{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T17:36:00Z","timestamp":1787679360356,"version":"build-2784847793"},"reference-count":125,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2016,12,15]],"date-time":"2016-12-15T00:00:00Z","timestamp":1481760000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0168177","type":"journal-article","created":{"date-parts":[[2016,12,15]],"date-time":"2016-12-15T18:57:35Z","timestamp":1481828255000},"page":"e0168177","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":31,"title":["Genome Analysis of Streptococcus pyogenes Associated with Pharyngitis and Skin Infections"],"prefix":"10.1371","volume":"11","author":[{"given":"Joe","family":"Ibrahim","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan A.","family":"Eisen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guillaume","family":"Jospin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David A.","family":"Coil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Georges","family":"Khazen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3653-8940","authenticated-orcid":true,"given":"Sima","family":"Tokajian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2016,12,15]]},"reference":[{"issue":"3","key":"ref1","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1128\/CMR.13.3.470-511.2000","article-title":"Pathogenesis of Group A Streptococcal Infections","volume":"13","author":"MW Cunningham","year":"2000","journal-title":"Clin Microbiol Rev"},{"issue":"2","key":"ref2","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1128\/CMR.00101-13","article-title":"Disease Manifestations and Pathogenic Mechanisms of Group A Streptococcus","volume":"27","author":"MJ Walker","year":"2014","journal-title":"Clin Microbiol Rev"},{"issue":"46","key":"ref3","article-title":"Epidemiology, treatment, and control of infection with Streptococcus pyogenes in Germany","volume":"4","author":"B Twisselmann","year":"2000","journal-title":"Euro Surveill"},{"issue":"3","key":"ref4","doi-asserted-by":"crossref","first-page":"514","DOI":"10.3201\/eid1003.030252","article-title":"Antibiotic Selection Pressure and Resistance in Streptococcus pneumoniae and Streptococcus pyogenes","volume":"10","author":"CW Albrich","year":"2004","journal-title":"Emerg Infect Diseases"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1038\/ng.3147","article-title":"Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance","volume":"47","author":"RM Davies","year":"2015","journal-title":"Nature Genet"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1016\/j.otohns.2007.07.033","article-title":"Systematic review of factors contributing to penicillin treatment failure in Streptococcus pyogenes pharyngitis","volume":"137","author":"ME Pichichero","year":"2007","journal-title":"Otolaryngol Head Neck Surg"},{"issue":"2","key":"ref7","doi-asserted-by":"crossref","first-page":"e2","DOI":"10.1038\/emi.2012.9","article-title":"Streptococcus pyogenes and reemergence of scarlet fever as a public health concern","volume":"1","author":"S Wong","year":"2012","journal-title":"Emerg Microbes Infect"},{"issue":"2","key":"ref8","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1086\/524687","article-title":"Lysogenic transfer of group A Streptococcus superantigen gene among streptococci","volume":"197","author":"I Vojtek","year":"2008","journal-title":"J Infect Dis"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1128\/JCM.02155-08","article-title":"Clinical and microbiological characteristics of severe Streptococcus pyogenes disease in Europe","volume":"47","author":"B Luca-Harari","year":"2009","journal-title":"J Clin Microbiol"},{"issue":"10","key":"ref10","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1016\/S1473-3099(09)70178-1","article-title":"Global emm type distribution of group A streptococci: Systematic review and implications for vaccine development","volume":"9","author":"AC Steer","year":"2009","journal-title":"Lancet Infect Dis"},{"issue":"11","key":"ref11","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1016\/S1473-3099(05)70267-X","article-title":"The global burden of group A streptococcal diseases","volume":"5","author":"JR Carapetis","year":"2005","journal-title":"Lancet Infect Dis"},{"issue":"1","key":"ref12","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1099\/jmm.0.023317-0","article-title":"emm typing, antibiotic resistance and PFGE analysis of Streptococcus pyogenes in Lebanon","volume":"60","author":"W Bahnan","year":"2011","journal-title":"J Med Microbiol"},{"issue":"9","key":"ref13","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1099\/jmm.0.063412-0","article-title":"Molecular characterization of Streptococcus pyogenes group A isolates from a tertiary hospital in Lebanon","volume":"63","author":"NM Karaky","year":"2014","journal-title":"J