, Brian
              G and Peacock, Sharon J and Feil, Edward J and Grundmann, Hajo",
  abstract = "Antibiotic resistance forms a serious threat to the health of
              hospitalised patients, rendering otherwise treatable bacterial
              infections potentially life-threatening. A thorough understanding
              of the mechanisms by which resistance spreads between patients in
              different hospitals is required in order to design effective
              control strategies. We measured the differences between bacterial
              populations of 52 hospitals in the United Kingdom and Ireland,
              using whole-genome sequences from 1085 MRSA clonal complex 22
              isolates collected between 1998 and 2012. The genetic differences
              between bacterial populations were compared with the number of
              patients transferred between hospitals and their regional
              structure. The MRSA populations within single hospitals, regions
              and countries were genetically distinct from the rest of the
              bacterial population at each of these levels. Hospitals from the
              same patient referral regions showed more similar MRSA
              populations, as did hospitals sharing many patients. Furthermore,
              the bacterial populations from different time-periods within the
              same hospital were generally more similar to each other than
              contemporaneous bacterial populations from different hospitals.
              We conclude that, while a large part of the dispersal and
              expansion of MRSA takes place among patients seeking care in
              single hospitals, inter-hospital spread of resistant bacteria is
              by no means a rare occurrence. Hospitals are exposed to constant
              introductions of MRSA on a number of levels: (1) most MRSA is
              received from hospitals that directly transfer large numbers of
              patients, while (2) fewer introductions happen between regions or
              (3) across national borders, reflecting lower numbers of
              transferred patients. A joint coordinated control effort between
              hospitals, is therefore paramount for the national control of
              MRSA, antibiotic-resistant bacteria and other hospital-associated
              pathogens.",
  journal  = "Microb Genom",
  volume   =  3,
  number   =  7,
  pages    = "e000113",
  month    =  jul,
  year     =  2017,
  keywords = "MRSA; antimicrobial Resistance; hospital
              network;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Yu2017-kx,
  title    = "Complete Genome Sequence of Super {Biofilm-Elaborating}
              \textit{Staphylococcus aureus} Isolated in Japan",
  author   = "Yu, Liansheng and Hisatsune, Junzo and Hirakawa, Hideki and
              Mizumachi, Emiri and Toyoda, Atsushi and Yahara, Koji and Sugai,
              Motoyuki",
  abstract = "Staphylococcus aureus JP080, previously named TF2758, is a
              clinical isolate from an atheroma and a super biofilm-elaborating
              strain whose biofilm elaboration is dependent solely on
              polysaccharide poly-N-acetylglucosamine/polysaccharide
              intercellular adhesin (PNAG/PIA). Here, we report the complete
              genome sequence of strain JP080, which consists of one chromosome
              and one circular plasmid.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  41,
  month    =  oct,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Hau2017-mo,
  title    = "Draft Genome Sequences of Nine {Livestock-Associated}
              {Methicillin-Resistant} \textit{Staphylococcus aureus} Sequence
              Type 5 Isolates from Humans with {Long-Term} Swine Contact",
  author   = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and
              Davies, Peter R and Haan, Jisun S and Nicholson, Tracy L",
  abstract = "Humans have been found to harbor livestock-associated
              methicillin-resistant Staphylococcus aureus (LA-MRSA) isolates.
              LA-MRSA isolates are considered adapted to colonizing livestock
              and less pathogenic in humans than their hospital- and
              community-acquired counterparts. Here, we present nine LA-MRSA
              sequence type 5 isolates from veterinarians with long-term swine
              contact.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  41,
  month    =  oct,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Toleman2017-de,
  title    = "Investigation of a Cluster of Sequence Type 22
              {Methicillin-Resistant} Staphylococcus aureus Transmission in a
              Community Setting",
  author   = "Toleman, Michelle S and Watkins, Emmeline R and Williams, Tom and
              Blane, Beth and Sadler, Belinda and Harrison, Ewan M and Coll,
              Francesc and Parkhill, Julian and Nazareth, Bernadette and Brown,
              Nicholas M and Peacock, Sharon J",
  abstract = "BackgroundWhole-genome sequencing (WGS) has typically been used
              to confirm or refute hospital/ward outbreaks of
              methicillin-resistant Staphylococcus aureus (MRSA) identified
              through routine practice. However, appropriately targeted WGS
              strategies that identify routinely ``undetectable'' transmission
              remain the ultimate aim.MethodsWGS of MRSA isolates sent to a
              regional microbiological laboratory was performed as part of a
              12-month prospective observational study. Phylogenetic analyses
              identified a genetically related cluster of E-MRSA15 isolated
              from patients registered to the same general practice (GP)
              surgery. This led to an investigation to identify epidemiological
              links, find additional cases, and determine potential for ongoing
              transmission.ResultsWe identified 15 MRSA-positive individuals
              with 27 highly related MRSA isolates who were linked to the GP
              surgery, 2 of whom died with MRSA bacteremia. Of the 13 cases
              that were further investigated, 11 had attended a leg
              ulcer/podiatry clinic. Cases lacked epidemiological links to
              hospitals, suggesting that transmission occurred elsewhere.
              Environmental and staff screening at the GP surgery did not
              identify an ongoing source of infection.ConclusionsSurveillance
              in the United Kingdom shows that the proportion of MRSA
              bacteremias apportioned to hospitals is decreasing, suggesting
              the need for greater focus on the detection of MRSA outbreaks and
              transmission in the community. This case study confirms that the
              typically nosocomial lineage (E-MRSA15) can transmit within
              community settings. Our study exemplifies the continued
              importance of WGS in detecting outbreaks, including those which
              may be missed by routine practice, and suggests that universal
              WGS of bacteremia isolates may help detect outbreaks in
              low-surveillance settings.",
  journal  = "Clin. Infect. Dis.",
  month    =  oct,
  year     =  2017,
  keywords = "genome; methicillin-resistant staphylococcus aureus; community;
              disease outbreaks; surgical procedures, operative;
              bacteremia;Staphylococcus;grants;interesting;transmission-epidemiology;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Coll_undated-fs,
  title    = "and the community",
  author   = "Coll, Francesc and Harrison, Ewan M and Toleman, Michelle S and
              Reuter, Sandra and Raven, Kathy E and Blane, Beth and Palmer,
              Beverley and Kappeler, A Ruth M and Brown, Nicholas M and
              Est{\'e}e T{\"o}r{\"o}k, M and Parkhill, Julian and Peacock,
              Sharon J",
  keywords = "transmission-epidemiology;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Donker2017-qu,
  title     = "Population genetic structuring of methicillin-resistant
               \textit{Staphylococcus aureus} clone {EMRSA-15} within {UK}
               reflects patient referral patterns",
  author    = "Donker, Tjibbe and Reuter, Sandra and Scriberras, James and
               Reynolds, Rosy and Brown, Nicholas M and Est{\'e}e
               T{\"o}r{\"o}k, M and James, Richard and {East of England
               Microbiology Research Network} and Aanensen, David M and
               Bentley, Stephen D and Holden, Matthew T G and Parkhill, Julian
               and Spratt, Brian G and Peacock, Sharon J and Feil, Edward J and
               Grundmann, Hajo",
  abstract  = "Antibiotic resistance forms a serious threat to the health of
               hospitalised patients, rendering otherwise treatable bacterial
               infections potentially life-threatening. A thorough
               understanding of the mechanisms by which resistance spreads
               between patients in different hospitals is required in order to
               design effective control strategies. We measured the differences
               between bacterial populations of 52 hospitals in the United
               Kingdom and Ireland, using whole-genome sequences from 1085 MRSA
               clonal complex 22 isolates collected between 1998 and 2012. The
               genetic differences between bacterial populations were compared
               with the number of patients transferred between hospitals and
               their regional structure. The MRSA populations within single
               hospitals, regions and countries were genetically distinct from
               the rest of the bacterial population at each of these levels.
               Hospitals from the same patient referral regions showed more
               similar MRSA populations, as did hospitals sharing many
               patients. Furthermore, the bacterial populations from different
               time-periods within the same hospital were generally more
               similar to each other than contemporaneous bacterial populations
               from different hospitals. We conclude that, while a large part
               of the dispersal and expansion of MRSA takes place among
               patients seeking care in single hospitals, inter-hospital spread
               of resistant bacteria is by no means a rare occurrence.
