{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T15:18:04Z","timestamp":1791299884618,"version":"4.1.0"},"reference-count":73,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,11,15]],"date-time":"2021-11-15T00:00:00Z","timestamp":1636934400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Coagulase-negative\n                    <jats:italic>Staphylococcus<\/jats:italic>\n                    (CoNS) is the most common pathogen causing traumatic endophthalmitis. Among which,\n                    <jats:italic>Staphylococcus epidermidis<\/jats:italic>\n                    is the most common species that colonizes human skin, eye surfaces, and nasal cavity. It is also the main cause of nosocomial infection, specially foreign body-related bloodstream infections (FBR-BSIs). Although some studies have reported the genome characteristics of\n                    <jats:italic>S. epidermidis<\/jats:italic>\n                    , the genome of ocular trauma-sourced\n                    <jats:italic>S. epidermidis<\/jats:italic>\n                    strain and a comprehensive understanding of its pathogenicity are still lacking. Our study sequenced, analyzed, and reported the whole genomes of 11 ocular trauma-sourced samples of\n                    <jats:italic>S. epidermidis<\/jats:italic>\n                    that caused traumatic endophthalmitis. By integrating publicly available genomes, we obtained a total of 187\n                    <jats:italic>S. epidermidis<\/jats:italic>\n                    samples from healthy and diseased eyes, skin, respiratory tract, and blood. Combined with pan-genome, phylogenetic, and comparative genomic analyses, our study showed that\n                    <jats:italic>S. epidermidis<\/jats:italic>\n                    , regardless of niche source, exhibits two founder lineages with different pathogenicity. Moreover, we identified several potential biomarkers associated with the virulence of\n                    <jats:italic>S. epidermidis<\/jats:italic>\n                    , including\n                    <jats:italic>essD<\/jats:italic>\n                    ,\n                    <jats:italic>uhpt<\/jats:italic>\n                    ,\n                    <jats:italic>sdrF<\/jats:italic>\n                    ,\n                    <jats:italic>sdrG<\/jats:italic>\n                    ,\n                    <jats:italic>fbe<\/jats:italic>\n                    , and\n                    <jats:italic>icaABCDR<\/jats:italic>\n                    .\n                    <jats:italic>EssD<\/jats:italic>\n                    and\n                    <jats:italic>uhpt<\/jats:italic>\n                    have high homology with\n                    <jats:italic>esaD<\/jats:italic>\n                    and\n                    <jats:italic>hpt<\/jats:italic>\n                    in\n                    <jats:italic>Staphylococcus aureus<\/jats:italic>\n                    , showing that the genomes of\n                    <jats:italic>S. epidermidis<\/jats:italic>\n                    and\n                    <jats:italic>S. aureus<\/jats:italic>\n                    may have communicated during evolution.\n                    <jats:italic>SdrF<\/jats:italic>\n                    ,\n                    <jats:italic>sdrG<\/jats:italic>\n                    ,\n                    <jats:italic>fbe<\/jats:italic>\n                    , and\n                    <jats:italic>icaABCDR<\/jats:italic>\n                    are related to biofilm formation. Compared to\n                    <jats:italic>S. epidermidis<\/jats:italic>\n                    from blood sources, ocular-sourced strains causing intraocular infection had no direct relationship with biofilm formation. In conclusion, this study provided additional data resources for studies on\n                    <jats:italic>S. epidermidis<\/jats:italic>\n                    and improved our understanding of the evolution and pathogenicity among strains of different sources.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2021.770191","type":"journal-article","created":{"date-parts":[[2021,11,15]],"date-time":"2021-11-15T01:25:07Z","timestamp":1636939507000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":15,"title":["Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains"],"prefix":"10.3389","volume":"12","author":[{"given":"Shudan","family":"Lin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bianjin","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinrui","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunfeng","family":"Gu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaobin","family":"Gu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueli","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tian","family":"Wan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianzhong","family":"Su","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongliang","family":"Lou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meiqin","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2021,11,15]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"D517","DOI":"10.1093\/nar\/gkz935","article-title":"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"Alcock","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"1037","DOI":"10.1016\/j.cell.2007.03.004","article-title":"Molecular mechanisms of antibacterial multidrug resistance","volume":"128","author":"Alekshun","year":"2007","journal-title":"Cell"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1097\/01.iae.0000225072.68265.ee","article-title":"Microbiologic spectrum and visual outcome of posttraumatic endophthalmitis","volume":"27","author":"Al-Omran","year":"2007","journal-title":"Retina"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1016\/j.jcrs.2008.01.016","article-title":"Increasing prevalence of methicillin resistance in serious ocular infections caused by Staphylococcus aureus in the United States: 2000 to 2005","volume":"34","author":"Asbell","year":"2008","journal-title":"J. Cataract Refract. Surg."