Med Microbiol"},{"issue":"13","key":"ref14","doi-asserted-by":"crossref","first-page":"4285","DOI":"10.1128\/JB.186.13.4285-4294.2004","article-title":"Multilocus sequence typing of Streptococcus pyogenes representing most known emm types and distinctions among subpopulation genetic structures","volume":"186","author":"KF McGregor","year":"2004","journal-title":"J Bacteriol"},{"issue":"4","key":"ref15","doi-asserted-by":"crossref","first-page":"2416","DOI":"10.1128\/IAI.69.4.2416-2427.2001","article-title":"Multilocus sequence typing of Streptococcus pyogenes and the relationships between emm type and clone","volume":"69","author":"MC Enright","year":"2001","journal-title":"Infect Immun"},{"issue":"9","key":"ref16","doi-asserted-by":"crossref","first-page":"e42304","DOI":"10.1371\/journal.pone.0042304","article-title":"An Integrated Pipeline for de Novo Assembly of Microbial Genomes","volume":"7","author":"A Tritt","year":"2012","journal-title":"PLoS ONE"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1093\/bioinformatics\/btu661","article-title":"A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data","volume":"31","author":"D Coil","year":"2015","journal-title":"Bioinfo"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST server: Rapid annotations using subsystems technology","volume":"9","author":"RK Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1093\/nar\/gkt1226","article-title":"The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)","volume":"42","author":"R Overbeek","year":"2014","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"ref20","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"E Zankari","year":"2012","journal-title":"Antimicrob Agents Chemother"},{"issue":"5","key":"ref21","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1128\/JCM.03617-13","article-title":"Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli","volume":"52","author":"KG Joensen","year":"2014","journal-title":"J Clin Microbiol"},{"issue":"10","key":"ref22","doi-asserted-by":"crossref","first-page":"e77302","DOI":"10.1371\/journal.pone.0077302","article-title":"PathogenFinder-distinguishing friend from foe using bacterial whole genome sequence data","volume":"8","author":"S Cosentino","year":"2013","journal-title":"PLoS ONE"},{"issue":"4","key":"ref23","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1128\/JCM.06094-11","article-title":"Multilocus sequence typing of total genome sequenced bacteria","volume":"50","author":"MV Larsen","year":"2012","journal-title":"J Clin Microbiol"},{"issue":"2","key":"ref24","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1093\/nar\/gkr485","article-title":"PHAST: A fast phage search tool","volume":"39","author":"Y Zhou","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"e243","DOI":"10.7717\/peerj.243","article-title":"PhyloSift: phylogenetic analysis of genomes and metagenomes","volume":"2","author":"AE Darling","year":"2014","journal-title":"PeerJ"},{"issue":"3","key":"ref26","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2014Approximately Maximum-Likelihood Trees for Large Alignments","volume":"5","author":"MN Price","year":"2010","journal-title":"PLoS ONE"},{"issue":"0","key":"ref27","first-page":"1","article-title":"Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks","volume":"0","author":"DH Huson","year":"2012","journal-title":"Syst Biol"},{"issue":"6","key":"ref28","doi-asserted-by":"crossref","first-page":"e11147","DOI":"10.1371\/journal.pone.0011147","article-title":"ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement","volume":"5","author":"AE Darling","year":"2010","journal-title":"PLoS ONE"},{"issue":"3","key":"ref29","doi-asserted-by":"crossref","first-page":"e00358","DOI":"10.1128\/genomeA.00358-14","article-title":"Draft Genome Sequences of Streptococcus pyogenes Strains Associated with Throat and Skin Infections in Lebanon","volume":"2","author":"S Tokajian","year":"2014","journal-title":"Genome Announc"},{"key":"ref30","unstructured":"National Center for Biotechnology Information. Genome. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.ncbi.nlm.nih.gov\/genome\/\" xlink:type=\"simple\">http:\/\/www.ncbi.nlm.nih.gov\/genome\/<\/ext-link> [Accessed 7th March 2015]."