               Hospitals are exposed to constant introductions of MRSA on a
               number of levels: (1) most MRSA is received from hospitals that
               directly transfer large numbers of patients, while (2) fewer
               introductions happen between regions or (3) across national
               borders, reflecting lower numbers of transferred patients. A
               joint coordinated control effort between hospitals, is therefore
               paramount for the national control of MRSA, antibiotic-resistant
               bacteria and other hospital-associated pathogens.",
  journal   = "Microbial Genomics",
  publisher = "Microbiology Society",
  volume    =  3,
  number    =  7,
  pages     = "e000113",
  month     =  jul,
  year      =  2017,
  keywords  = "MRSA; antimicrobial Resistance; hospital
               network;Staphylococcus;Teaching antibiotic resistance
               genomics;Staphylococcus\_aureus\_genome\_papers",
  language  = "en"
 }

 @ARTICLE{Kumar2017-ri,
  title    = "Tuning of the Lethal Response to Multiple Stressors with a
              {Single-Site} Mutation during Clinical Infection by
              Staphylococcus aureus",
  author   = "Kumar, Krishan and Chen, John and Drlica, Karl and Shopsin, Bo",
  abstract = "The agr system of Staphylococcus aureus promotes invasion of host
              tissues, and as expected, agents that block agr quorum sensing
              have anti-infective properties. Paradoxically, agr-defective
              mutants are frequently recovered from patients, especially those
              persistently infected with S. aureus. We found that an agr
              deficiency increased survival of cultured bacteria during severe
              stress, such as treatment with gentamicin, ciprofloxacin, heat,
              or low pH. With daptomycin, deletion of agr decreased survival.
              Therefore, agr activity can be either detrimental or protective,
              depending on the type of lethal stress. Deletion of agr had no
              effect on the ability of the antimicrobials to block bacterial
              growth, indicating that agr effects are limited to lethal action.
              Thus, the effect of an agr deletion is on bacterial tolerance,
              not resistance. For gentamicin and daptomycin, activity can be
              altered by agr-regulated secreted factors. For ciprofloxacin, a
              detrimental function was downregulation of glutathione peroxidase
              (bsaA), an enzyme responsible for defense against oxidative
              stress. Deficiencies in agr and bsaA were epistatic for survival,
              consistent with agr having a destructive role mediated by
              reactive oxygen species. Enhanced susceptibility to lethal stress
              by wild-type agr, particularly antimicrobial stress, helps
              explain why inactivating mutations in S. aureus agr commonly
              occur in hospitalized patients during infection. Moreover, the
              agr quorum-sensing system of S. aureus provides a clinically
              relevant example in which a single-step change in the response to
              severe stress alters the evolutionary path of a pathogen during
              infection.IMPORTANCE When phenotypes produced in response to an
              environmental stress are inadequate to buffer against that
              stress, changes that do buffer may become genetically encoded by
              natural selection. A clinically relevant example is seen with S.
              aureus mutants that are deficient in the key virulence regulator
              agr. Paradoxically, defects in agr are selected during serious
              hospital infection and have been associated with worse outcome.
              The current work helps resolve this paradox: agr mutants are
              often less readily killed by lethal stressors without affecting
              MIC, a phenomenon known as tolerance. Our results indicate that
              tolerance, which would not be detected as resistance, can be
              selected in clinical settings. The data also support the ideas
              that (i) S. aureus broadly hedges against environmental change
              and stress through genome plasticity, (ii) reactive oxygen can be
              involved in the self-destructive response in bacteria, and (iii)
              therapeutic targeting of agr and virulence can be
              counterproductive.",
  journal  = "MBio",
  volume   =  8,
  number   =  5,
  month    =  nov,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Hau2017-di,
  title    = "Draft Genome Sequences of One {Methicillin-Sensitive} and Seven
              {Methicillin-Resistant} \textit{Staphylococcus aureus} Sequence
              Type 5 Isolates Obtained in California",
  author   = "Hau, Samantha J and Bayles, Darrell O and Alt, David P and
              Nicholson, Tracy L",
  abstract = "Staphylococcus aureus is a commensal bacterium of humans that can
              cause a spectrum of diseases. An isolate's capacity to cause
              disease is partially attributed to the acquisition of novel
              mobile genetic elements. This report provides the draft genome
              sequence of one methicillin-susceptible and seven
              methicillin-resistant clinical human S. aureus isolates.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  42,
  month    =  oct,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Lepuschitz2017-oz,
  title    = "Draft Genome Sequence of a {Community-Acquired}
              {Methicillin-Resistant} \textit{Staphylococcus aureus} {USA300}
              Isolate from a River Sample",
  author   = "Lepuschitz, Sarah and Mach, Robert and Springer, Burkhard and
              Allerberger, Franz and Ruppitsch, Werner",
  abstract = "The increasing emergence of multiresistant bacteria in health
              care settings in the community and in the environment represents
              a major health threat worldwide. Here, we report the draft genome
              sequence of a community-acquired methicillin-resistant
              Staphylococcus aureus (CA-MRSA) USA300 isolate (W1) from a small
              river in southern Austria.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  42,
  month    =  oct,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Nemet2017-kj,
  title    = "Draft Genome Sequence of an Atypical Highly Virulent Rabbit
              \textit{Staphylococcus aureus} Strain",
  author   = "N{\'e}met, Zolt{\'a}n and Albert, Ervin and Nagy, Tibor and
              Olasz, Ferenc and Barta, Endre and Kiss, J{\'a}nos and D{\'a}n,
              {\'A}d{\'a}m and B{\'a}nyai, Kriszti{\'a}n and Hermans, Katleen
              and Biksi, Imre",
  abstract = "Rabbit staphylococcosis is one of the most important diseases in
              industrial rabbit production. We report here the draft genome
              sequence of Staphylococcus aureus strain 380/11, an atypical
              highly virulent (aHV) rabbit Staphylococcus aureus strain.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  42,
  month    =  oct,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Mohamed2017-ly,
  title    = "First Complete Genome Sequence of {Methicillin-Resistant}
              \textit{Staphylococcus aureus} Strain {SO-1977} Isolated from
              Khartoum, Sudan",
  author   = "Mohamed, Sofia B and Ali, Mohamed S and Alamir, Faisal M and
              Alyas, Tahani B and Ahmed, Abdallah E and Seed, Almeen O and
              Omer, Rihab A",
  abstract = "Methicillin-resistant Staphylococcus aureus is increasingly
              becoming resistant to most antibiotics and consequently has
              become a challenging public health problem in Sudan. The present
              study documented the first complete genome sequence of strain
              SO-1977, isolated from a contaminated wound in Sudan.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  42,
  month    =  oct,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Senok2017-ku,
  title    = "Investigating a rare methicillin-resistant \textit{Staphylococcus
              aureus} strain: first description of genome sequencing and
              molecular characterization of {CC15-MRSA}",
  author   = "Senok, Abiola C and Somily, Ali M and Slickers, Peter and Raji,
              Muhabat A and Garaween, Ghada and Shibl, Atef and Monecke, Stefan
              and Ehricht, Ralf",
  abstract = "PURPOSE: Methicillin resistant Staphylococcus aureus CC15 strains
              (CC15-MRSA) have only been sporadically described in literature.
              This study was carried out to describe the genetic make-up for
              this rare MRSA strain. METHODS: Four CC15-MRSA isolates collected
              in Riyadh, Saudi Arabia, between 2013 and 2014 were studied. Two
              isolates were from clinical infection and 2 from retail meat
              products. Whole genome sequencing was carried out using Illumina
              HiSeq2500 genome analyzer. RESULTS: All the CC15-MRSA isolates
              had the multilocus sequence typing profile ST1535,
              13-13-1-1-81-11-13, which is a single locus variant of ST15. Of
              the 6 contigs related to the SCC element, one comprised a
              recombinase gene ccrAA, ccrC-PM1, fusC and a helicase, another
              one included mvaS, dru, mecA and 1 had yobV and Q4LAG7. The SCC
              element had 5 transposase genes, namely 3 identical paralogs of
              tnpIS431 and 2 identical paralogs of tnpIS256. Two identical
              copies of a tnpIS256-based insertion element flank the aacA-aphD
              gene. Two copies of this insertion element were present with 1
              located in the SCC element and another inserted into the sasC
              gene. A short 3 kb region, which lacks any bacteriophage
              structural genes and site-specific DNA integrase, was inserted
              into the hlb gene. The hsdM and the 5'-part of the hsdS gene are
              replaced by a copy of the hsdM/hsdS paralogs from $\nu$Sa$\beta$
              giving rise to a new chimeric paralog of hsdS in $\nu$Sa$\alpha$.
              CONCLUSION: CC15-MRSA shows a novel SCCmecV/SCCfus composite
              element. Its variant of hsdM/hsdS probably facilitated uptake of
              foreign mobile genetic elements that promoted emergence of
              CC15-MRSA. Close surveillance is needed to monitor spread and
              emergence of further CC15 MRSA strains.",
  journal  = "Infect. Drug Resist.",
  volume   =  10,
  pages    = "307--315",
  month    =  oct,
  year     =  2017,
  keywords = "MLST; MRSA; SCCmec; Saudi Arabia; clonal complex; whole genome
              sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Kanjilal2017-dv,
  title    = "Trends in antibiotic susceptibility in Staphylococcus aureus in
              Boston, Massachusetts, 2000-2014",
  author   = "Kanjilal, Sanjat and Sater, Mohamad R Abdul and Thayer, Maile and
              Lagoudas, Georgia K and Kim, Soohong and Blainey, Paul C and
              Grad, Yonatan H",
  abstract = "The rate of infection by methicillin-resistant S. aureus (MRSA)
              has declined over the past decade, but it is unclear whether this
              represents a decline in S. aureus infections overall. To evaluate
              trends in the annual rates of infection by S. aureus subtype and
              mean antibiotic resistance, we conducted a 15-year retrospective
              observational study at two tertiary care institutions in Boston,
              MA of 31 753 adult inpatients with S. aureus isolated from
              clinical specimens. We inferred gain and loss of methicillin
              resistance through genome sequencing of 180 isolates from 2016.
