{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T16:59:04Z","timestamp":1789750744226,"version":"4.0.1"},"reference-count":72,"publisher":"Elsevier BV","issue":"1","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T00:00:00Z","timestamp":1764892800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001704","name":"European Society of Clinical Microbiology and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001704","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["PTDC\/FIS-NAN\/0117\/2014"],"award-info":[{"award-number":["PTDC\/FIS-NAN\/0117\/2014"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["LISBOA-01-0145-FEDER-016417"],"award-info":[{"award-number":["LISBOA-01-0145-FEDER-016417"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["PTDC\/BIA-EVF\/117507\/2010"],"award-info":[{"award-number":["PTDC\/BIA-EVF\/117507\/2010"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UID\/CBQ\/04612\/2013"],"award-info":[{"award-number":["UID\/CBQ\/04612\/2013"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["SFRH\/BD\/72675\/2010"],"award-info":[{"award-number":["SFRH\/BD\/72675\/2010"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["2022.11966"],"award-info":[{"award-number":["2022.11966"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Genomics"],"published-print":{"date-parts":[[2026,1]]},"DOI":"10.1016\/j.ygeno.2025.111167","type":"journal-article","created":{"date-parts":[[2025,12,6]],"date-time":"2025-12-06T23:18:35Z","timestamp":1765063115000},"page":"111167","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"title":["Remodeling of Staphylococcus epidermidis genome over three decades of nosocomial exposure"],"prefix":"10.1016","volume":"118","author":[{"given":"Joana","family":"Rolo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Botelho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diana","family":"Espadinha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peder","family":"Worning","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rita","family":"Sobral","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henrik","family":"Westh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Miragaia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.ygeno.2025.111167_bb0005","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1111\/j.1462-5822.2008.01264.x","article-title":"Staphylococcus epidermidis polysaccharide intercellular adhesin induces IL-8 expression in human astrocytes via a mechanism involving TLR2","volume":"11","author":"Stevens","year":"2009","journal-title":"Cell. Microbiol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0010","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1001\/archinte.1958.00030010375005","article-title":"Observations on Staphylococcus albus septicemia in mice and men","volume":"102","author":"Smith","year":"1958","journal-title":"Arch. Intern. Med."},{"key":"10.1016\/j.ygeno.2025.111167_bb0015","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1128\/CMR.7.1.117","article-title":"Update on clinical significance of coagulase-negative staphylococci","volume":"7","author":"Kloos","year":"1994","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.ygeno.2025.111167_bb0020","doi-asserted-by":"crossref","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":"10.1016\/j.ygeno.2025.111167_bb0025","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1038\/nrmicro2182","article-title":"Staphylococcus epidermidis \u2014 the \u201caccidental\u201d pathogen","volume":"7","author":"Otto","year":"2009","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0030","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1093\/jac\/dkq410","article-title":"High prevalence of the arginine catabolic mobile element in carriage isolates of methicillin-resistant Staphylococcus epidermidis","volume":"66","author":"Barbier","year":"2011","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.ygeno.2025.111167_bb0035","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0007722","article-title":"Genetic diversity of arginine catabolic mobile element in Staphylococcus epidermidis","volume":"4","author":"Miragaia","year":"2009","journal-title":"PloS One"},{"key":"10.1016\/j.ygeno.2025.111167_bb0040","doi-asserted-by":"crossref","first-page":"1523","DOI":"10.1086\/587907","article-title":"The arginine catabolic Mobile element and staphylococcal chromosomal cassette mec linkage: convergence of virulence and resistance in the USA300 clone of methicillin-resistant Staphylococcus aureus","volume":"197","author":"Diep","year":"2008","journal-title":"J Infect Dis"},{"key":"10.1016\/j.ygeno.2025.111167_bb0045","doi-asserted-by":"crossref","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":"10.1016\/j.ygeno.2025.111167_bb0050","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/S1473-3099(11)70126-8","article-title":"Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study","volume":"11","author":"Garc\u00eda-\u00c1lvarez","year":"2011","journal-title":"Lancet Infect. Dis."