},{"issue":"8","key":"ref31","doi-asserted-by":"crossref","first-page":"4658","DOI":"10.1073\/pnas.071559398","article-title":"Complete genome sequence of an M1 strain of Streptococcus pyogenes","volume":"98","author":"JJ Ferretti","year":"2001","journal-title":"PNAS"},{"issue":"6657","key":"ref32","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/36786","article-title":"The complete genome sequence of the gram-positive bacterium Bacillus subtilis","volume":"390","author":"F Kunst","year":"1997","journal-title":"Nature"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1146\/annurev-micro-092412-155737","article-title":"Bacterial sigma factors: A historical, structural, and genomic perspective","volume":"68","author":"A Fekl\u00edstov","year":"2014","journal-title":"Annu Rev Microbiol"},{"issue":"1","key":"ref34","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1128\/JB.185.1.349-358.2003","article-title":"Transient association of an alternative sigma factor, ComX, with RNA polymerase during the period of competence for genetic transformation in Streptococcus pneumoniae","volume":"185","author":"P Luo","year":"2003","journal-title":"J Bacteriol"},{"issue":"2","key":"ref35","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1046\/j.1365-2958.2001.02657.x","article-title":"A secondary RNA polymerase sigma factor from Streptococcus pyogenes","volume":"42","author":"JA Opdyke","year":"2001","journal-title":"Mol. Microbiol."},{"issue":"21","key":"ref36","doi-asserted-by":"crossref","first-page":"6862","DOI":"10.1128\/jb.179.21.6862-6864.1997","article-title":"Sigma E is an essential sigma factor in Escherichia coli","volume":"179","author":"AD Las Pe\u00f1as","year":"1997","journal-title":"J Bacteriol"},{"issue":"8","key":"ref37","doi-asserted-by":"crossref","first-page":"2690","DOI":"10.1128\/JB.01393-07","article-title":"Identification of two gene clusters and a transcriptional regulator required for Pseudomonas aeruginosa glycine betaine catabolism","volume":"190","author":"MJ Wargo","year":"2008","journal-title":"J Bacteriol"},{"issue":"4","key":"ref38","first-page":"555","article-title":"Role of F1F0-ATPase in the growth of Streptococcus mutans GS5","volume":"88","author":"T Suzuki","year":"2000","journal-title":"Appl Microbiol Biotechnol"},{"issue":"2","key":"ref39","first-page":"125","article-title":"Recent developments in bacterial cold-shock response","volume":"6","author":"S Phadtare","year":"2004","journal-title":"Curr. Issues Mol. Biol"},{"issue":"4","key":"ref40","doi-asserted-by":"crossref","first-page":"1153","DOI":"10.1128\/jb.179.4.1153-1164.1997","article-title":"The dnaK operon of Bacillus subtilis is heptacistronic","volume":"179","author":"G Homuth","year":"1997","journal-title":"J Bacteriol"},{"issue":"3","key":"ref41","doi-asserted-by":"crossref","first-page":"1364","DOI":"10.1128\/IAI.72.3.1364-1373.2004","article-title":"The DnaK\/DnaJ chaperone machinery of Salmonella enterica serovar Typhimurium is essential for invasion of epithelial cells and survival within macrophages, leading to systemic infection","volume":"72","author":"A Takaya","year":"2004","journal-title":"Infect Immun"},{"issue":"1","key":"ref42","doi-asserted-by":"crossref","first-page":"e5","DOI":"10.1371\/journal.ppat.0020005","article-title":"Genome-wide analysis of group A streptococci reveals a mutation that modulates global phenotype and disease specificity","volume":"2","author":"P Sumby","year":"2006","journal-title":"PLoS Pathog"},{"issue":"9","key":"ref43","doi-asserted-by":"crossref","first-page":"2455","DOI":"10.1172\/JCI38095","article-title":"A decade of molecular pathogenomic analysis of group A Streptococcus","volume":"119","author":"JM Musser","year":"2009","journal-title":"J. Clin. Invest."},{"issue":"12","key":"ref44","doi-asserted-by":"crossref","first-page":"3928","DOI":"10.1128\/JB.186.12.3928-3937.2004","article-title":"CovS inactivates CovR and is required for growth under conditions of general stress in Streptococcus pyogenes","volume":"186","author":"TL Dalton","year":"2004","journal-title":"J Bacteriol"},{"issue":"8","key":"ref45","doi-asserted-by":"crossref","first-page":"3141","DOI":"10.1128\/IAI.01560-08","article-title":"CovC simultaneously activates and inhibits the CovR-mediated repression of distinct subsets of group A Streptococcus virulence factor-encoding genes","volume":"77","author":"J Trevino","year":"2009","journal-title":"Infect Immun"},{"issue":"8","key":"ref46","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1038\/nm1612","article-title":"DNase Sda1 provides selection pressure for a switch to invasive group A streptococcal infection","volume":"13","author":"MJ Walker","year":"2007","journal-title":"Nat Med"},{"issue":"2","key":"ref47","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1111\/j.1365-2958.2006.05381.x","article-title":"Defining the Mga regulon: Comparative transcriptome analysis reveals both direct and indirect regulation by Mga in the group A Streptococcus","volume":"62","author":"DA Ribardo","year":"2006","journal-title":"Mol Microbiol"},{"issue":"6","key":"ref48","doi-asserted-by":"crossref","first-page":"1176","DOI":"10.1111\/mmi.12250","article-title":"PTS phosphorylation of Mga modulates regulon expression and virulence in the group A Streptococcus","volume":"88","author":"ER Hondorp","year":"2013","journal-title":"Mol Microbiol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1006\/jmbi.1993.1481","article-title":"Replicatively active complexes of DnaA protein and the Escherichia coli chromosomal origin observed in the electron microscope","volume":"233","author":"E Crooke","year":"1993","journal-title":"J. Mol. Biol."