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1128\/CMR.00109-13","article-title":"Coagulase-negative staphylococci","volume":"27","author":"Becker","year":"2014","journal-title":"Clin. Microbiol. Rev."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1016\/j.survophthal.2010.09.002","article-title":"Post-traumatic infectious endophthalmitis","volume":"56","author":"Bhagat","year":"2011","journal-title":"Surv. Ophthalmol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1412","DOI":"10.1128\/JCM.03098-13","article-title":"Characterization of ocular methicillin-resistant Staphylococcus epidermidis isolates belonging predominantly to clonal complex 2 subcluster II","volume":"52","author":"Bispo","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"16183","DOI":"10.1038\/nmicrobiol.2016.183","article-title":"The type VII secretion system of Staphylococcus aureus secretes a nuclease toxin that targets competitor bacteria","volume":"2","author":"Cao","year":"2016","journal-title":"Nat. Microbiol."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"24373","DOI":"10.1038\/srep24373","article-title":"BPGA- an ultra-fast pan-genome analysis pipeline","volume":"6","author":"Chaudhari","year":"2016","journal-title":"Sci. Rep."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"e8557","DOI":"10.1371\/journal.pone.0008557","article-title":"Staphylococcus epidermidis antimicrobial delta-toxin (phenol-soluble modulin-gamma) cooperates with host antimicrobial peptides to kill group A Streptococcus","volume":"5","author":"Cogen","year":"","journal-title":"PLoS One"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1038\/jid.2009.243","article-title":"Selective antimicrobial action is provided by phenol-soluble modulins derived from Staphylococcus epidermidis, a normal resident of the skin","volume":"130","author":"Cogen","year":"","journal-title":"J. Invest. Dermatol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"R64","DOI":"10.1186\/gb-2012-13-7-r64","article-title":"Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates","volume":"13","author":"Conlan","year":"2012","journal-title":"Genome Biol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1111\/j.1755-3768.2011.02349.x","article-title":"A multicentre prospective study of post-traumatic endophthalmitis","volume":"91","author":"Cornut","year":"2013","journal-title":"Acta Ophthalmol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1093\/molbev\/mss236","article-title":"The rhizome of the multidrug-resistant Enterobacter aerogenes genome reveals how new \u201ckiller bugs\u201d are created because of a sympatric lifestyle","volume":"30","author":"Diene","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1038\/s41564-021-00913-z","article-title":"Staphylococcus epidermidis clones express Staphylococcus aureus-type wall teichoic acid to shift from a commensal to pathogen lifestyle","volume":"6","author":"Du","year":"2021","journal-title":"Nat. Microbiol."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1111\/1469-0691.12118","article-title":"Endophthalmitis","volume":"19","author":"Durand","year":"2013","journal-title":"Clin. Microbiol. Infect."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1002\/cpt.698","article-title":"The association of the skin microbiota with health, immunity, and disease","volume":"102","author":"Egert","year":"2017","journal-title":"Clin. Pharmacol. Ther."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"37464","DOI":"10.1074\/jbc.M206063200","article-title":"A novel ligand-binding domain involved in regulation of amino acid metabolism in prokaryotes","volume":"277","author":"Ettema","year":"2002","journal-title":"J. Biol. Chem."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1093\/femsre\/fux007","article-title":"Antibiotic resistance in Staphylococcus aureus. Current status and future prospects","volume":"41","author":"Foster","year":"2017","journal-title":"FEMS Microbiol. Rev."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1038\/nrmicro3161","article-title":"Adhesion, invasion and evasion: the many functions of the surface proteins of Staphylococcus aureus","volume":"12","author":"Foster","year":"2014","journal-title":"Nat. Rev. Microbiol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"D274","DOI":"10.1093\/nar\/gkaa1018","article-title":"COG database update: focus on microbial diversity, model organisms, and widespread pathogens","volume":"49","author":"Galperin","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"2877","DOI":"10.1093\/bioinformatics\/btv271","article-title":"kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome","volume":"31","author":"Gardner","year":"2015","journal-title":"Bioinformatics"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"151","DOI":"10.3389\/fmicb.2010.00151","article-title":"Defining pathogenic bacterial species in the genomic era","volume":"1","author":"Georgiades","year":"2010","journal-title":"Front. Microbiol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"5616","DOI":"10.1167\/iovs.07-0588","article-title":"Ocular pathogen or commensal: a PCR-based study of surface bacterial flora in normal and dry eyes","volume":"48","author":"Graham","year":"2007","journal-title":"Invest. Ophthalmol. Vis. Sci."