},{"key":"10.1016\/j.ygeno.2025.111167_bb0055","doi-asserted-by":"crossref","first-page":"4961","DOI":"10.1128\/AAC.00579-09","article-title":"Classification of staphylococcal cassette chromosome mec (SCCmec): guidelines for reporting novel SCCmec elements","volume":"53","author":"Ito","year":"2009","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.ygeno.2025.111167_bb0060","doi-asserted-by":"crossref","first-page":"3046","DOI":"10.1128\/AAC.01475-10","article-title":"Novel types of staphylococcal cassette chromosome mec elements identified in clonal complex 398 methicillin-resistant Staphylococcus aureus strains","volume":"55","author":"Li","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.ygeno.2025.111167_bb0065","doi-asserted-by":"crossref","first-page":"3765","DOI":"10.1128\/AAC.00187-11","article-title":"Detection of staphylococcal cassette chromosome mec type XI carrying highly divergent mecA, mecI, mecR1, blaZ, and ccr genes in human clinical isolates of clonal complex 130 methicillin-resistant Staphylococcus aureus","volume":"55","author":"Shore","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.ygeno.2025.111167_bb0070","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/j.meegid.2018.03.013","article-title":"Novel SCCmec type XIII (9A) identified in an ST152 methicillin-resistant Staphylococcus aureus","volume":"61","author":"Baig","year":"2018","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0075","first-page":"46","article-title":"Novel staphylococcal cassette chromosome mec (SCCmec) type XIV (5A) and a truncated SCCmec element in SCC composite islands carrying speG in ST5 MRSA in Japan","volume":"75","author":"Urushibara","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.ygeno.2025.111167_bb0080","doi-asserted-by":"crossref","first-page":"7597","DOI":"10.1128\/AAC.01692-15","article-title":"Novel type XII staphylococcal cassette chromosome mec harboring a new cassette chromosome recombinase, CcrC2","volume":"59","author":"Wu","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.ygeno.2025.111167_bb0085","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1089\/mdr.2005.11.83","article-title":"Genetic diversity among methicillin-resistant Staphylococcus epidermidis (MRSE)","volume":"11","author":"Miragaia","year":"2005","journal-title":"Microb. Drug Resist."},{"key":"10.1016\/j.ygeno.2025.111167_bb0090","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1093\/jac\/dks068","article-title":"Strategies of adaptation of Staphylococcus epidermidis to hospital and community: amplification and diversification of SCCmec","volume":"67","author":"Rolo","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.ygeno.2025.111167_bb0095","doi-asserted-by":"crossref","first-page":"2540","DOI":"10.1128\/JB.01484-06","article-title":"Inferring a population structure for Staphylococcus epidermidis from multilocus sequence typing data","volume":"189","author":"Miragaia","year":"2007","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0100","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.vetmic.2015.04.019","article-title":"Antimicrobial resistance and population structure of Staphylococcus epidermidis recovered from animals and humans","volume":"178","author":"Argud\u00edn","year":"2015","journal-title":"Vet. Microbiol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0105","doi-asserted-by":"crossref","first-page":"4751","DOI":"10.1128\/JCM.43.9.4751-4757.2005","article-title":"Clonal analysis of Staphylococcus epidermidis isolates carrying or lacking biofilm-mediating genes by multilocus sequence typing","volume":"43","author":"Kozitskaya","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0110","doi-asserted-by":"crossref","first-page":"1313","DOI":"10.1093\/gbe\/evv066","article-title":"Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis","volume":"7","author":"M\u00e9ric","year":"2015","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0115","doi-asserted-by":"crossref","first-page":"5034","DOI":"10.1038\/s41467-018-07368-7","article-title":"Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis","volume":"9","author":"M\u00e9ric","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ygeno.2025.111167_bb0120","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1128\/JCM.40.2.430-438.2002","article-title":"Molecular