},{"key":"ref50","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/1471-2105-9-79","article-title":"Ori-Finder: A web-based system for finding oriC s in unannotated bacterial genomes","volume":"9","author":"F Gao","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1093\/nar\/gks990","article-title":"DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes","volume":"41","author":"F Gao","year":"2013","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"ref52","doi-asserted-by":"crossref","first-page":"2683","DOI":"10.1128\/JB.181.9.2683-2688.1999","article-title":"DnaA boxes are important elements in setting the initiation mass of Escherichia coli","volume":"181","author":"BB Christensen","year":"1999","journal-title":"J Bacteriol"},{"issue":"15","key":"ref53","doi-asserted-by":"crossref","first-page":"3757","DOI":"10.1111\/j.1742-4658.2005.04768.x","article-title":"Origins of DNA replication in the three domains of life","volume":"272","author":"NP Robinson","year":"2005","journal-title":"FEBS J"},{"issue":"5","key":"ref54","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1007\/s004380050679","article-title":"Unique organization of the dnaA region from Prochlorococcus marinus CCMP1375, a marine cyanobacterium","volume":"257","author":"S Richter","year":"1998","journal-title":"Mol. Gen. Genet."},{"issue":"3","key":"ref55","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1086\/315299","article-title":"Genomic differences in Streptococcus pyogenes serotype M3 between recent isolates associated with toxic shock-like syndrome and past clinical isolates","volume":"181","author":"Y Inagaki","year":"2000","journal-title":"J Infect Dis"},{"issue":"9","key":"ref56","doi-asserted-by":"crossref","first-page":"4725","DOI":"10.1128\/IAI.67.9.4725-4731.1999","article-title":"Identification, cloning, and expression of the CAMP factor gene (cfa) of group A streptococci","volume":"67","author":"K Gase","year":"1999","journal-title":"Infect Immun"},{"issue":"5","key":"ref57","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1007\/BF00198458","article-title":"Molecular characterization of the cfb gene encoding group B streptococcal CAMP-factor","volume":"183","author":"A Podbielski","year":"1994","journal-title":"Med. Microbiol. Immun."},{"issue":"2","key":"ref58","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1074\/jbc.M804632200","article-title":"Streptolysin O promotes group A Streptococcus immune evasion by accelerated macrophage apoptosis","volume":"284","author":"AM Timmer","year":"2009","journal-title":"J Biol Chem"},{"issue":"7","key":"ref59","doi-asserted-by":"crossref","first-page":"4245","DOI":"10.1128\/IAI.68.7.4245-4254.2000","article-title":"Genetic locus for streptolysin S production by group A Streptococcus","volume":"68","author":"V Nizet","year":"2000","journal-title":"Infect. Immun."},{"issue":"1","key":"ref60","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1086\/430617","article-title":"Cytocidal effect of Streptococcus pyogenes on mouse neutrophils in vivo and the critical role of streptolysin S","volume":"192","author":"T Miyoshi-Akiyama","year":"2005","journal-title":"J. Infect. Dis."},{"issue":"4","key":"ref61","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1128\/IAI.6.4.459-464.1972","article-title":"Oxygen-stable hemolysins of group A Streptococci VIII. Leukotoxic and antiphagocytic effects of Sstreptolysins S and O","volume":"6","author":"I Ofek","year":"1972","journal-title":"Infect. Immun."},{"issue":"8","key":"ref62","doi-asserted-by":"crossref","first-page":"e800","DOI":"10.1371\/journal.pone.0000800","article-title":"Contribution of exogenous genetic elements to the group A Streptococcus metagenome","volume":"2","author":"SB Beres","year":"2007","journal-title":"PLoS ONE"},{"issue":"2","key":"ref63","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.1074\/jbc.271.2.1081","article-title":"Protein SIC, a novel extracellular protein of Streptococcus pyogenes interfering with complement function","volume":"271","author":"P Akesson","year":"1996","journal-title":"J Biol Chem"},{"issue":"4","key":"ref64","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1086\/318543","article-title":"Distribution of streptococcal inhibitor of complement variants in pharyngitis and invasive isolates in an epidemic of serotype M1 group A Streptococcus infection","volume":"183","author":"NP Hoe","year":"2001","journal-title":"J Infect Dis"},{"issue":"3","key":"ref65","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1093\/glycob\/1.3.257","article-title":"Purification