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In this study, 40 Enterococcus spp. isolates of human clinical (n = 10), veterinary commensal (n = 10), veterinary clinical (n = 10) and veterinary environmental (hospital surfaces) (n = 10) origins, were exposed to a high concentration of ciprofloxacin. Time\u2013kill curves were established, after which antimicrobial susceptibility profiles were reassessed. Subsequently, the only presumptive persister was selected for Whole-Genome Sequencing, together with one isolate showing no evidence of persister formation. Comparative genomic analyses were conducted to identify genetic variations between exposed and non-exposed isolates and to explore potential genetic determinants associated with persistence. Observed genetic features present in the persister isolate included toxin\u2013antitoxin systems, a cold-shock protein and the tyrosine-type recombinase\/integrase XerC, which may represent putative candidates for further investigation. Interestingly, the majority of toxin\u2013antitoxin system-associated genes were found in plasmids. This study represents an important step towards a better understanding of persistence development in Enterococcus spp.; however, validation using other methodologies such as RNA-sequencing is an important next step.<\/jats:p>","DOI":"10.3390\/microorganisms14040921","type":"journal-article","created":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T13:22:47Z","timestamp":1776691367000},"page":"921","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Candidate Genomic Features Associated with Persistence in Enterococcus spp."],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7885-1820","authenticated-orcid":false,"given":"Catarina","family":"Geraldes","sequence":"first","affiliation":[{"name":"CIISA\u2014Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal"},{"name":"AL4AnimalS\u2014Associate 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Lisbon, 1300-477 Lisbon, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu\u00eds","family":"Tavares","sequence":"additional","affiliation":[{"name":"CIISA\u2014Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal"},{"name":"AL4AnimalS\u2014Associate Laboratory for Animal and Veterinary Science, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1960-603X","authenticated-orcid":false,"given":"Joana Fernandes","family":"Guerreiro","sequence":"additional","affiliation":[{"name":"CIISA\u2014Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal"},{"name":"AL4AnimalS\u2014Associate Laboratory for Animal and Veterinary Science, Faculty of Veterinary Medicine, University of Lisbon, 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