characterization of methicillin-resistant Staphylococcus epidermidis clones: evidence of geographic dissemination","volume":"40","author":"Miragaia","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0125","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1128\/AAC.35.4.632","article-title":"Multiple mechanisms of methicillin resistance and improved methods for detection in clinical isolates of Staphylococcus aureus","volume":"35","author":"de Lencastre","year":"1991","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.ygeno.2025.111167_bb0130","series-title":"Performance Standards for Antimicrobial Susceptibility Testing - CLSI Supplement M100","author":"CLSI","year":"2014"},{"key":"10.1016\/j.ygeno.2025.111167_bb0135","series-title":"Methods Enzymol","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1016\/S0076-6879(95)53040-1","article-title":"Methods for studying microbial colonization of plastics","author":"Christensen","year":"1995"},{"issue":"2010","key":"10.1016\/j.ygeno.2025.111167_bb0140","first-page":"469","article-title":"Evolution of MRSA during hospital transmission and intercontinental spread","volume":"327","author":"Harris","year":"1979","journal-title":"Science"},{"key":"10.1016\/j.ygeno.2025.111167_bb0145","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2 \u2013 approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PloS One"},{"key":"10.1016\/j.ygeno.2025.111167_bb0150","series-title":"snippy: Fast Bacterial Variant Calling From NGS Reads","author":"Seemann","year":"2015"},{"key":"10.1016\/j.ygeno.2025.111167_bb0155","article-title":"Microreact: visualizing and sharing data for genomic epidemiology and phylogeography","volume":"2","author":"Argim\u00f3n","year":"2016","journal-title":"Microb. Genom."},{"key":"10.1016\/j.ygeno.2025.111167_bb0160","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for de novo short read assembly using de Bruijn graphs","volume":"18","author":"Zerbino","year":"2008","journal-title":"Genome Res."},{"key":"10.1016\/j.ygeno.2025.111167_bb0165","doi-asserted-by":"crossref","first-page":"1518","DOI":"10.1128\/JB.186.5.1518-1530.2004","article-title":"eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data","volume":"186","author":"Feil","year":"2004","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0170","doi-asserted-by":"crossref","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":"10.1016\/j.ygeno.2025.111167_bb0175","doi-asserted-by":"crossref","first-page":"D32","DOI":"10.1093\/nar\/gkj014","article-title":"ISfinder: the reference Centre for bacterial insertion sequences","volume":"34","author":"Siguier","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ygeno.2025.111167_bb0180","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.ygeno.2025.111167_bb0185","doi-asserted-by":"crossref","first-page":"W347","DOI":"10.1093\/nar\/gkr485","article-title":"PHAST: a fast phage search tool","volume":"39","author":"Zhou","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ygeno.2025.111167_bib361","doi-asserted-by":"crossref","first-page":"4289","DOI":"10.1128\/JCM.40.11.4289-4294.2002","article-title":"Dissemination of New Methicillin-Resistant Staphylococcus aureus Clones in the Community","volume":"40","author":"Okuma","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.ygeno.2025.111167_bib362","doi-asserted-by":"crossref","first-page":"2637","DOI":"10.1128\/AAC.48.7.2637-2651.2004","article-title":"Novel type V staphylococcal cassette chromosome mec driven by a novel cassette chromosome recombinase, ccrC","volume":"48","author":"Ito","year":"2004","journal-title":"Antimicrob Agents Chemother"},{"key":"10.1016\/j.ygeno.2025.111167_bib363","doi-asserted-by":"crossref","first-page":"2155","DOI":"10.1128\/AAC.46.7.2155-2161.2002","article-title":"Multiplex PCR Strategy for Rapid Identification of Structural Types and Variants of the mec Element in Methicillin-Resistant Staphylococcus aureus","volume":"46","author":"Oliveira","year":"2002","journal-title":"Antimicrob Agents Chemother"},{"key":"10.1016\/j.ygeno.2025.111167_bb0190","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: multiple alignment of conserved genomic sequence with rearrangements","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Res."