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Therefore, we analyze its population structure through genomic analysis integrated with metadata.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      We performed whole-genome sequencing-based population genomic analyses by integrating 1742 publicly available\n                      <jats:italic>S. epidermidis<\/jats:italic>\n                      genomes (accessed by August 2025) with 94 newly sequenced isolates. Our analyses revealed that\n                      <jats:italic>S. epidermidis<\/jats:italic>\n                      represents a species complex composed of four phylogenetic lineages (phylogroups 1-4) with diverse clonal backgrounds and a broad global distribution. The species harbors an open pan-genome and demonstrates a strong capacity to acquire novel genetic traits through mobile genetic elements. Extensive antimicrobial resistance and substantial virulence potential were observed across lineages. Notably, phylogroup 1, dominated by ST 2, exhibited a 97.8% detection rate of the methicillin resistance gene\n                      <jats:italic>mecA<\/jats:italic>\n                      , likely driven by clonal expansion and horizontal gene transfer, identifying it as a high-risk lineage. The analysis of enriched genes in blood-derived strains showed that the adaptability of\n                      <jats:italic>S. epidermidis<\/jats:italic>\n                      in bloodstream-associated environments is controlled by multiple genes, involving antimicrobial resistance, cell wall remodeling, environmental adaptation, and core metabolism.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      This study provides a comprehensive population genomic framework for\n                      <jats:italic>S. epidermidis<\/jats:italic>\n                      , elucidating its population structure, genomic diversity, antimicrobial resistance, and virulence-associated genetic features. These findings offer valuable insights into the evolutionary dynamics and pathogenic potential of\n                      <jats:italic>S. epidermidis<\/jats:italic>\n                      and provide an important genomic resource to inform infection control strategies and clinical management.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12864-026-12922-5","type":"journal-article","created":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T10:27:55Z","timestamp":1778754475000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Global distribution, antimicrobial resistance, and virulence factors of Staphylococcus epidermidis revealed through population genomics"],"prefix":"10.1186","volume":"27","author":[{"given":"Yan","family":"Yang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian-Hua","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cong-Ran","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan-Biao","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xue","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,5,14]]},"reference":[{"issue":"7","key":"12922_CR1","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1016\/j.tim.2023.01.001","volume":"31","author":"TL Burke","year":"2023","unstructured":"Burke TL, Rupp ME, Fey PD. 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