of the oligosaccharide-cleaving enzymes of Flavobacterium meningosepticum","volume":"1","author":"TH Plummer","year":"1991","journal-title":"Glycobiology"},{"issue":"1","key":"ref66","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1042\/BJ20130126","article-title":"EndoS2 is a unique and conserved enzyme of serotype M49 group A Streptococcus that hydrolyzes N-linked glycans on IgG and alpha1-acid glycoprotein","volume":"455","author":"J Sjogren","year":"2013","journal-title":"Biochem J"},{"issue":"120","key":"ref67","article-title":"Nizet, Hollands A. Study of the IgG endoglycosidase EndoS in group A streptococcal phagocyte resistance and virulence","volume":"11","author":"J Sjogren","year":"2011","journal-title":"BMC Microbiology"},{"issue":"1","key":"ref68","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1111\/j.1365-2958.2004.04255.x","article-title":"Post-proteomic identification of a novel phage-encoded streptodornase, Sda1, in invasive M1T1 Streptococcus pyogenes","volume":"54","author":"RK Aziz","year":"2004","journal-title":"Mol Microbiol"},{"issue":"50","key":"ref69","doi-asserted-by":"crossref","first-page":"52789","DOI":"10.1074\/jbc.M410698200","article-title":"Insight of host immune evasion mediated by two variants of group A Streptococcus Mac protein","volume":"279","author":"J Agniswamy","year":"2004","journal-title":"J Biol Chem"},{"issue":"12","key":"ref70","doi-asserted-by":"crossref","first-page":"1298","DOI":"10.1038\/nm1201-1298","article-title":"Evasion of human innate and acquired immunity by a bacterial homolog of CD11b that inhibits opsonophagocytosis","volume":"7","author":"B Lei","year":"2001","journal-title":"Nat Med"},{"issue":"4","key":"ref71","doi-asserted-by":"crossref","first-page":"e00499","DOI":"10.1128\/mBio.00499-13","article-title":"IgG protease Mac\/IdeS is not essential for phagocyte resistance or mouse virulence of M1T1 group A Streptococcus","volume":"4","author":"CY Okumura","year":"2013","journal-title":"mBio"},{"issue":"6A","key":"ref72","doi-asserted-by":"crossref","first-page":"1042","DOI":"10.1101\/gr.1096703","article-title":"Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution","volume":"13","author":"I Nakagawa","year":"2003","journal-title":"Genome Research"},{"issue":"3","key":"ref73","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1128\/IAI.70.3.1159-1167.2002","article-title":"Genomic localization of a T serotype locus to a recombinatorial zone encoding extracellular matrix-binding proteins in Streptococcus pyogenes","volume":"70","author":"DE Bessen","year":"2002","journal-title":"Infect Immun"},{"issue":"4","key":"ref74","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1128\/JB.01301-06","article-title":"Population genetics and linkage analysis of loci within the FCT region of Streptococcus pyogenes","volume":"189","author":"Z Kratovac","year":"2007","journal-title":"J Bacteriol"},{"issue":"5","key":"ref75","doi-asserted-by":"crossref","first-page":"1657","DOI":"10.1073\/pnas.85.5.1657","article-title":"Antiphagocytic activity of streptococcal M protein: Selective binding of complement control protein factor H","volume":"85","author":"RD Horstmann","year":"1988","journal-title":"PNAS"},{"issue":"35\u201336","key":"ref76","doi-asserted-by":"crossref","first-page":"6088","DOI":"10.1016\/j.vaccine.2006.05.024","article-title":"Intranasal vaccination with SfbI or M protein-derived peptides conjugated to diphtheria toxoid confers protective immunity against a lethal challenge with Streptococcus pyogenes","volume":"24","author":"K Schulze","year":"2006","journal-title":"Vaccine"},{"issue":"4","key":"ref77","doi-asserted-by":"crossref","first-page":"1426","DOI":"10.1128\/JB.01179-06","article-title":"Role of Streptococcal T Antigens in Superficial Skin Infection","volume":"189","author":"S Lizano","year":"2007","journal-title":"J Bacteriol"},{"issue":"3","key":"ref78","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1016\/S0882-4010(95)90013-6","article-title":"Analysis of the interaction of group A streptococci with fibrinogen, streptokinase and plasminogen","volume":"18","author":"H Wang","year":"1995","journal-title":"Microb Pathog"},{"issue":"6","key":"ref79","doi-asserted-by":"crossref","first-page":"3161","DOI":"10.1016\/S0021-9258(19)39748-0","article-title":"Complete nucleotide sequence of the streptococcal C5a peptidase gene of Streptococcus pyogenes","volume":"265","author":"CC Chen","year":"1990","journal-title":"J Biol Chem"},{"issue":"5","key":"ref80","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1111\/j.1365-2958.2007.06006.x","article-title":"The Mga virulence regulon: Infection where the grass is greener","volume":"66","author":"ER Hondorp","year":"2007","journal-title":"Mol