              Annual rates of infection by S. aureus declined from 2003 to 2014
              by 4.2\% (2.7\%-5.6\%), attributable to an annual decline in MRSA
              of 10.9\% (9.3\%-12.6\%). Penicillin-susceptible S. aureus (PSSA)
              increased by 6.1\% (4.2\%-8.1\%) annually and rates of
              methicillin-susceptible, penicillin-resistant S. aureus (MSSA)
              did not change. Resistance in S. aureus decreased from 2000 to
              2014 by 0.8 antibiotics (0.7-0.8). Within common MRSA clonal
              complexes, 3/14 MSSA and 2/21 PSSA isolates arose from the loss
              of resistance-conferring genes. Overall, in two tertiary care
              institutions in Boston, MA, a decline in S. aureus infections has
              been accompanied by a shift towards increased antibiotic
              susceptibility. The rise in PSSA makes penicillin an increasingly
              viable treatment option.",
  journal  = "J. Clin. Microbiol.",
  month    =  nov,
  year     =  2017,
  keywords = "Staphylococcus;antibiotics;transmission-epidemiology;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Zhang2017-ar,
  title    = "Preliminary comparative genomics revealed pathogenic potential
              and international spread of Staphylococcus argenteus",
  author   = "Zhang, Dao-Feng and Zhi, Xiao-Yang and Zhang, Jing and Paoli,
              George C and Cui, Yan and Shi, Chunlei and Shi, Xianming",
  abstract = "BACKGROUND: Staphylococcus argenteus and S. schweitzeri, were
              recently proposed as novel species within S. aureus complex
              (SAC). S. argenteus has been reported in many countries and can
              threaten human health. S. schweitzeri has not been associated
              with human infections, but has been isolated from non-human
              primates. Questions regarding the evolution of pathogenicity of
              these two species will remain elusive until an exploratory
              evolutionary framework is established. RESULTS: We present
              genomic comparison analysis among members of SAC based on a
              pan-genome definition, which included 15 S. argenteus genomes
              (five newly sequenced), six S. schweitzeri genomes and 30
              divergent S. aureus genomes. The three species had divergent core
              genomes and rare interspecific recombination was observed among
              the core genes. However, some subtypes of staphylococcal cassette
              chromosome mec (SCCmec) elements and prophages were present in
              different species. Of 111 tested virulence genes of S. aureus, 85
              and 86 homologous genes were found in S. argenteus and S.
              schweitzeri, respectively. There was no difference in virulence
              gene content among the three species, but the sequence of most
              core virulence genes was divergent. Analysis of the agr locus and
              the genes in the capsular polysaccharides biosynthetic operon
              revealed that they both diverged before the speciation of SAC
              members. Furthermore, the widespread geographic distribution of
              S. argenteus, sequence type 2250, showed ambiguous
              biogeographical structure among geographically isolated
              populations, demonstrating an international spread of this
              pathogen. CONCLUSIONS: S. argenteus has spread among several
              countries, and invasive infections and persistent carriage may be
              not limited to currently reported regions. S. argenteus probably
              had undergone a recent host adaption and can cause human
              infections with a similar pathogenic potential.",
  journal  = "BMC Genomics",
  volume   =  18,
  number   =  1,
  pages    = "808",
  month    =  oct,
  year     =  2017,
  keywords = "Agr; Biogeographical structure; Capsular polysaccharides;
              Comparative genomics; Staphylococcus argenteus; Staphylococcus
              aureus; Staphylococcus schweitzeri; Virulence
              gene;Staphylococcus;confirmed\_SA-resistance-mutation;pangenome;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Amissah2017-yh,
  title    = "Methicillin Resistant \textit{Staphylococcus aureus} Transmission
              in a Ghanaian Burn Unit: The Importance of Active Surveillance in
              {Resource-Limited} Settings",
  author   = "Amissah, Nana Ama and Buultjens, Andrew H and Ablordey, Anthony
              and van Dam, Lieke and Opoku-Ware, Ampomah and Baines, Sarah L
              and Bulach, Dieter and Tetteh, Caitlin S and Prah, Isaac and van
              der Werf, Tjip S and Friedrich, Alexander W and Seemann, Torsten
              and van Dijl, Jan Maarten and Stienstra, Ymkje and Stinear,
              Timothy P and Rossen, John W",
  abstract = "Objectives:Staphylococcus aureus infections in burn patients can
              lead to serious complications and death. The frequency of S.
              aureus infection is high in low- and middle-income countries
              presumably due to limited resources, misuse of antibiotics and
              poor infection control. The objective of the present study was to
              apply population genomics to precisely define, for the first
              time, the transmission of antibiotic resistant S. aureus in a
              resource-limited setting in sub-Saharan Africa.
              Methods:Staphylococcus aureus surveillance was performed amongst
              burn patients and healthcare workers during a 7-months survey
              within the burn unit of the Korle Bu Teaching Hospital in Ghana.
              Results: Sixty-six S. aureus isolates (59 colonizing and 7
              clinical) were obtained from 31 patients and 10 healthcare
              workers. Twenty-one of these isolates were ST250-IV
              methicillin-resistant S. aureus (MRSA). Notably, 25 (81\%) of the
              31 patients carried or were infected with S. aureus within 24 h
              of admission. Genome comparisons revealed six distinct S. aureus
              clones circulating in the burn unit, and demonstrated multiple
              transmission events between patients and healthcare workers.
              Further, the collected S. aureus isolates exhibited a wide range
              of genotypic resistances to antibiotics, including trimethoprim
              (21\%), aminoglycosides (33\%), oxacillin (33\%), chloramphenicol
              (50\%), tetracycline (59\%) and fluoroquinolones (100\%).
              Conclusion: Population genomics uncovered multiple transmission
              events of S. aureus, especially MRSA, within the investigated
              burn unit. Our findings highlight lapses in infection control and
              prevention, and underscore the great importance of active
              surveillance to protect burn victims against multi-drug resistant
              pathogens in resource-limited settings.",
  journal  = "Front. Microbiol.",
  volume   =  8,
  pages    = "1906",
  month    =  oct,
  year     =  2017,
  keywords = "Staphylococcus aureus; burn patients; comparative genomics;
              healthcare workers; transmission
              events;Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Coll2017-jb,
  title    = "Longitudinal genomic surveillance of {MRSA} in the {UK} reveals
              transmission patterns in hospitals and the community",
  author   = "Coll, Francesc and Harrison, Ewan M and Toleman, Michelle S and
              Reuter, Sandra and Raven, Kathy E and Blane, Beth and Palmer,
              Beverley and Kappeler, A Ruth M and Brown, Nicholas M and
              T{\"o}r{\"o}k, M Est{\'e}e and Parkhill, Julian and Peacock,
              Sharon J",
  abstract = "Genome sequencing has provided snapshots of the transmission of
              methicillin-resistant Staphylococcus aureus (MRSA) during
              suspected outbreaks in isolated hospital wards. Scale-up to
              populations is now required to establish the full potential of
              this technology for surveillance. We prospectively identified all
              individuals over a 12-month period who had at least one
              MRSA-positive sample processed by a routine diagnostic
              microbiology laboratory in the East of England, which received
              samples from three hospitals and 75 general practitioner (GP)
              practices. We sequenced at least 1 MRSA isolate from 1465
              individuals (2282 MRSA isolates) and recorded epidemiological
              data. An integrated epidemiological and phylogenetic analysis
              revealed 173 transmission clusters containing between 2 and 44
              cases and involving 598 people (40.8\%). Of these, 118 clusters
              (371 people) involved hospital contacts alone, 27 clusters (72
              people) involved community contacts alone, and 28 clusters (157
              people) had both types of contact. Community- and
              hospital-associated MRSA lineages were equally capable of
              transmission in the community, with instances of spread in
              households, long-term care facilities, and GP practices. Our
              study provides a comprehensive picture of MRSA transmission in a
              sampled population of 1465 people and suggests the need to review
              existing infection control policy and practice.",
  journal  = "Sci. Transl. Med.",
  volume   =  9,
  number   =  413,
  month    =  oct,
  year     =  2017,
  keywords = "Staphylococcus;confirmed\_SA-resistance-mutation;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Wan2017-xr,
  title    = "Genomic comparison between Staphylococcus aureus {GN} strains
              clinically isolated from a familial infection case: {IS1272}
              transposition through a novel inverted repeat-replacing mechanism",
  author   = "Wan, Tsai-Wen and Higuchi, Wataru and Khokhlova, Olga E and Hung,
              Wei-Chun and Iwao, Yasuhisa and Wakayama, Masataka and Inomata,
              Noriyoshi and Takano, Tomomi and Lin, Yu-Tzu and Peryanova, Olga
              V and Kojima, Kenji K and Salmina, Alla B and Teng, Lee-Jene and
              Yamamoto, Tatsuo",
  abstract = "A bacterial insertion sequence (IS) is a mobile DNA sequence
              carrying only the transposase gene (tnp) that acts as a mutator
              to disrupt genes, alter gene expressions, and cause genomic
              rearrangements. ``Canonical'' ISs have historically been
              characterized by their terminal inverted repeats (IRs), which may
              form a stem-loop structure, and duplications of a short (non-IR)
              target sequence at both ends, called target site duplications
              (TSDs). The IS distributions and virulence potentials of
              Staphylococcus aureus genomes in familial infection cases are
              unclear. Here, we determined the complete circular genome
              sequences of familial strains from a Panton-Valentine leukocidin
              (PVL)-positive ST50/agr4 S. aureus (GN) infection of a 4-year old
              boy with skin abscesses. The genomes of the patient strain (GN1)
              and parent strain (GN3) were rich for ``canonical'' IS1272 with
              terminal IRs, both having 13 commonly-existing copies
              (ce-IS1272). Moreover, GN1 had a newly-inserted IS1272
              (ni-IS1272) on the PVL-converting prophage, while GN3 had two
              copies of ni-IS1272 within the DNA helicase gene and near rot.
