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Antimicrobial use is the major treatment, but there are many flaws linked to resistance, tolerance or persistence. This study aimed to verify changes in resistance, virulence and clonal profiles of <jats:italic>S. aureus<\/jats:italic> isolated from persistent mastitis goat milk before and after enrofloxacin treatment.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>MIC increased to at least one antimicrobial in <jats:italic>S. aureus<\/jats:italic> isolates after enrofloxacin treatment compared to before. The most detected resistance genes before and after treatment were <jats:italic>tetK<\/jats:italic>, <jats:italic>tetM<\/jats:italic>, and <jats:italic>blaZ<\/jats:italic>, with more resistance genes detected after enrofloxacin treatment (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.05). Occasional variations in efflux system gene detection were observed before and after treatment. Nine virulence genes (<jats:italic>hla<\/jats:italic>, <jats:italic>fnbA<\/jats:italic>, <jats:italic>fnbB<\/jats:italic>, <jats:italic>eta<\/jats:italic>, <jats:italic>etb<\/jats:italic>, <jats:italic>sea<\/jats:italic>, <jats:italic>sec<\/jats:italic>, <jats:italic>seh<\/jats:italic>, and <jats:italic>sej<\/jats:italic>) were detected at both times, and between these, the <jats:italic>hla<\/jats:italic> and <jats:italic>eta<\/jats:italic> genes were detected more in isolates after treatment. All isolates of <jats:italic>S. aureus<\/jats:italic> belonged to the same sequence type (ST) 133, except for two <jats:italic>S. aureus<\/jats:italic> isolates prior to enrofloxacin treatment which were classified as ST5 and the other as a new one, ST4966. Isolates of <jats:italic>S. aureus<\/jats:italic> 4, 8, and 100 from before and after treatment had identical pulse types, while others obtained from other animals before and after treatment were classified into distinct pulse types.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>There were occasional changes in the studied profiles of <jats:italic>S. aureus<\/jats:italic> isolated before and after treatment of animals with enrofloxacin, which may have contributed to the permanence of bacteria in the mammary gland, even when using traditional treatment, resulting in persistent mastitis.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12866-020-01793-9","type":"journal-article","created":{"date-parts":[[2020,5,24]],"date-time":"2020-05-24T08:02:32Z","timestamp":1590307352000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["Profiles of Staphyloccocus aureus isolated from goat persistent mastitis before and after treatment with enrofloxacin"],"prefix":"10.1186","volume":"20","author":[{"given":"Magna Coroa","family":"Lima","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariana","family":"de Barros","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thalita Moreira","family":"Scatamburlo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard Costa","family":"Polveiro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"La\u00eds Karolyne","family":"de Castro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel Henrique Sales","family":"Guimar\u00e3es","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanely Louren\u00e7o","family":"da Costa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mateus Matiuzzi","family":"da Costa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6902-2502","authenticated-orcid":false,"given":"Maria Aparecida Scatamburlo","family":"Moreira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,5,24]]},"reference":[{"key":"1793_CR1","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1051\/vetres:2003030","volume":"34","author":"D Bergonier","year":"2003","unstructured":"Bergonier D, de Cr\u00e9moux R, Rupp R, Lagriffoul G, Berthelot X. 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