Microbiol"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"6619","DOI":"10.1128\/jb.177.22.6619-6624.1995","article-title":"Specific binding of the activator Mga to promoter sequences of the emm and scpA genes in the group A streptococcus","volume":"177","author":"KS McIver","year":"1995","journal-title":"J Bacteriol"},{"issue":"4","key":"ref82","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1111\/j.1365-2958.1993.tb01614.x","article-title":"Structural heterogeneity of the emm gene cluster in group A streptococci","volume":"8","author":"SK Hollingshead","year":"1993","journal-title":"Mol Microbiol"},{"issue":"5","key":"ref83","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1007\/s10096-011-1385-9","article-title":"Streptococcus pyogenes bacteraemia, emm types and superantigen profiles","volume":"31","author":"S Rantala","year":"2012","journal-title":"Eur J Clin Microbiol Infect Dis"},{"issue":"3","key":"ref84","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1128\/CMR.00104-12","article-title":"Staphylococcal and streptococcal superantigen exotoxins","volume":"26","author":"AR Spaulding","year":"2013","journal-title":"Clin Microbiol Rev"},{"issue":"1","key":"ref85","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1056\/NEJM198907063210101","article-title":"Severe group A streptococcal infections associated with a toxic shock-like syndrome and scarlet fever toxin A","volume":"321","author":"DL Stevens","year":"1989","journal-title":"N Engl J Med"},{"issue":"1","key":"ref86","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.molmed.2013.10.004","article-title":"Streptococcal superantigens: Categorization and clinical associations","volume":"20","author":"RJ Commons","year":"2014","journal-title":"Trends Mol Med"},{"key":"ref87","first-page":"789","article-title":"Streptococcal diseases and the immune response","author":"AL Bisno","year":"1980"},{"issue":"9056","key":"ref88","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1016\/S0140-6736(96)06364-7","article-title":"Rheumatic fever","volume":"349","author":"GH Stollerman","year":"1997","journal-title":"Lancet"},{"issue":"10","key":"ref89","doi-asserted-by":"crossref","first-page":"1765","DOI":"10.1084\/jem.191.10.1765","article-title":"The streptococcal superantigen SMEZ exhibits wide allelic variation, mosaic structure, and significant antigenic variation","volume":"191","author":"T Proft","year":"2000","journal-title":"J Exp Med"},{"issue":"10","key":"ref90","doi-asserted-by":"crossref","first-page":"1238","DOI":"10.1099\/jmm.0.2008\/001156-0","article-title":"Superantigen genes in group A streptococcal isolates and their relationship with emm types","volume":"57","author":"RJ Commons","year":"2008","journal-title":"J Med Microbiol"},{"issue":"3","key":"ref91","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1128\/IAI.69.3.1381-1388.2001","article-title":"Functional Characterization of Streptococcal Pyrogenic Exotoxin J, a Novel Superantigen","volume":"69","author":"JK McCormick","year":"2001","journal-title":"Infect Immun"},{"issue":"4","key":"ref92","doi-asserted-by":"crossref","first-page":"1473","DOI":"10.1128\/JB.01227-06","article-title":"Complete genome of acute rheumatic fever-associated serotype M5 Streptococcus pyogenes strain Manfredo","volume":"189","author":"MTG Holden","year":"2007","journal-title":"J. Bacteriol."},{"issue":"4","key":"ref93","doi-asserted-by":"crossref","first-page":"1522","DOI":"10.1016\/j.ajpath.2011.12.037","article-title":"Full-genome dissection of an epidemic of severe invasive disease caused by a hypervirulent, recently emerged clone of group A Streptococcus","volume":"180","author":"N Fittipaldi","year":"2012","journal-title":"Am J Pathol"},{"issue":"5","key":"ref94","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1086\/430618","article-title":"Genome sequence of a serotype M28 strain of group A Streptococcus: Potential new insights into puerperal sepsis and bacterial disease specificity","volume":"192","author":"NM Green","year":"2005","journal-title":"Int J Infect Dis"},{"issue":"6","key":"ref95","doi-asserted-by":"crossref","first-page":"3227","DOI":"10.1128\/IAI.70.6.3227-3233.2002","article-title":"Dissemination of the phage-associated novel superantigen gene speL in recent invasive and noninvasive Streptococcus pyogenes M3\/T3 isolates in Japan","volume":"70","author":"T Ikebe","year":"2002","journal-title":"Infect Immun"},{"issue":"1","key":"ref96","first-page":"79","article-title":"Clinical and epidemiological aspects of invasive Streptococcus pyogenes infections in Denmark during 2003 and 2004","volume":"46","author":"B Luca-Harari","year":"2008","journal-title":"J Med Microbiol"},{"issue":"7","key":"ref97","doi-asserted-by":"crossref","first-page":"681","DOI":"10.3109\/00313020903257723","article-title":"Epidemiological analysis of Streptococcus pyogenes