              The GN3 genome also had a small deletion. The targets of
              ni-IS1272 transposition were IR structures, in contrast with
              previous ``canonical'' ISs. There were no TSDs. Based on a
              database search, the targets for ce-IS1272 were IRs or
              ``non-IRs''. IS1272 included a larger structure with tandem
              duplications of the left (IRL) side sequence; tnp included minor
              cases of a long fusion form and truncated form. One ce-IS1272 was
              associated with the segments responsible for immune evasion and
              drug resistance. Regarding virulence, GN1 expressed cytolytic
              peptides (phenol-soluble modulin $\alpha$ and $\delta$-hemolysin)
              and PVL more strongly than some other familial strains. These
              results suggest that IS1272 transposes through an IR-replacing
              mechanism, with an irreversible process unlike that of
              ``canonical'' transpositions, resulting in genomic variations,
              and that, among the familial strains, the patient strain has
              strong virulence potential based on community-associated
              virulence factors.",
  journal  = "PLoS One",
  volume   =  12,
  number   =  11,
  pages    = "e0187288",
  month    =  nov,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Stieber2017-ig,
  title    = "{PVL} overexpression due to genomic rearrangements and mutations
              in the S. aureus reference strain {ATCC25923}",
  author   = "Stieber, Bettina and Sabat, Artur and Monecke, Stefan and
              Slickers, Peter and Akkerboom, Viktoria and M{\"u}ller, Elke and
              Friedrich, Alexander W and Ehricht, Ralf",
  abstract = "OBJECTIVE: ATCC25923 is a Staphylococcus aureus strain that is
              positive for the Panton Valentin leukocidin. It has been used for
              decades as reference strain. We observed that two separately
              maintained clones of ATCC25923 (``G477 and G478'') differed
              grossly in the expression of this toxin. For that reason, both
              clones were sequenced using an Illumina MiSeq instrument. After
              assembling, the final sequences were analyzed and mapped to a
              previously published ATCC25923 sequence (GenBank CP009361) using
              bl2seq from the NCBI Blast2 package. RESULTS: The genomes of G477
              and G478 size 2778,859 and 2792,213 nucleotides, respectively.
              Both genomes include a circular plasmid of 27,490 nucleotides.
              The sequence of the G477 chromosome maps nearly exactly to
              CP009361. G478 has a slightly larger size because of the presence
              of an additional transposable element tnp13k. The second copy of
              that tnp13k element is located in an intergenic region between
              the genes mazF and rsbU. The sequences of the ATCC25923 clones
              G477 and G478 differ mainly in the insertion of a second tnp13k
              element between the genes mazF and rsbU. That insertion may lead
              to a different transcription of that genome region resulting in
              upregulation of the expression of the Panton-Valentine leukocidin
              in the ATCC25923 clone G478.",
  journal  = "BMC Res. Notes",
  volume   =  10,
  number   =  1,
  pages    = "576",
  month    =  nov,
  year     =  2017,
  keywords = "Panton-Valentine leukocidin (PVL); Protein expression; Sequence
              mutation; Staphylococcus
              aureus;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Takeuchi2016-jc,
  title    = "The Presence of Two {Receptor-Binding} Proteins Contributes to
              the Wide Host Range of Staphylococcal {Twort-Like} Phages",
  author   = "Takeuchi, Ippei and Osada, Keita and Azam, Aa Haeruman and
              Asakawa, Hiroaki and Miyanaga, Kazuhiko and Tanji, Yasunori",
  abstract = "UNLABELLED: Thanks to their wide host range and virulence,
              staphylococcal bacteriophages (phages) belonging to the genus
              Twortlikevirus (staphylococcal Twort-like phages) are regarded as
              ideal candidates for clinical application for Staphylococcus
              aureus infections due to the emergence of antibiotic-resistant
              bacteria of this species. To increase the usability of these
              phages, it is necessary to understand the mechanism underlying
              host recognition, especially the receptor-binding proteins (RBPs)
              that determine host range. In this study, we found that the
              staphylococcal Twort-like phage $\Phi$SA012 possesses at least
              two RBPs. Genomic analysis of five mutant phages of $\Phi$SA012
              revealed point mutations in orf103, in a region unique to
              staphylococcal Twort-like phages. Phages harboring mutated ORF103
              could not infect S. aureus strains in which wall teichoic acids
              (WTAs) are glycosylated with $\alpha$-N-acetylglucosamine
              ($\alpha$-GlcNAc). A polyclonal antibody against ORF103 also
              inhibited infection by $\Phi$SA012 in the presence of
              $\alpha$-GlcNAc, suggesting that ORF103 binds to $\alpha$-GlcNAc.
              In contrast, a polyclonal antibody against ORF105, a short tail
              fiber component previously shown to be an RBP, inhibited phage
              infection irrespective of the presence of $\alpha$-GlcNAc.