},{"key":"10.1016\/j.ygeno.2025.111167_bb0195","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using gubbins","volume":"43","author":"Croucher","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ygeno.2025.111167_bb0200","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1093\/bioinformatics\/btx610","article-title":"Phandango: an interactive viewer for bacterial population genomics","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ygeno.2025.111167_bb0205","doi-asserted-by":"crossref","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":"10.1016\/j.ygeno.2025.111167_bb0210","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ygeno.2025.111167_bb0215","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-016-1108-8","article-title":"Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary","volume":"17","author":"Brynildsrud","year":"2016","journal-title":"Genome Biol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0220","unstructured":"GraphPad | Analyze a 2x2 Contingency Table, (n.d.). https:\/\/www.graphpad.com\/quickcalcs\/contingency1\/ (accessed May 2, 2021)."},{"key":"10.1016\/j.ygeno.2025.111167_bb0225","doi-asserted-by":"crossref","first-page":"1020","DOI":"10.1111\/j.1469-0691.2008.02080.x","article-title":"Molecular characterization of methicillin-resistant Staphylococcus epidermidis strains from bacteraemic patients","volume":"14","author":"Ibrahem","year":"2008","journal-title":"Clin. Microbiol. Infect."},{"key":"10.1016\/j.ygeno.2025.111167_bb0230","doi-asserted-by":"crossref","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":"10.1016\/j.ygeno.2025.111167_bb0235","doi-asserted-by":"crossref","first-page":"14","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"},{"key":"10.1016\/j.ygeno.2025.111167_bb0240","doi-asserted-by":"crossref","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":"10.1016\/j.ygeno.2025.111167_bb0245","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0104561","article-title":"Comparison of biofilm formation between major clonal lineages of methicillin resistant Staphylococcus aureus","volume":"9","author":"Vanhommerig","year":"2014","journal-title":"PloS One"},{"key":"10.1016\/j.ygeno.2025.111167_bb0250","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1086\/653483","article-title":"Methicillin-resistant coagulase-negative staphylococci in the community: high homology of SCCmec IVa between Staphylococcus epidermidis and major clones of methicillin-resistant Staphylococcus aureus","volume":"202","author":"Barbier","year":"2010","journal-title":"J Infect Dis"},{"key":"10.1016\/j.ygeno.2025.111167_bb0255","doi-asserted-by":"crossref","first-page":"2426","DOI":"10.1128\/JB.187.7.2426-2438.2005","article-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","volume":"187","author":"Gill","year":"2005","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0260","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1111\/j.1574-6968.2007.00688.x","article-title":"ica and beyond: biofilm mechanisms and regulation in Staphylococcus epidermidis and Staphylococcus aureus","volume":"270","author":"O\u2019Gara","year":"2007","journal-title":"FEMS Microbiol. Lett."},{"key":"10.1016\/j.ygeno.2025.111167_bb0265","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1128\/AAC.00724-08","article-title":"Diversity of staphylococcal cassette chromosome mec structures in methicillin-resistant Staphylococcus epidermidis and Staphylococcus haemolyticus strains among outpatients from four countries","volume":"53","author":"Rupp\u00e9","year":"2009","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.ygeno.2025.111167_bb0270","doi-asserted-by":"crossref","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":"10.1016\/j.ygeno.2025.111167_bb0275","doi-asserted-by":"crossref","first-page":"3574","DOI":"10.1128\/AAC.47.11.3574-3579.2003","article-title":"Related clones containing SCCmec type IV predominate among clinically significant Staphylococcus epidermidis isolates","volume":"47","author":"Wisplinghoff","year":"2003","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.ygeno.2025.111167_bb0280","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1003539","article-title":"Enterococcus faecalis prophage dynamics and contributions to pathogenic traits","volume":"9","author":"Matos","year":"2013","journal-title":"PLoS Genet."