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However, identification techniques do not routinely differentiate\n                    <jats:italic>Elc<\/jats:italic>\n                    from\n                    <jats:italic>Efm<\/jats:italic>\n                    . As part of a longitudinal study to investigate the antimicrobial resistance of\n                    <jats:italic>Enterococcus<\/jats:italic>\n                    in dairy cattle, isolates initially identified as\n                    <jats:italic>Efm<\/jats:italic>\n                    were confirmed as\n                    <jats:italic>Elc<\/jats:italic>\n                    after Oxford-Nanopore long-fragment whole-genome sequencing and genome comparisons. An\n                    <jats:italic>Efm<\/jats:italic>\n                    -specific PCR assay was developed and used to identify isolates recovered from animal feces on five farms, resulting in 44\n                    <jats:italic>Efs<\/jats:italic>\n                    , 23\n                    <jats:italic>Efm<\/jats:italic>\n                    , and 59\n                    <jats:italic>Elc<\/jats:italic>\n                    . Resistance, determined by broth microdilution, was more frequent in\n                    <jats:italic>Efs<\/jats:italic>\n                    than in\n                    <jats:italic>Efm<\/jats:italic>\n                    and\n                    <jats:italic>Elc<\/jats:italic>\n                    but all isolates were susceptible to ampicillin, daptomycin, teicoplanin, tigecycline, and vancomycin. Genome sequencing analysis of 32 isolates identified 23 antimicrobial resistance genes (ARGs, mostly plasmid-located) and 2 single nucleotide polymorphisms associated with resistance to 10 antimicrobial classes, showing high concordance with phenotypic resistance. Notably, linezolid resistance in\n                    <jats:italic>Efm<\/jats:italic>\n                    was encoded by the\n                    <jats:italic>optrA<\/jats:italic>\n                    gene, located in plasmids downstream of the\n                    <jats:italic>fexA<\/jats:italic>\n                    gene. Although most\n                    <jats:italic>Elc<\/jats:italic>\n                    lacked virulence factors and genetic determinants of resistance, one isolate carried a plasmid with eight ARGs. This study showed that\n                    <jats:italic>Elc<\/jats:italic>\n                    is more prevalent than\n                    <jats:italic>Efm<\/jats:italic>\n                    in dairy cattle but carries fewer ARGs and virulence genes. However,\n                    <jats:italic>Elc<\/jats:italic>\n                    can carry multi-drug-resistant plasmids like those harbored by\n                    <jats:italic>Efm<\/jats:italic>\n                    and could act as a donor of ARGs for other pathogenic enterococcal species.\n                  <\/jats:p>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Enterococcus<\/jats:italic>\n                      species identification is crucial due to differences in pathogenicity and antibiotic resistance profiles. The failure of traditional methods or whole-genome sequencing-based taxonomic classifiers to distinguish\n                      <jats:italic>Enterococcus lactis<\/jats:italic>\n                      (\n                      <jats:italic>Elc<\/jats:italic>\n                      ) from\n                      <jats:italic>Enterococcus faecium<\/jats:italic>\n                      (\n                      <jats:italic>Efm<\/jats:italic>\n                      ) results in a biased interpretation of\n                      <jats:italic>Efm<\/jats:italic>\n                      epidemiology. The\n                      <jats:italic>Efm<\/jats:italic>\n                      species-specific real-time PCR assay developed here will help to properly identify\n                      <jats:italic>Efm<\/jats:italic>\n                      (only the formerly known clade A) in future studies. Here, we showed that\n                      <jats:italic>Elc<\/jats:italic>\n                      is prevalent in dairy cattle, and although this species carries fewer genetic determinants of resistance (GDRs) than\n                      <jats:italic>Enterococcus faecalis<\/jats:italic>\n                      (\n                      <jats:italic>Efs<\/jats:italic>\n                      ) and\n                      <jats:italic>Efm<\/jats:italic>\n                      , it can carry multi-drug-resistant (MDR) plasmids and could act as a donor of resistance genes for other pathogenic enterococcal species. Although all isolates (\n                      <jats:italic>Efs<\/jats:italic>\n                      ,\n                      <jats:italic>Efm<\/jats:italic>\n                      , and\n                      <jats:italic>Elc<\/jats:italic>\n                      ) were susceptible to critically or highly important antibiotics like daptomycin, teicoplanin, tigecycline, and vancomycin, the presence of GDRs in MDR-plasmids is a concern since antimicrobials commonly used in livestock could co-select and confer resistance to critically important antimicrobials not used in food-producing animals.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.03672-23","type":"journal-article","created":{"date-parts":[[2024,1,17]],"date-time":"2024-01-17T09:00:44Z","timestamp":1705482044000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":13,"title":["Whole-genome long-read sequencing to unveil\n                    <i>Enterococcus<\/i>\n                    antimicrobial resistance in dairy cattle farms exposed a widespread occurrence of\n                    <i>Enterococcus lactis<\/i>"],"prefix":"10.1128","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5136-956X","authenticated-orcid":false,"given":"Medelin","family":"Ocejo","sequence":"first","affiliation":[{"name":"Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-2315-1505","authenticated-orcid":false,"given":"Maitane","family":"Mugica","sequence":"additional","affiliation":[{"name":"Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8896-6245","authenticated-orcid":false,"given":"Beatriz","family":"Oporto","sequence":"additional","affiliation":[{"name":"Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0914-3211","authenticated-orcid":false,"given":"Jos\u00e9 Luis","family":"Lav\u00edn","sequence":"additional","affiliation":[{"name":"Applied Mathematics Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, 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