              Immunoelectron microscopy indicated that ORF103 is a tail fiber
              component localized at the bottom of the baseplate. From these
              results, we conclude that ORF103 binds $\alpha$-GlcNAc in WTAs,
              whereas ORF105, the primary RBP, is likely to bind the WTA
              backbone. These findings provide insight into the infection
              mechanism of staphylococcal Twort-like phages. IMPORTANCE:
              Staphylococcus phages belonging to the genus Twortlikevirus
              (called staphylococcal Twort-like phages) are considered
              promising agents for control of Staphylococcus aureus due to
              their wide host range and highly lytic capabilities. Although
              staphylococcal Twort-like phages have been studied widely for
              therapeutic purposes, the host recognition process of
              staphylococcal Twort-like phages remains unclear. This work
              provides new findings about the mechanisms of host recognition of
              the staphylococcal Twort-like phage $\Phi$SA012. The details of
              the host recognition mechanism of $\Phi$SA012 will allow us to
              analyze the mechanisms of infection and expand the utility of
              staphylococcal Twort-like phages for the control of S. aureus.",
  journal  = "Appl. Environ. Microbiol.",
  volume   =  82,
  number   =  19,
  pages    = "5763--5774",
  month    =  oct,
  year     =  2016,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Sivaraman2017-ta,
  title    = "Draft Genome Sequence of a {Methicillin-Resistant} Sequence Type
              39 Staphylococcal Isolate Obtained from Seafood",
  author   = "Sivaraman, G K and Vanik, Deesha and Visnuvinayagam, S and
              Prasad, Mothadaka Mukteswar and Murugadas, V and Nadella, Ranjit
              Kumar and Ravishankar, C N",
  abstract = "The draft genome sequence of a methicillin-resistant
              Staphylococcus aureus (MRSA) sequence type 39 (ST 39) isolate
              obtained from the dried ribbonfish of Gujarat, India, is reported
              here. Staphylococcus-specific genes were present in this MRSA
              isolate. The whole-genome sequence of this strain contains 2,693
              protein-coding genes and 70 RNAs within the 2.82-Mb genome.",
  journal  = "Genome Announc.",
  volume   =  5,
  number   =  45,
  month    =  nov,
  year     =  2017,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Shylo_E_Wardyn2018-vx,
  title    = "{Whole-Genome} Analysis of Recurrent Staphylococcus aureus
              {t571/ST398} Infection in Farmer, Iowa, {USA}",
  author   = "{Shylo E. Wardyn} and {Marc Stegger} and {Lance B. Price} and
              {Tara C. Smith}",
  abstract = "Staphylococcus aureus strain sequence type (ST) 398 has emerged
              during the last decade, largely among persons who have contact
              with swine or other livestock. Although colonization with ST398
              is common in livestock workers, infections are not frequently
              documented. We report recurrent ST398-IIa infection in an Iowa
              farmer in contact with swine and cattle.",
  journal  = "Emerging Infectious Disease journal",
  volume   =  24,
  number   =  1,
  year     =  2018,
  keywords = "antibiotic resistance; antimicrobial resistance; bacteria;
              farmer; farming; Iowa; livestock; methicillin-resistant
              Staphylococcus aureus; methicillin-sensitive S. aureus; MRSA;
              MSSA; sequence types; swine; United States; whole-genome
              analysis;
              zoonosis;Staphylococcus;Staphylococcus\_aureus\_genome\_papers"
 }

 @ARTICLE{Lilje2017-hx,
  title    = "Whole-genome sequencing of bloodstream Staphylococcus aureus
              isolates does not distinguish bacteraemia from endocarditis",
  author   = "Lilje, Berit and Rasmussen, Rasmus Vedby and Dahl, Anders and
              Stegger, Marc and Skov, Robert Leo and Fowler, Vance G and Ng,
              Kim Lee and Kiil, Kristoffer and Larsen, Anders Rhod and
              Petersen, Andreas and Johansen, Helle Krogh and Sch{\o}nheyder,
              Henrik Carl and Arpi, Magnus and Rosenvinge, Flemming S and
              Korup, Eva and H{\o}st, Ulla and Hassager, Christian and Gill,
              Sabine Ute Alice and Hansen, Thomas Fritz and Johannesen, Thor
              Bech and Smit, Jesper and S{\o}gaard, Peter and Skytt Andersen,
              Paal and Eske-Bruun, Niels",
  abstract = "Most Staphylococcus aureus isolates can cause invasive disease
              given the right circumstances, but it is unknown if some isolates
              are more likely to cause severe infections than others. S. aureus
              bloodstream isolates from 120 patients with definite infective
              endocarditis and 121 with S. aureus bacteraemia without infective
              endocarditis underwent whole-genome sequencing. Genome-wide
              association analysis was performed using a variety of
              bioinformatics approaches including SNP analysis, accessory
              genome analysis and k-mer based analysis. Core and accessory
              genome analyses found no association with either of the two
              clinical groups. In this study, the genome sequences of S. aureus
              bloodstream isolates did not discriminate between bacteraemia and
              infective endocarditis. Based on our study and the current
              literature, it is not convincing that a specific S. aureus
              genotype is clearly associated to infective endocarditis in
              patients with S. aureus bacteraemia.",
  journal  = "Microb Genom",
  volume   =  3,
  number   =  11,
  month    =  nov,
  year     =  2017,
  keywords = "Staphylococcus aureus; bacteraemia; genome-wide association;
              infective
              endocarditis;Staphylococcus;Staphylococcus\_aureus\_genome\_papers;GWAS-bacteria",
  language = "en"
 }

 @ARTICLE{Carter2017-go,
  title    = "Topical antibiotic use co-selects for the carriage of mobile
              genetic elements conferring resistance to unrelated
              antimicrobials in \textit{Staphylococcus aureus}",
  author   = "Carter, Glen P and Schultz, Mark B and Baines, Sarah L and
              Goncalves da Silva, Anders and Heffernan, Helen and Tiong, Audrey
              and Pham, Peter H and Monk, Ian R and Stinear, Timothy P and
              Howden, Benjamin P and Williamson, Deborah A",
  abstract = "Topical antibiotics such as mupirocin and fusidic acid are
              commonly used in the prevention and treatment of skin infections,
              particularly those caused by staphylococci. However, widespread
              use of these agents is associated with increased resistance to
              these agents, potentially limiting their efficacy. Of particular
              concern is the observation that resistance to topical antibiotics
              is often associated with multidrug resistance, suggesting that
              topical antibiotics may play a role in the emergence of
              multidrug-resistant (MDR) strains.New Zealand (NZ) has some of
              the highest globally recorded rates of topical antibiotic usage
              and resistance. Using a combination of Pacific Biosciences Single
              Molecule Real Time (SMRT) whole genome sequencing, Illumina short
              read sequencing and Bayesian phylogenomic modelling on 118 new
              multilocus sequence type 1 (ST1) community Staphylococcus aureus
              isolates from New Zealand and 61 publically available
              international ST1 genome sequences, we demonstrate a strong
              correlation between the clinical introduction of topical
              antibiotics and the emergence of MDR ST1 S. aureus We also
              provide in vitro experimental evidence showing that exposure to
              topical antibiotics can lead to the rapid selection of MDR S.
              aureus isolates carrying plasmids that confer resistance to
              multiple unrelated antibiotics, from within a mixed population of
              competitor strains. These findings have important implications
              regarding the impact of the indiscriminate use of topical
              antibiotics.",
  journal  = "Antimicrob. Agents Chemother.",
  month    =  dec,
  year     =  2017,
  keywords = "Staphylococcus;antibiotics;chlorhexidine;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Chen2018-bt,
  title    = "Draft Genome Sequence of {USA100} {Methicillin-Resistant}
              \textit{Staphylococcus aureus} Strain 209",
  author   = "Chen, Yingfeng and Crosby, Heidi A and Oosthuysen, 2nd, Wilhelm F
              and Diekema, Daniel J and Kelley, Scott T and Horswill, Alexander
              R",
  abstract = "USA100 strains are significant contributors to the overall burden
              of health care-associated methicillin-resistant Staphylococcus
              aureus (MRSA) infections. Strain 209 is a representative MRSA
              isolate that serves as a model organism for agr type II studies
              and USA100 virulence assessments. We present a draft genome
              sequence of this strain.",
  journal  = "Genome Announc.",
  volume   =  6,
  number   =  1,
  month    =  jan,
  year     =  2018,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Challagundla2018-vw,
  title    = "Range Expansion and the Origin of {USA300} North American
              Epidemic {Methicillin-Resistant} Staphylococcus aureus",
  author   = "Challagundla, Lavanya and Luo, Xiao and Tickler, Isabella A and
              Didelot, Xavier and Coleman, David C and Shore, Anna C and
              Coombs, Geoffrey W and Sordelli, Daniel O and Brown, Eric L and
              Skov, Robert and Larsen, Anders Rhod and Reyes, Jinnethe and
              Robledo, Iraida E and Vazquez, Guillermo J and Rivera, Raul and
              Fey, Paul D and Stevenson, Kurt and Wang, Shu-Hua and Kreiswirth,
              Barry N and Mediavilla, Jose R and Arias, Cesar A and Planet,
              Paul J and Nolan, Rathel L and Tenover, Fred C and Goering,
              Richard V and Robinson, D Ashley",
  abstract = "The USA300 North American epidemic (USA300-NAE) clone of
              methicillin-resistant Staphylococcus aureus has caused a wave of
              severe skin and soft tissue infections in the United States since
              it emerged in the early 2000s, but its geographic origin is
              obscure. Here we use the population genomic signatures expected
              from the serial founder effects of a geographic range expansion
              to infer the origin of USA300-NAE and identify polymorphisms
              associated with its spread. Genome sequences from 357 isolates
              from 22 U.S. states and territories and seven other countries are
              compared. We observe two significant signatures of range
              expansion, including decreases in genetic diversity and increases
              in derived allele frequency with geographic distance from the
              Pennsylvania region. These signatures account for approximately
              half of the core nucleotide variation of this clone, occur genome
              wide, and are robust to heterogeneity in temporal sampling of
              isolates, human population density, and recombination detection
              methods. The potential for positive selection of a gyrA
              fluoroquinolone resistance allele and several intergenic regions,
              along with a 2.4 times higher recombination rate in a resistant
              subclade, is noted. These results are the first to show a pattern
              of genetic variation that is consistent with a range expansion of
              an epidemic bacterial clone, and they highlight a rarely
              considered but potentially common mechanism by which genetic
              drift may profoundly influence bacterial genetic
              variation.IMPORTANCE The process of geographic spread of an
              origin population by a series of smaller populations can result
              in distinctive patterns of genetic variation. We detect these
              patterns for the first time with an epidemic bacterial clone and
              use them to uncover the clone's geographic origin and variants
              associated with its spread. We study the USA300 clone of
              methicillin-resistant Staphylococcus aureus, which was first
              noticed in the early 2000s and subsequently became the leading
              cause of skin and soft tissue infections in the United States.
              The eastern United States is the most likely origin of epidemic
              USA300. Relatively few variants, which include an antibiotic
              resistance mutation, have persisted during this clone's spread.
