{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T09:25:13Z","timestamp":1787736313447,"version":"build-2784847793"},"reference-count":64,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T00:00:00Z","timestamp":1787702400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001807","name":"S\u00e3o Paulo Research Foundation","doi-asserted-by":"publisher","award":["2021\/12215-8"],"award-info":[{"award-number":["2021\/12215-8"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"award":["2021\/12215-8"],"award-info":[{"award-number":["2021\/12215-8"]}],"id":[{"id":"https:\/\/ror.org\/02ddkpn78","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002322","name":"Brazilian Federal Agency for Support and Evaluation of Graduate Education","doi-asserted-by":"publisher","award":["001"],"award-info":[{"award-number":["001"]}],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]},{"award":["001"],"award-info":[{"award-number":["001"]}],"id":[{"id":"https:\/\/ror.org\/00x0ma614","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Antimicrobial resistance (AMR) is a global public health concern, and animal food production contributes to its spread. This study compared antimicrobial resistance gene (ARG) profiles in Salmonella spp., Escherichia coli, and Enterococcus spp. isolated from chicken meat produced under conventional (CONV) and antibiotic-free (ATB-Free) systems using whole-genome sequencing of 207 phenotypically selected isolates. We hypothesized that the ATB-Free production would be associated with fewer resistance genes, but the observed patterns differed among the bacterial groups. In E. coli (41 genes; 61.0% shared between chains), the gene load per isolate was similar between the production systems (median of four in both chains). In Salmonella spp., only five ATB-Free isolates were available, precluding a meaningful comparison between the production systems; a rarefaction analysis showed that the lower gene count observed in this group was consistent with the sampling effort. In Enterococcus spp., the CONV isolates carried a higher gene load (median of two vs. one) and a higher proportion of enzymatic determinants (48.4% vs. 11.8%). This difference was concentrated in isolates carrying the ionophore resistance genes narA and narB (CONV 41.9% vs. ATB-Free 5.9%; p &lt; 0.001), which were not associated with transferable vancomycin or high-level aminoglycoside resistance determinants in this dataset. The resistance determinants associated with the clinically important antimicrobial classes, including blaCTX-M-8, quinolone resistance genes, and fosfomycin resistance genes, were detected in isolates from both production systems. Overall, the observed ARG profiles differed among the bacterial groups, indicating that the relationship between the production system and the resistome was not uniform. Since the sequenced isolates constituted a phenotypically selected subset, the observed ARG frequencies should not be interpreted as population-level prevalence estimates for either production system.<\/jats:p>","DOI":"10.3390\/pathogens15090899","type":"journal-article","created":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T09:05:46Z","timestamp":1787735146000},"page":"899","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Antimicrobial Resistance Gene Profiles in Salmonella spp., Escherichia coli, and Enterococcus spp. from Conventional and Antibiotic-Free Chicken Meat"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1222-6544","authenticated-orcid":false,"given":"Camila Koutsodontis","family":"Cerqueira-C\u00e9zar","sequence":"first","affiliation":[{"name":"Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, S\u00e3o Paulo State University (UNESP), Prof. Dr. Walter Mauricio Correa Street, Botucatu 18618-681, SP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0722-7710","authenticated-orcid":false,"given":"Evelyn Cristine","family":"da Silva","sequence":"additional","affiliation":[{"name":"Institute for Biotechnology, S\u00e3o Paulo State University (UNESP), Tecomarias Avenue, Botucatu 18607-440, SP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3648-2382","authenticated-orcid":false,"given":"Aryele Nunes","family":"da Cruz Encide Sampaio","sequence":"additional","affiliation":[{"name":"Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, S\u00e3o Paulo State University (UNESP), Prof. Dr. Walter Mauricio Correa Street, Botucatu 18618-681, SP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evelyn Fernanda Flores","family":"Caron","sequence":"additional","affiliation":[{"name":"Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, S\u00e3o Paulo State University (UNESP), Prof. Dr. Walter Mauricio Correa Street, Botucatu 18618-681, SP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanderson Sirley Reis","family":"Teixeira","sequence":"additional","affiliation":[{"name":"Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, S\u00e3o Paulo State University (UNESP), Prof. Dr. Walter Mauricio Correa Street, Botucatu 18618-681, SP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emanoelli Aparecida Rodrigues","family":"dos Santos","sequence":"additional","affiliation":[{"name":"Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, S\u00e3o Paulo State University (UNESP), Prof. Dr. Walter Mauricio Correa Street, Botucatu 18618-681, SP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Larissa","family":"de Abreu Albano","sequence":"additional","affiliation":[{"name":"Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, S\u00e3o Paulo State University (UNESP), Prof. Dr. Walter Mauricio Correa Street, Botucatu 18618-681, SP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-9054-9518","authenticated-orcid":false,"given":"Gustavo Guimar\u00e3es Fernandes","family":"Viana","sequence":"additional","affiliation":[{"name":"Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, S\u00e3o Paulo State University (UNESP), Prof. Dr. Walter Mauricio Correa Street, Botucatu 18618-681, SP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0711-6455","authenticated-orcid":false,"given":"Larissa Soares","family":"de Araujo","sequence":"additional","affiliation":[{"name":"Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, S\u00e3o Paulo State University (UNESP), Prof. Dr. Walter Mauricio Correa Street, Botucatu 18618-681, SP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9153-1485","authenticated-orcid":false,"given":"Jo\u00e3o Pessoa","family":"Ara\u00fajo Junior","sequence":"additional","affiliation":[{"name":"Institute for Biotechnology, S\u00e3o Paulo State University (UNESP), Tecomarias Avenue, Botucatu 18607-440, SP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9065-1277","authenticated-orcid":false,"given":"Carlo","family":"Spanu","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Sassari (UNISS), 07100 Sassari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0118-6164","authenticated-orcid":false,"given":"F\u00e1bio Sossai","family":"Possebon","sequence":"additional","affiliation":[{"name":"Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, S\u00e3o Paulo State University (UNESP), Prof. Dr. Walter Mauricio Correa Street, Botucatu 18618-681, SP, Brazil"},{"name":"Institute for Biotechnology, S\u00e3o Paulo State University (UNESP), Tecomarias Avenue, Botucatu 18607-440, SP, 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