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We report the identification of\n                      <jats:italic>S. nepalensis<\/jats:italic>\n                      of a hypersaline lagoon in Brazil, along with in-depth phylogeographical and resistome analysis of publicly available genomes.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods and results<\/jats:title>\n                    <jats:p>\n                      During a local survey from hypersaline aquatic environments in Rio de Janeiro, Brazil, two staphylococcal strains were recovered, designated as COLB and AM1. These isolates were subjected to antimicrobial susceptibility testing, genomic sequencing, and comprehensive phylogenomic analyses. Genomic analysis confirmed the taxonomic identity of COLB and AM1 as\n                      <jats:italic>S. nepalensis.<\/jats:italic>\n                      Both isolates harbored the\n                      <jats:italic>sal<\/jats:italic>\n                      (E) conferring resistance to pleuromutilins and streptogramin A, whereas\n                      <jats:italic>tet<\/jats:italic>\n                      (K) conferring to tetracyclines. Additionally, AM1 carried\n                      <jats:italic>lnu<\/jats:italic>\n                      (A), consistent with the reduced susceptibility to clindamycin (MIC\u2009=\u20092\u00a0\u00b5g\/mL) relative to COLB. Genes associated with arsenic and copper tolerance, and the replicons\n                      <jats:italic>rep7a<\/jats:italic>\n                      and\n                      <jats:italic>rep19c<\/jats:italic>\n                      , were confirmed. Phylogenomic analysis indicated that COLB and AM1 were clonally related (1 cgSNP-difference) but distinct from global isolates. Phylogeographic analysis revealed wide geographic occurrence, with some lineages carrying\n                      <jats:italic>blaZ<\/jats:italic>\n                      and\n                      <jats:italic>mecA<\/jats:italic>\n                      associated with beta-lactamase production and methicillin resistance, respectively. Strikingly,\n                      <jats:italic>sal<\/jats:italic>\n                      (E) is conserved across all\n                      <jats:italic>S. nepalensis<\/jats:italic>\n                      genomes.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      The findings confirm the presence of\n                      <jats:italic>S. nepalensis<\/jats:italic>\n                      in South America as early as 2016 and documented among available genomes from environmental, human, and animal-associated sources. Furthermore, reveal the circulation of some lineages carrying clinically relevant antimicrobial genes, underscoring the importance of accurate species identification and continuous genomic surveillance and potential One Health relevance.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1007\/s11033-026-12601-4","type":"journal-article","created":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T13:41:33Z","timestamp":1788529293000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Phylogeographic analysis of Staphylococcus nepalensis reveals global occurrence of antimicrobial-resistant lineages carrying the sal(E) resistance gene"],"prefix":"10.1007","volume":"53","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9813-1556","authenticated-orcid":false,"given":"Johana","family":"Becerra","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabella","family":"Gai\u00e3o","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberta Almeida","family":"Vincenzi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Davi Gabriel Salustiano","family":"Merighi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felipe","family":"V\u00e1squez-Ponce","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Santiago Justo","family":"Arevalo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jesus","family":"Pariona","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory","family":"Melocco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernanda","family":"Esposito","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabio","family":"Rodrigues","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nilton","family":"Lincopan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,4]]},"reference":[{"key":"12601_CR1","doi-asserted-by":"publisher","first-page":"1092632","DOI":"10.1155\/2018\/1092632","volume":"2018","author":"LA Onyango","year":"2018","unstructured":"Onyango LA, Alreshidi MM (2018) Adaptive metabolism in staphylococci: survival and persistence in environmental and clinical settings. 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