              Our study suggests that an early chapter in the genetic history
              of this epidemic bacterial clone was greatly influenced by random
              subsampling of isolates during the clone's geographic spread.",
  journal  = "MBio",
  volume   =  9,
  number   =  1,
  month    =  jan,
  year     =  2018,
  keywords = "epidemics; fluoroquinolones; founder effects; genetic drift;
              population genetics; range
              expansion;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Delgado-Baquerizo2018-zw,
  title     = "A global atlas of the dominant bacteria found in soil",
  author    = "Delgado-Baquerizo, Manuel and Oliverio, Angela M and Brewer,
               Tess E and Benavent-Gonz{\'a}lez, Alberto and Eldridge, David J
               and Bardgett, Richard D and Maestre, Fernando T and Singh,
               Brajesh K and Fierer, Noah",
  abstract  = "The immense diversity of soil bacterial communities has stymied
               efforts to characterize individual taxa and document their
               global distributions. We analyzed soils from 237 locations
               across six continents and found that only 2\% of bacterial
               phylotypes (~500 phylotypes) consistently accounted for almost
               half of the soil bacterial communities worldwide. Despite the
               overwhelming diversity of bacterial communities, relatively few
               bacterial taxa are abundant in soils globally. We clustered
               these dominant taxa into ecological groups to build the first
               global atlas of soil bacterial taxa. Our study narrows down the
               immense number of bacterial taxa to a ``most wanted'' list that
               will be fruitful targets for genomic and cultivation-based
               efforts aimed at improving our understanding of soil microbes
               and their contributions to ecosystem functioning.",
  journal   = "Science",
  publisher = "American Association for the Advancement of Science",
  volume    =  359,
  number    =  6373,
  pages     = "320--325",
  month     =  jan,
  year      =  2018,
  keywords  = "microbiome;climate;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language  = "en"
 }

 @ARTICLE{Becker2018-xs,
  title    = "{Plasmid-Encoded} Transferable {mecB-Mediated} Methicillin
              Resistance in Staphylococcus aureus",
  author   = "Becker, Karsten and van Alen, Sarah and Idelevich, Evgeny A and
              Schleimer, Nina and Seggewi{\ss}, Jochen and Mellmann, Alexander
              and Kaspar, Ursula and Peters, Georg",
  abstract = "During cefoxitin-based nasal screening, phenotypically
              categorized methicillin-resistant Staphylococcus aureus (MRSA)
              was isolated and tested negative for the presence of the mecA and
              mecC genes as well as for the SCCmec-orfX junction region. The
              isolate was found to carry a mecB gene previously described for
              Macrococcus caseolyticus but not for staphylococcal species. The
              gene is flanked by $\beta$-lactam regulatory genes similar to
              mecR, mecI, and blaZ and is part of an 84.6-kb
              multidrug-resistance plasmid that harbors genes encoding
              additional resistances to aminoglycosides (aacA-aphD, aphA, and
              aadK) as well as macrolides (ermB) and tetracyclines (tetS). This
              further plasmidborne $\beta$-lactam resistance mechanism harbors
              the putative risk of acceleration or reacceleration of MRSA
              spread, resulting in broad ineffectiveness of $\beta$-lactams as
              a main therapeutic application against staphylococcal infections.",
  journal  = "Emerg. Infect. Dis.",
  volume   =  24,
  number   =  2,
  pages    = "242--248",
  month    =  feb,
  year     =  2018,
  keywords = "MRSA; Macrococcus; Staphylococcaceae; Staphylococcus aureus;
              antibacterial agents; antimicrobial resistance; bacteria; mecB;
              methicillin-resistant Staphylococcus aureus; microbial genome;
              plasmids;
              staphylococci;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Ronco2018-qi,
  title    = "Genomic investigation of Staphylococcus aureus isolates from bulk
              tank milk and dairy cows with clinical mastitis",
  author   = "Ronco, Troels and Klaas, Ilka C and Stegger, Marc and Svennesen,
              Line and Astrup, L{\ae}rke B and Farre, Michael and Pedersen,
              Karl",
  abstract = "Staphylococcus aureus is one of the most common pathogens that
              cause mastitis in dairy cows. Various subtypes, virulence genes
              and mobile genetic elements have been associated with isolates
              from bulk tank milk and clinical mastitis. So far, no Danish
              cattle associated S. aureus isolates have been whole-genome
              sequenced and further analyzed. Thus, the main objective was to
              investigate the population structure and genomic content of
              isolates from bulk tank milk and clinical mastitis, using
              whole-genome sequencing. This may reveal the origin of strains
              that cause clinical mastitis. S. aureus isolates from bulk tank
              milk (n = 94) and clinical mastitis (n = 63) were collected from
              91 and 24 different farms, respectively and whole-genome
              sequenced. The genomic content was analyzed and a phylogenetic
              tree based on single nucleotide polymorphisms was constructed. In
              general, the isolates from both bulk tank milk and clinical
              mastitis were of similar genetic background. This suggests that
              dairy cows are natural carriers of the S. aureus subtypes that
              cause clinical mastitis if the right conditions are present and
              that a broad range of subtypes cause mastitis. A phylogenetic
              cluster that mostly consisted of ST151 isolates carried three
              mobile genetic elements that were primarily found in this group.
              The prevalence of resistance genes was generally low. However,
              the first ST398 methicillin resistant S. aureus isolate from a
              Danish dairy cow with clinical mastitis was detected.",
  journal  = "Vet. Microbiol.",
  volume   =  215,
  pages    = "35--42",
  month    =  feb,
  year     =  2018,
  keywords = "Bulk tank milk; Clinical mastitis; Genomic analysis; S. aureus;
              Virulence and resistance
              genes;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Choe2018-me,
  title    = "Genome-scale analysis of Methicillin-resistant Staphylococcus
              aureus {USA300} reveals a tradeoff between pathogenesis and drug
              resistance",
  author   = "Choe, Donghui and Szubin, Richard and Dahesh, Samira and Cho,
              Suhyung and Nizet, Victor and Palsson, Bernhard and Cho,
              Byung-Kwan",
  abstract = "Staphylococcus aureus infection is a rising public health care
              threat. S. aureus is believed to have elaborate regulatory
              networks that orchestrate its virulence. Despite its importance,
              the systematic understanding of the transcriptional landscape of
              S. aureus is limited. Here, we describe the primary transcriptome
              landscape of an epidemic USA300 isolate of community-acquired
              methicillin-resistant S. aureus. We experimentally determined
              1,861 transcription start sites with their principal promoter
              elements, including well-conserved -35 and -10 elements and
              weakly conserved -16 element and 5' untranslated regions
              containing AG-rich Shine-Dalgarno sequence. In addition, we
              identified 225 genes whose transcription was initiated from
              multiple transcription start sites, suggesting potential
              regulatory functions at transcription level. Along with the
              transcription unit architecture derived by integrating the
              primary transcriptome analysis with operon prediction, the
              measurement of differential gene expression revealed the
              regulatory framework of the virulence regulator Agr, the
              SarA-family transcriptional regulators, and $\beta$-lactam
              resistance regulators. Interestingly, we observed a complex
              interplay between virulence regulation, $\beta$-lactam
              resistance, and metabolism, suggesting a possible tradeoff
              between pathogenesis and drug resistance in the USA300 strain.
              Our results provide platform resource for the location of
              transcription initiation and an in-depth understanding of
              transcriptional regulation of pathogenesis, virulence, and
              antibiotic resistance in S. aureus.",
  journal  = "Sci. Rep.",
  volume   =  8,
  number   =  1,
  pages    = "2215",
  month    =  feb,
  year     =  2018,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Suligoy2018-de,
  title    = "Mutation of Agr Is Associated with the Adaptation
              ofStaphylococcus aureusto the Host during Chronic Osteomyelitis",
  author   = "Suligoy, Carlos M and Lattar, Santiago M and Noto Llana,
              Mari{\'a}ngeles and Gonz{\'a}lez, Cintia D and Alvarez,
              Luc{\'\i}a P and Robinson, D Ashley and G{\'o}mez, Marisa I and
              Buzzola, Fernanda R and Sordelli, Daniel O",
  abstract = "Selection pressures exerted onStaphylococcus aureusby host
              factors may lead to the emergence of mutants better adapted to
              the evolving conditions at the infection site. This study was
              aimed at identifying the changes that occur inS. aureusexposed to
              the host defense mechanisms during chronic osteomyelitis and
              evaluating whether these changes affect the virulence of the
              organism. Genome assessment of twoS. aureusisolates collected 13
              months apart (HU-85a and HU-85c) from a host with chronic
              osteomyelitis was made by whole genome sequencing. Agr
              functionality was assessed by qRT-PCR. Isolates were tested in a
              rat model of osteomyelitis and the bacterial load (CFU/tibia) and
              the morphometric osteomyelitic index (OI) were determined. The
              ability of the isolates to trigger the release of proinflammatory
              cytokines was determined on macrophages in culture. Persistence
              ofS. aureuswithin the host resulted in anagrCframeshift mutation
              that likely led to the observed phenotype. The capacity to cause
              bone tissue damage and trigger proinflammatory cytokines by
              macrophages of theagr-deficient, unencapsulated derivative
              (HU-85c) was decreased when compared with those of the isogenic
              CP8-capsulated parental strain (HU-85a). By comparison, no
              significant differences were found in the bacterial load or the
              OI from rats challenged with isogenic Reynolds strains [CP5, CP8,
              and non-typeable (NT)], indicating that lack of CP expression
              alone was not likely responsible for the reduced capacity to
              cause tissue damage in HU-85c compared with HU-85a. The
              production of biofilm was significantly increased in the isogenic
              derivative HU-85c. Lack ofagr-dependent factors makesS.