infections in Hong Kong","volume":"41","author":"JC Chan","year":"2009","journal-title":"Pathology"},{"issue":"18","key":"ref98","doi-asserted-by":"crossref","first-page":"7059","DOI":"10.1073\/pnas.0510279103","article-title":"Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen group A Streptococcus","volume":"103","author":"SB Beres","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"3","key":"ref99","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1111\/j.1574-695X.2010.00652.x","article-title":"Epidemiology of invasive Streptococcus pyogenes disease in Germany during 2003\u20132007","volume":"58","author":"M Imohl","year":"2010","journal-title":"Immunol Med Mic"},{"issue":"2","key":"ref100","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1128\/AAC.42.2.257","article-title":"A novel erythromycin resistance methylase gene (ermTR) in Streptococcus pyogenes","volume":"42","author":"H Seppala","year":"1998","journal-title":"Antimicrob Agents Chemother"},{"issue":"5","key":"ref101","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1007\/s10096-011-1362-3","article-title":"Significant decline in the erythromycin resistance of group A Streptococcus isolates at a German paediatric tertiary care centre","volume":"31","author":"S Farmand","year":"2012","journal-title":"Eur J Clin Microbiol"},{"issue":"11","key":"ref102","doi-asserted-by":"crossref","first-page":"2602","DOI":"10.1093\/jac\/dks281","article-title":"Increase in fluoroquinolone non-susceptibility among clinical Streptococcus pyogenes in Belgium during 2007\u201310","volume":"67","author":"L Van Heirstraeten","year":"2012","journal-title":"J Antimicrob Chemother"},{"issue":"4","key":"ref103","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1093\/jac\/dkq006","article-title":"Molecular characterization of macrolide- and multidrug-resistant Streptococcus pyogenes isolated from adult patients in Barcelona, Spain (1993\u20132008)","volume":"65","author":"C Ardanuy","year":"2010","journal-title":"J Antimicrob Chemother"},{"issue":"11","key":"ref104","doi-asserted-by":"crossref","first-page":"1383","DOI":"10.1099\/jmm.0.2008\/002642-0","article-title":"Distribution of emm type and antibiotic susceptibility of group A streptococci causing invasive and noninvasive disease","volume":"57","author":"T Wajima","year":"2008","journal-title":"J Med Microbiol"},{"issue":"2","key":"ref105","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/j.diagmicrobio.2008.04.018","article-title":"An intrinsic pattern of reduced susceptibility to fluoroquinolones in pediatric isolates of Streptococcus pyogenes","volume":"62","author":"SS Yan","year":"2008","journal-title":"Diagn Microbiol Infect Dis"},{"issue":"1","key":"ref106","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1128\/AAC.00780-09","article-title":"Prevalence and clonal characterization of Streptococcus pyogenes clinical isolates with reduced fluoroquinolone susceptibility in Spain","volume":"54","author":"M Montes","year":"2010","journal-title":"J. Antimicrob. Chemother."},{"issue":"5","key":"ref107","doi-asserted-by":"crossref","first-page":"2406","DOI":"10.1128\/AAC.01665-10","article-title":"In vitro activities of retapamulin and 16 other antimicrobial agents against recently obtained Streptococcus pyogenes isolates","volume":"55","author":"E Perez-Trallero","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"issue":"2","key":"ref108","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1128\/MMBR.65.2.232-260.2001","article-title":"Tetracycline antibiotics: Mode of action, applications, molecular biology, and epidemiology of bacterial resistance","volume":"65","author":"I Chopra","year":"2001","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref109","doi-asserted-by":"crossref","first-page":"1477","DOI":"10.1038\/ncomms2470","article-title":"Mechanism of tetracycline resistance by ribosomal protection protein Tet(O)","volume":"4","author":"W Li","year":"2013","journal-title":"Nat Commun"},{"issue":"8","key":"ref110","doi-asserted-by":"crossref","first-page":"3844","DOI":"10.1128\/JCM.42.8.3844-3846.2004","article-title":"Clonal spread of emm type 28 isolates of Streptococcus pyogenes that are multiresistant to antibiotics","volume":"42","author":"L Mihaila-Amrouche","year":"2004","journal-title":"J Clin Microbiol"},{"issue":"11","key":"ref111","doi-asserted-by":"crossref","first-page":"4798","DOI":"10.1128\/AAC.49.11.4798-4800.2005","article-title":"Multiplex PCR for simultaneous detection of macrolide and tetracycline resistance determinants in streptococci","volume":"49","author":"S Malhotra-Kumar","year":"2005","journal-title":"Antimicrob Agents Chemother"},{"issue":"5","key":"ref112","doi-asserted-by":"crossref","first-page":"1865","DOI":"10.1128\/AAC.49.5.1865-1871.2005","article-title":"A novel MATE family