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1128\/jb.158.2.513-516.1984","article-title":"Low-affinity penicillin-binding protein associated with beta-lactam resistance in Staphylococcus aureus","volume":"158","author":"Hartman","year":"1984","journal-title":"J. Bacteriol."},{"key":"ref27","doi-asserted-by":"crossref","first-page":"6602","DOI":"10.1073\/pnas.85.18.6602","article-title":"A large family of bacterial activator proteins","volume":"85","author":"Henikoff","year":"1988","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"2115","DOI":"10.1093\/molbev\/msx148","article-title":"Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper","volume":"34","author":"Huerta-Cepas","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Huerta-Cepas","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"55","DOI":"10.4161\/mge.1.1.16432","article-title":"The influence of the accessory genome on bacterial pathogen evolution","volume":"1","author":"Jackson","year":"2011","journal-title":"Mob. Genet. Elements"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"1549","DOI":"10.1128\/AAC.44.6.1549-1555.2000","article-title":"A new class of genetic element, Staphylococcus cassette chromosome mec, encodes methicillin resistance in Staphylococcus aureus","volume":"44","author":"Katayama","year":"2000","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/j.ophtha.2005.08.013","article-title":"Microbial keratitis predisposing factors and morbidity","volume":"113","author":"Keay","year":"2006","journal-title":"Ophthalmology"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"4126","DOI":"10.1038\/s41598-018-22416-4","article-title":"Genomics-based identification of microorganisms in human ocular body fluid","volume":"8","author":"Kirstahler","year":"2018","journal-title":"Sci. Rep."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"1859","DOI":"10.2217\/fmb.15.98","article-title":"Staphylococcus epidermidis as a cause of bacteremia","volume":"10","author":"Kleinschmidt","year":"2015","journal-title":"Future Microbiol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation","volume":"27","author":"Koren","year":"2017","journal-title":"Genome Res."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1128\/JCM.06094-11","article-title":"Multilocus sequence typing of total-genome-sequenced bacteria","volume":"50","author":"Larsen","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"1175","DOI":"10.1038\/s41564-018-0230-7","article-title":"Global spread of three multidrug-resistant lineages of Staphylococcus epidermidis","volume":"3","author":"Lee","year":"2018","journal-title":"Nat. Microbiol."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive tree Of life (iTOL) v5: an online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"1785","DOI":"10.1016\/j.ophtha.2012.03.031","article-title":"Shifting trends in bacterial keratitis in Toronto: an 11-year review","volume":"119","author":"Lichtinger","year":"2012","journal-title":"Ophthalmology"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"784.e718","DOI":"10.1016\/j.cell.2017.12.033","article-title":"Non-classical immunity controls microbiota impact on skin immunity and tissue repair","volume":"172","author":"Linehan","year":"2018","journal-title":"Cell"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"D687","DOI":"10.1093\/nar\/gky1080","article-title":"VFDB 2019: a comparative pathogenomic platform with an interactive web interface","volume":"47","author":"Liu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"4647","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes","volume":"38","author":"Manni","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"e0138079","DOI":"10.1371\/journal.pone.0138079","article-title":"Comparative genotypes, staphylococcal cassette chromosome mec (SCCmec) genes and antimicrobial resistance amongst Staphylococcus epidermidis and Staphylococcus haemolyticus isolates from infections in humans and companion animals","volume":"10","author":"McManus","year":"2015","journal-title":"PLoS One"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"459","DOI":"10.3389\/fcimb.2017.00459","article-title":"Comparative pan-genome analysis of piscirickettsia salmonis reveals genomic divergences within genogroups","volume":"7","author":"Nourdin-Galindo","year":"2017","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"854","DOI":"10.1016\/j.cell.2016.04.008","article-title":"Temporal stability of the human skin microbiome","volume":"165","author":"Oh","year":"2016","journal-title":"Cell"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"841","DOI":"10.2741\/1295","article-title":"Virulence factors of the coagulase-negative staphylococci","volume":"9","author":"Otto","year":"2004","journal-title":"Front. Biosci."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1038\/nrmicro2182","article-title":"Staphylococcus epidermidis\u2013the \u2018accidental\u2019 pathogen","volume":"7","author":"Otto","year":"2009","journal-title":"Nat. Rev. Microbiol."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"1620","DOI":"10.1128\/IAI.03109-14","article-title":"Characterization of a novel two-component regulatory system, HptRS, the regulator for the hexose phosphate transport system in Staphylococcus aureus","volume":"83","author":"Park","year":"","journal-title":"Infect. Immun."