              aureusless virulent during chronic osteomyelitis and alteration
              of theagrfunctionality seems to permit better adaptation ofS.
              aureusto the chronically infected host.",
  journal  = "Front. Cell. Infect. Microbiol.",
  volume   =  8,
  pages    = "18",
  month    =  feb,
  year     =  2018,
  keywords = "Staphylococcus aureus; adaptation; agr; biofilm; capsular
              polysaccharide; chronic; infection;
              osteomyelitis;Staphylococcus;host-pathogen;within-host-evolution;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Argemi2018-ot,
  title    = "Comparative Genomics and Identification of an
              {Enterotoxin-Bearing} Pathogenicity Island, {SEPI-1/SECI-1}, in
              Staphylococcus epidermidis Pathogenic Strains",
  author   = "Argemi, Xavier and Nanoukon, Chim{\`e}ne and Affolabi, Dissou and
              Keller, Daniel and Hansmann, Yves and Riegel, Philippe and
              Baba-Moussa, Lamine and Pr{\'e}vost, Gilles",
  abstract = "Staphylococcus epidermidis is a leading cause of nosocomial
              infections, majorly resistant to beta-lactam antibiotics, and may
              transfer several mobile genetic elements among the members of its
              own species, as well as toStaphylococcus aureus; however, a
              genetic exchange fromS. aureustoS. epidermidisremains
              controversial. We recently identified two pathogenic clinical
              strains ofS. epidermidisthat produce a staphylococcal enterotoxin
              C3-like (SEC) similar to that byS. aureuspathogenicity islands.
              This study aimed to determine the genetic environment of the
              SEC-coding sequence and to identify the mobile genetic elements.
              Whole-genome sequencing and annotation of theS.
              epidermidisstrains were performed using Illumina technology and a
              bioinformatics pipeline for assembly, which provided evidence
              that the SEC-coding sequences were located in a composite
              pathogenicity island that was previously described in theS.
              epidermidisstrain FRI909, called SePI-1/SeCI-1, with 83.8-89.7\%
              nucleotide similarity. Various other plasmids were identified,
              particularly p\_3\_95 and p\_4\_95, which carry antibiotic
              resistance genes (hsrAanddfrG, respectively), and share
              homologies with SAP085A and pUSA04-2-SUR11, two plasmids
              described inS. aureus. Eventually, one complete prophage was
              identified, $\Phi$SE90, sharing 30 out of 52 coding sequences
              with theAcinetobacterphage vB\_AbaM\_IME200. Thus, the
              SePI-1/SeCI-1 pathogenicity island was identified in two
              pathogenic strains ofS. epidermidisthat produced a SEC
              enterotoxin causing septic shock. These findings suggest the
              existence of in vivo genetic exchange fromS. aureustoS.
              epidermidis.",
  journal  = "Toxins",
  volume   =  10,
  number   =  3,
  month    =  feb,
  year     =  2018,
  keywords = "Staphylococcus aureus; Staphylococcus epidermidis; core genome;
              enterotoxin; pan-genome; pathogenicity
              island;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Kumburu2018-uw,
  title    = "Hospital Epidemiology of {Methicillin-ResistantStaphylococcus}
              aureusin a Tertiary Care Hospital in Moshi, Tanzania, as
              Determined by Whole Genome Sequencing",
  author   = "Kumburu, Happiness H and Sonda, Tolbert and Leekitcharoenphon,
              Pimlapas and van Zwetselaar, Marco and Lukjancenko, Oksana and
              Alifrangis, Michael and Lund, Ole and Mmbaga, Blandina T and
              Kibiki, Gibson and Aarestrup, Frank M",
  abstract = "Objective: To determine molecular epidemiology of
              methicillin-resistantS. aureusin Tanzania using whole genome
              sequencing. Methods: DNA from 33Staphylococcusspecies was
              recovered from subcultured archivedStaphylococcusisolates. Whole
              genome sequencing was performed on Illumina Miseq using
              paired-end 2 $\times$ 250 bp protocol. Raw sequence data were
              analyzed using online tools. Results: Full susceptibility to
              vancomycin and chloramphenicol was observed. Thirteen isolates
              (43.3\%) resisted cefoxitin and other antimicrobials tested.
              Multilocus sequence typing revealed 13 different sequence types
              among the 30S. aureusisolates, with ST-8 (n= seven, 23\%) being
              the most common. Gene detection inS.aureusstains were as
              follows:mecA, 10 (33.3\%);pvl, 5 (16.7\%);tst, 2 (6.7\%). The SNP
              difference among the six Tanzanian ST-8 MRSA isolates ranged from
              24 to 196 SNPs and from 16 to 446 SNPs when using the
              USA300\_FPR3757 or the USA500\_2395 as a reference, respectively.
              The mutation rate was 1.38 $\times$ 10-11SNPs/site/year or 1.4
              $\times$ 10-6SNPs/site/year as estimated by USA300\_FPR3757 or
              the USA500\_2395, respectively. Conclusion: S. aureus isolates
              causing infections in hospitalized patients in Moshi are highly
              diverse and epidemiologically unrelated. Temporal phylogenetic
              analysis provided better resolution on transmission and
              introduction of MRSA and it may be important to include this in
              future routines.",
  journal  = "Biomed Res. Int.",
  volume   =  2018,
  pages    = "2087693",
  month    =  jan,
  year     =  2018,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Bazaid2018-tp,
  title    = "Fatty Acid Supplementation Reverses the Small Colony Variant
              Phenotype in {Triclosan-Adapted} Staphylococcus aureus: Genetic,
              Proteomic and Phenotypic Analyses",
  author   = "Bazaid, Abdulrahman S and Forbes, Sarah and Humphreys, Gavin J
              and Ledder, Ruth G and O'Cualain, Ronan and McBain, Andrew J",
  abstract = "Staphylococcus aureus can develop a small colony variant (SCV)
              phenotype in response to sub-lethal exposure to the biocide
              triclosan. In the current study, whole genome sequencing was
              performed and changes in virulence were investigated in five
              Staphylococcus aureus strains following repeated exposure to
              triclosan. Following exposure, 4/5 formed SCV and exhibited point
              mutations in the triclosan target gene fabI with 2/4 SCVs showing
              mutations in both fabI and fabD. The SCV phenotype was in all
              cases immediately reversed by nutritional supplementation with
              fatty acids or by repeated growth in the absence of triclosan,
              although fabI mutations persisted in 3/4 reverted SCVs.
              Virulence, determined using keratinocyte invasion and Galleria
              mellonella pathogenicity assays was significantly (p < 0.05)
              attenuated in 3/4 SCVs and in the non-SCV triclosan-adapted
              bacterium. Proteomic analysis revealed elevated FabI in 2/3 SCV
              and down-regulation in a protein associated with virulence in 1/3
              SCV. In summary, attenuated keratinocyte invasion and larval
              virulence in triclosan-induced SCVs was associated with decreases
              in growth rate and virulence factor expression. Mutation occurred
              in fabI, which encodes the main triclosan target in all SCVs and
              the phenotype was reversed by fatty acid supplementation,
              demonstrating an association between fatty acid metabolism and
              triclosan-induced SCV.",
  journal  = "Sci. Rep.",
  volume   =  8,
  number   =  1,
  pages    = "3876",
  month    =  mar,
  year     =  2018,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{You2018-er,
  title    = "Genomic differences between nasal Staphylococcus aureus from hog
              slaughterhouse workers and their communities",
  author   = "You, Yaqi and Song, Li and Nonyane, Bareng A S and Price, Lance B
              and Silbergeld, Ellen K",
  abstract = "New human pathogens can emerge from the livestock-human interface
              and spread into human populations through many pathways including
              livestock products. Occupational contact with livestock is a risk
              factor for exposure to those pathogens and may cause further
              spreading of those pathogens in the community. The current study
              used whole genome sequencing to explore nasal Staphylococcus
              aureus obtained from hog slaughterhouse workers and their
              community members, all of whom resided in a livestock-dense
              region in rural North Carolina. Sequence data were analyzed for
              lineage distribution, pathogenicity-related genomic features, and
              mobile genetic elements. We observed evidence of nasal S. aureus
              differences between hog workers and non-workers. Nasal S. aureus
              from hog workers showed a greater lineage diversity than nasal S.
              aureus from community residents. Hog worker isolates were less
              likely to carry the $\varphi$Sa3 prophage and human-specific
              immune evasion cluster genes than community resident isolates
              ($\varphi$Sa3 prophage: 54.5\% vs. 91.7\%, Benjamini-Hochberg
              (BH) corrected p = 0.035; immune evasion cluster genes: 66.7\%
              vs. 100\%, BH p = 0.021). Hog worker isolates had a lower
              prevalence and diversity of enterotoxins than community resident
              isolates, particularly lacking the enterotoxin gene cluster
              (39.4\% vs. 70.8\%, BH p = 0.125). Moreover, hog worker isolates
              harbored more diverse antibiotic resistance genes, with a higher
              prevalence of carriage of multiple resistance genes, than
              community resident isolates (75.8\% vs. 29.2\%, BH p = 0.021).