efflux pump contributes to the reduced susceptibility of laboratory-derived Staphylococcus aureus mutants to tigecycline","volume":"49","author":"F McAleese","year":"2005","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"ref113","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1128\/AAC.00499-09","article-title":"Phim46.1, the main Streptococcus pyogenes element carrying mef(A) and tet(O) genes","volume":"54","author":"A Brenciani","year":"2010","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"ref114","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1128\/AAC.05352-11","article-title":"ICESp2905, the erm(TR)-tet(O) element of Streptococcus pyogenes, is formed by two independent integrative and conjugative elements","volume":"56","author":"E Giovanetti","year":"2012","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"ref115","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1111\/j.1365-2958.2004.04113.x","article-title":"The impact of prophages on bacterial chromosomes","volume":"53","author":"C Canchaya","year":"2004","journal-title":"Mol Microbiol"},{"issue":"4","key":"ref116","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/S1473-3099(03)00576-0","article-title":"Molecular basis of group A streptococcal virulence","volume":"3","author":"AL Bisno","year":"2003","journal-title":"Lancet Infect Dis"},{"issue":"6","key":"ref117","doi-asserted-by":"crossref","first-page":"1461","DOI":"10.1016\/S0002-9440(10)61232-1","article-title":"Toward a genome-wide systems biology analysis of host-pathogen interactions in group A Streptococcus","volume":"167","author":"JM Musser","year":"2005","journal-title":"Am. J. Pathol."},{"issue":"7","key":"ref118","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/j.tim.2007.05.003","article-title":"In vivo acquisition of prophage in Streptococcus pyogenes","volume":"15","author":"VA Fischetti","year":"2007","journal-title":"Trends in Microbiol"},{"issue":"1","key":"ref119","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.jhin.2010.01.012","article-title":"High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak","volume":"75","author":"T Lewis","year":"2010","journal-title":"J Hosp Infect"},{"issue":"7","key":"ref120","doi-asserted-by":"crossref","first-page":"2224","DOI":"10.1128\/JCM.00675-12","article-title":"Analysis of a Streptococcus pyogenes puerperal sepsis cluster by use of whole-genome sequencing","volume":"50","author":"NL Ben Zakour","year":"2012","journal-title":"J Clin Microbiol"},{"issue":"10","key":"ref121","doi-asserted-by":"crossref","first-page":"e77033","DOI":"10.1371\/journal.pone.0077033","article-title":"Systematic identification of gene families for use as markers for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups","volume":"8","author":"D Wu","year":"2013","journal-title":"PLoS ONE"},{"issue":"4","key":"ref122","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1086\/422697","article-title":"Progress toward characterization of the group A Streptococcus metagenome: Complete genome sequence of a macrolide-resistant serotype M6 strain","volume":"190","author":"DJ Banks","year":"2004","journal-title":"J Infect Dis"},{"issue":"12","key":"ref123","doi-asserted-by":"crossref","first-page":"1898","DOI":"10.1086\/379897","article-title":"Structure and distribution of an unusual chimeric genetic element encoding macrolide resistance in phylogenetically diverse clones of group A Streptococcus","volume":"188","author":"DJ Banks","year":"2003","journal-title":"J Infect Dis"},{"issue":"1","key":"ref124","doi-asserted-by":"crossref","first-page":"e00149","DOI":"10.1128\/genomeA.00149-12","article-title":"Complete Genome Sequence of emm1 Streptococcus pyogenes A20, a Strain with an Intact Two-Component System, CovRS, Isolated from a Patient with Necrotizing Fasciitis","volume":"1","author":"PX Zheng","year":"2013","journal-title":"Genome Announc"},{"issue":"8","key":"ref125","doi-asserted-by":"crossref","first-page":"1325","DOI":"10.1093\/infdis\/jiu260","article-title":"A Systematic and Functional Classification of Streptococcus pyogenes That Serves as a New Tool for Molecular Typing and Vaccine Development","volume":"210","author":"M Sanderson-Smith","year":"2014","journal-title":"J Infect Dis"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0168177","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,17]],"date-time":"2022-07-17T11:46:09Z","timestamp":1658058369000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0168177"}},"subtitle":[],"editor":[{"given":"Feng","family":"Gao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,12,15]]},"references-count":125,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2016,12,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0168177","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,12,15]]}}}