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1097\/ICL.0000000000000068","article-title":"Microbiological study of therapeutic soft contact lenses used in the treatment of recurrent corneal erosion syndrome","volume":"41","author":"Park","year":"","journal-title":"Eye Contact Lens"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1016\/j.vetmic.2008.09.009","article-title":"Role of coagulase-negative staphylococci in human disease","volume":"134","author":"Piette","year":"2009","journal-title":"Vet. Microbiol."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"1293","DOI":"10.3389\/fmicb.2016.01293","article-title":"PSM-Mec-A virulence determinant that connects transcriptional regulation, virulence, and antibiotic resistance in staphylococci","volume":"7","author":"Qin","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"W320","DOI":"10.1093\/nar\/gku316","article-title":"Deciphering key features in protein structures with the new ENDscript server","volume":"42","author":"Robert","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"D84","DOI":"10.1093\/nar\/gkz956","article-title":"GenBank","volume":"48","author":"Sayers","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"50.e51","DOI":"10.1016\/j.ajo.2013.01.027","article-title":"Endophthalmitis isolates and antibiotic susceptibilities: a 10-year review of culture-proven cases","volume":"156","author":"Schimel","year":"2013","journal-title":"Am J. Ophthalmol."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1016\/j.ijmm.2010.04.011","article-title":"Success through diversity \u2013 how Staphylococcus epidermidis establishes as a nosocomial pathogen","volume":"300","author":"Schoenfelder","year":"2010","journal-title":"Int. J. Med. Microbiol."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"660","DOI":"10.1016\/j.tim.2013.10.001","article-title":"Structure and function of the human skin microbiome","volume":"21","author":"Schommer","year":"2013","journal-title":"Trends Microbiol."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"333","DOI":"10.3389\/fmicb.2018.00333","article-title":"Phylogenomic based comparative studies on Indian and American commensal Staphylococcus epidermidis isolates","volume":"9","author":"Sharma","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal omega","volume":"7","author":"Sievers","year":"2011","journal-title":"Mol. Syst. Biol."},{"key":"ref62","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"ref63","doi-asserted-by":"publisher","first-page":"566080","DOI":"10.3389\/fgene.2020.566080","article-title":"Comparative genome analysis reveals the molecular basis of niche adaptation of Staphylococcus epidermidis strains","volume":"11","author":"Su","year":"2020","journal-title":"Front. Genet."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"274","DOI":"10.3389\/fcimb.2020.00274","article-title":"Determining the genetic characteristics of resistance and virulence of the \u201cEpidermidis Cluster Group\u201d through pan-genome analysis","volume":"10","author":"Sun","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial \u201cpan-genome\u201d","volume":"102","author":"Tettelin","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"29797","DOI":"10.1074\/jbc.M110.214981","article-title":"Fibrinogen is a ligand for the Staphylococcus aureus microbial surface components recognizing adhesive matrix molecules (MSCRAMM) bone sialoprotein-binding protein (Bbp)","volume":"286","author":"Vazquez","year":"2011","journal-title":"J. Biol. Chem."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.exer.2013.06.003","article-title":"Characterization of the normal microbiota of the ocular surface","volume":"117","author":"Willcox","year":"2013","journal-title":"Exp. Eye Res."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1086\/421946","article-title":"Nosocomial bloodstream infections in US hospitals: analysis of 24,179 cases from a prospective nationwide surveillance study","volume":"39","author":"Wisplinghoff","year":"2004","journal-title":"Clin. Infect. Dis."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1038\/ismej.2010.15","article-title":"A poke into the diversity and associations within human anterior nare microbial communities","volume":"4","author":"Wos-Oxley","year":"2010","journal-title":"ISME J."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"452","DOI":"10.3980\/j.issn.2222-3959.2013.04.08","article-title":"Comparison on conjunctival sac bacterial flora of the seniors with dry eye in Ganzi autonomous prefecture","volume":"6","author":"Zhang","year":"2013","journal-title":"Int. J. Ophthalmol."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"454.e418","DOI":"10.1016\/j.cell.2020.01.006","article-title":"Host-specific evolutionary and transmission dynamics shape the functional diversification of Staphylococcus epidermidis in human skin","volume":"180","author":"Zhou","year":"2020","journal-title":"Cell"},{"key":"ref73","doi-asserted-by":"publisher","first-page":"S14","DOI":"10.1016\/j.ijantimicag.2006.05.012","article-title":"Nosocomial infections by Staphylococcus epidermidis: how a commensal bacterium turns into a pathogen","volume":"28","author":"Ziebuhr","year":"2006","journal-title":"Int. J. Antimicrob. Agents"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2021.770191\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,11,15]],"date-time":"2021-11-15T01:25:13Z","timestamp":1636939513000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2021.770191\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,15]]},"references-count":73,"alternative-id":["10.3389\/fmicb.2021.770191"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2021.770191","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.08.12.456181","asserted-by":"object"}]},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,11,15]]},"article-number":"770191"}}