              Phylogenetic analysis of all ST5 isolates, the most abundant
              lineage in the collection, further supported separation of
              isolates from hog workers and non-workers. Together, our
              observations suggest impact of occupational contact with
              livestock on nasal S. aureus colonization and highlight the need
              for further research on the complex epidemiology of S. aureus at
              the livestock-human interface.",
  journal  = "PLoS One",
  volume   =  13,
  number   =  3,
  pages    = "e0193820",
  month    =  mar,
  year     =  2018,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Worthing2018-ee,
  title    = "Qac genes and biocide tolerance in clinical veterinary
              methicillin-resistant and methicillin-susceptible Staphylococcus
              aureus and Staphylococcus pseudintermedius",
  author   = "Worthing, Kate A and Marcus, Alan and Abraham, Sam and Trott,
              Darren J and Norris, Jacqueline M",
  abstract = "Qac genes are associated with increased tolerance to quaternary
              ammonium compounds and other cationic biocides such as
              chlorhexidine. This study aimed to determine whether qac genes
              and increased biocide tolerance were present in 125 clinical
              methicillin-resistant and susceptible veterinary staphylococci. A
              total of 125 methicillin-resistant Staphylococcus aureus (MRSA)
              and methicillin-resistant and -susceptible Staphylococcus
              pseudintermedius (MRSP and MSSP) from three archived Australian
              veterinary staphylococci collections underwent whole genome
              sequencing, multilocus sequence typing and qac gene screening.
              Two MRSA isolates (12\%) harboured qacA/B genes; both isolates
              were ST8 from horses. QacJ, qacG and smr genes were identified in
              28/90 (31\%) MRSP and 1/18 (6\%) MSSP isolates. ST71 MRSP was
              significantly more likely to harbour qac genes than other MRSP
              clones (p < 0.05). A random subset of 31 isolates underwent
              minimum bactericidal concentration (MBC) testing against
              F10SCTM(benzalkonium chloride and biguanide), and
              HexaconTM(chlorhexidine gluconate), with and without the addition
              of bovine serum albumin (BSA) as an in vitro substitute for
              organic matter contamination. Qac genes were not associated with
              increased phenotypic biocide tolerance but biocide efficacy was
              significantly affected by the presence of BSA. In the absence of
              BSA, all MBC values were well below the recommended usage
              concentration. When BSA was present, regardless of qac gene
              presence, 50\% of MRSA and 43\% of MRSP had an F10SCTMMBC above
              the recommended concentration for general disinfection. Qac genes
              did not confer increased in vitro biocide tolerance to veterinary
              staphylococci. Organic matter contamination must be minimized to
              ensure the efficacy of biocides against MRSA and MRSP.",
  journal  = "Vet. Microbiol.",
  volume   =  216,
  pages    = "153--158",
  month    =  mar,
  year     =  2018,
  keywords = "Biocide tolerance; Methicillin-resistance; Qac genes;
              Staphylococcus; Veterinary;
              Zoonosis;Staphylococcus;chlorhexidine;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 % The entry below contains non-ASCII chars that could not be converted
 % to a LaTeX equivalent.
 @ARTICLE{Anson2018-he,
  title    = "{DNA} extraction from primary liquid blood cultures for
              bloodstream infection diagnosis using whole genome sequencing",
  author   = "Anson, Luke W and Chau, Kevin and Sanderson, Nicholas and
              Hoosdally, Sarah and Bradley, Phelim and Iqbal, Zamin and Phan,
              Hang and Foster, Dona and Oakley, Sarah and Morgan, Marcus and
              Peto, Tim E A and {Modernizing Medical Microbiology Informatics
              Group Mmmig} and Crook, Derrick W and Pankhurst, Louise J",
  abstract = "PURPOSE: Speed of bloodstream infection diagnosis is vital to
              reduce morbidity and mortality. Whole genome sequencing (WGS)
              performed directly from liquid blood culture could provide
              single-assay species and antibiotic susceptibility prediction;
              however, high inhibitor and human cell/DNA concentrations limit
              pathogen recovery. We develop a method for the preparation of
              bacterial DNA for WGS-based diagnostics direct from liquid blood
              culture. METHODOLOGY: We evaluate three commercial DNA extraction
              kits: BiOstic Bacteraemia, Amplex Hyplex and MolYsis Plus.
              Differential centrifugation, filtration, selective lysis and
              solid-phase reversible immobilization bead clean-up are tested to
              improve human cells/DNA and inhibitor removal. Using WGS
              (Illumina/MinION), we assess human DNA removal, pathogen
              recovery, and predict species and antibiotic susceptibility
              inpositive blood cultures of 44 Gram-negative and 54
              Staphylococcus species.Results/Key findings. BiOstic kit
              extractions yield the greatest mean DNA concentration, 94-301 ng
              µl-1, versus 0-2.5 ng µl-1using Amplex and MolYsis kits. However,
              we note higher levels of inhibition (260/280 ratio 0.9-2.1) and
              human DNA (0.0-4.4$\times$106 copies) in BiOstic extracts.
              Differential centrifugation (2000 g, 1 min) prior to BiOstic
              extraction reduces human DNA by 63-89 \% with selective lysis
              minimizing by a further 62 \%. Post-extraction bead clean-up
              lowers inhibition. Overall, 67 \% of sequenced samples (Illumina
              MiSeq) contain 93 \% concordance between WGS-based species and
              susceptibility predictions and clinical diagnosis. If >60 \% of
              sequencing reads are human (7/98 samples) susceptibility
              prediction becomes compromised. Novel MinION-based WGS (n=9)
              currently gives rapid species identification but not
              susceptibility prediction. CONCLUSION: Our method for DNA
              preparation allows WGS-based diagnosis direct from blood culture
              bottles, providing species and antibiotic susceptibility
              prediction in a single assay.",
  journal  = "J. Med. Microbiol.",
  volume   =  67,
  number   =  3,
  pages    = "347--357",
  month    =  mar,
  year     =  2018,
  keywords = "bacteraemia; bloodstream infection; sepsis; whole genome
              sequencing;Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }

 @ARTICLE{Purves2018-im,
  title    = "A horizontally gene transferred copper resistance locus confers
              hyper-resistance to antibacterial copper toxicity and enables
              survival of community acquired methicillin resistant
              Staphylococcus aureus {USA300} in macrophages",
  author   = "Purves, Joanne and Thomas, Jamie and Riboldi, Gustavo Pelicoli
              and Zapotoczna, Marta and Tarrant, Emma and Andrew, Peter W and
              Londo{\~n}o, Alejandra and Planet, Paul J and Geoghegan, Joan A
              and Waldron, Kevin J and Morrissey, Julie A",
  abstract = "Excess copper is highly toxic and forms part of the host innate
              immune system's antibacterial arsenal, accumulating at sites of
              infection and acting within macrophages to kill engulfed
              pathogens. We show for the first time that a novel, horizontally
              gene transferred copper resistance locus (copXL), uniquely
              associated with the SCCmec elements of the highly virulent,
              epidemic, community acquired methicillin resistant Staphylococcus
              aureus (CA-MRSA) USA300, confers copper hyper-resistance. These
              genes are additional to existing core genome copper resistance
              mechanisms, and are not found in typical S. aureus lineages, but
              are increasingly identified in emerging pathogenic isolates. Our
              data show that CopX, a putative P1B-3-ATPase efflux transporter,
              and CopL, a novel lipoprotein, confer copper hyper-resistance
              compared to typical S. aureus strains. The copXL genes form an
              operon that is tightly repressed in low copper environments by
              the copper regulator CsoR. Significantly, CopX and CopL are
              important for S. aureus USA300 intracellular survival within
              macrophages. Therefore the emergence of new S. aureus clones with
              the copXL locus has significant implications for public health
              because these genes confer increased resistance to antibacterial
              copper toxicity, enhancing bacterial fitness by altering S.
              aureus interaction with innate immunity. This article is
              protected by copyright. All rights reserved.",
  journal  = "Environ. Microbiol.",
  month    =  mar,
  year     =  2018,
  keywords = "Staphylococcus;Staphylococcus\_aureus\_genome\_papers",
  language = "en"
 }