},{"key":"10.1016\/j.ygeno.2025.111167_bb0285","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1186\/1471-2164-13-228","article-title":"Genomic characterization of two Staphylococcus epidermidis bacteriophages with anti-biofilm potential","volume":"13","author":"Guti\u00e9rrez","year":"2012","journal-title":"BMC Genomics"},{"key":"10.1016\/j.ygeno.2025.111167_bb0290","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0107307","article-title":"Effective removal of staphylococcal biofilms by the endolysin LysH5","volume":"9","author":"Guti\u00e9rrez","year":"2014","journal-title":"PloS One"},{"key":"10.1016\/j.ygeno.2025.111167_bb0295","doi-asserted-by":"crossref","first-page":"3336","DOI":"10.1128\/AEM.03560-14","article-title":"Two phages, phiIPLA-RODI and phiIPLA-C1C, lyse mono- and dual-species staphylococcal biofilms","volume":"81","author":"Guti\u00e9rrez","year":"2015","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0300","doi-asserted-by":"crossref","first-page":"6208","DOI":"10.1128\/JB.186.18.6208-6219.2004","article-title":"Inactivations of rsbU and sarA by IS256 represent novel mechanisms of biofilm phenotypic variation in Staphylococcus epidermidis","volume":"186","author":"Conlon","year":"2004","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0305","doi-asserted-by":"crossref","first-page":"1210","DOI":"10.1128\/IAI.72.2.1210-1215.2004","article-title":"The bacterial insertion sequence element IS256 occurs preferentially in nosocomial Staphylococcus epidermidis isolates: association with biofilm formation and resistance to aminoglycosides","volume":"72","author":"Kozitskaya","year":"2004","journal-title":"Infect. Immun."},{"key":"10.1016\/j.ygeno.2025.111167_bb0310","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1046\/j.1365-2958.1999.01353.x","article-title":"A novel mechanism of phase variation of virulence in Staphylococcus epidermidis: evidence for control of the polysaccharide intercellular adhesin synthesis by alternating insertion and excision of the insertion sequence element IS256","volume":"32","author":"Ziebuhr","year":"1999","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0315","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1128\/jb.95.4.1335-1342.1968","article-title":"Plasmid-linked resistance to inorganic salts in Staphylococcus aureus","volume":"95","author":"Novick","year":"1968","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0320","doi-asserted-by":"crossref","first-page":"2690","DOI":"10.1128\/AEM.00036-15","article-title":"Methicillin-resistant Staphylococcus aureus in commercial swine herds is associated with disinfectant and zinc usage","volume":"81","author":"Slifierz","year":"2015","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0325","first-page":"1635","article-title":"Erythromycin-resistant staphylococci. Incidence and mode of development","volume":"122","author":"Eriksen","year":"1960","journal-title":"Ugeskr Laeger"},{"key":"10.1016\/j.ygeno.2025.111167_bb0330","doi-asserted-by":"crossref","first-page":"3320","DOI":"10.1021\/bi00874a034","article-title":"On the mode of action of fusidic acid","volume":"5","author":"Harvey","year":"1966","journal-title":"Biochemistry"},{"key":"10.1016\/j.ygeno.2025.111167_bb0335","first-page":"359","article-title":"Staphylococcus aureus strains isolated in Danish hospitals from January 1st, 1966, to December 31st, 1974","volume":"84B","author":"Rosendal","year":"1976","journal-title":"Acta Pathol. Microbiol. Scand. Sec. B Microbiol."},{"key":"10.1016\/j.ygeno.2025.111167_bb0340","doi-asserted-by":"crossref","first-page":"9865","DOI":"10.1073\/pnas.161272898","article-title":"The evolution of methicillin resistance in Staphylococcus aureus: similarity of genetic backgrounds in historically early methicillin-susceptible and -resistant isolates and contemporary epidemic clones","volume":"98","author":"Cris\u00f3stomo","year":"2001","journal-title":"Proc. Natl. Acad. Sci."},{"key":"10.1016\/j.ygeno.2025.111167_bb0345","doi-asserted-by":"crossref","first-page":"5465","DOI":"10.1128\/JB.185.18.5465-5472.2003","article-title":"H the barrier to \u03b2-lactam resistance in Staphylococcus aureus","volume":"185","author":"Katayama","year":"2003","journal-title":"J. Bacteriol."}],"container-title":["Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0888754325001831?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0888754325001831?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,11]],"date-time":"2026-05-11T23:44:52Z","timestamp":1778543092000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0888754325001831"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":72,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1]]}},"alternative-id":["S0888754325001831"],"URL":"https:\/\/doi.org\/10.1016\/j.ygeno.2025.111167","relation":{},"ISSN":["0888-7543"],"issn-type":[{"value":"0888-7543","type":"print"}],"subject":[],"published":{"date-parts":[[2026,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Remodeling of Staphylococcus epidermidis genome over three decades of nosocomial exposure","name":"articletitle","label":"Article Title"},{"value":"Genomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ygeno.2025.111167","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"111167"}}