{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T17:48:27Z","timestamp":1791654507230,"version":"4.3.4"},"reference-count":47,"publisher":"Elsevier BV","issue":"3","license":[{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,1,24]],"date-time":"2025-01-24T00:00:00Z","timestamp":1737676800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007917","name":"USDA Agricultural Research Service","doi-asserted-by":"publisher","award":["6040-32000-085-002-S"],"award-info":[{"award-number":["6040-32000-085-002-S"]}],"id":[{"id":"10.13039\/100007917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007917","name":"USDA Agricultural Research Service","doi-asserted-by":"publisher","award":["6040-32000-012-006-S"],"award-info":[{"award-number":["6040-32000-012-006-S"]}],"id":[{"id":"10.13039\/100007917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008745","name":"Alabama Agricultural Experiment Station","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008745","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Poultry Science"],"published-print":{"date-parts":[[2025,3]]},"DOI":"10.1016\/j.psj.2025.104855","type":"journal-article","created":{"date-parts":[[2025,1,28]],"date-time":"2025-01-28T18:54:37Z","timestamp":1738090477000},"page":"104855","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":9,"title":["Genotypic and phenotypic characterization of antimicrobial resistance in Salmonella strains isolated from both No-Antibiotics-Ever (NAE) and conventional broiler complexes"],"prefix":"10.1016","volume":"104","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-0414-384X","authenticated-orcid":false,"given":"Yagya","family":"Adhikari","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0209-9465","authenticated-orcid":false,"given":"Dianna V.","family":"Bourassa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5421-4256","authenticated-orcid":false,"given":"Sabin","family":"Poudel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5149-4456","authenticated-orcid":false,"given":"Matthew A.","family":"Bailey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9291-2418","authenticated-orcid":false,"given":"Richard J.","family":"Buhr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2707-8866","authenticated-orcid":false,"given":"Kenneth S.","family":"Macklin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.psj.2025.104855_bib0001","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.02090-24","article-title":"Whole-genome sequencing and phylogenetic analysis of Salmonella isolated from pullets through final raw product in the processing plant of a conventional broiler complex: a longitudinal study","author":"Adhikari","year":"2025","journal-title":"Microbiol. Spectr."},{"key":"10.1016\/j.psj.2025.104855_bib0002","doi-asserted-by":"crossref","DOI":"10.1016\/j.psj.2024.104212","article-title":"Assessment and genomic analysis of Salmonella and Campylobacter from different stages of an integrated No-antibiotics-ever (NAE) broiler complex: a longitudinal study","author":"Adhikari","year":"2024","journal-title":"Poult. Sci."},{"key":"10.1016\/j.psj.2025.104855_bib0003","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.cmi.2015.12.004","article-title":"Salmonellosis: the role of poultry meat","volume":"22","author":"Antunes","year":"2016","journal-title":"Clin. Microbiol. Infect."},{"issue":"2","key":"10.1016\/j.psj.2025.104855_bib0004","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1111\/j.1574-6968.1999.tb13586.x","article-title":"A new chloramphenicol and florfenicol resistance gene flanked by two integron structures in Salmonella typhimurium DT104","volume":"174","author":"Arcangioli","year":"1999","journal-title":"FEMS Microbiol. Letters"},{"issue":"3","key":"10.1016\/j.psj.2025.104855_bib0005","doi-asserted-by":"crossref","first-page":"491","DOI":"10.4315\/0362-028X.JFP-19-269","article-title":"Prevalence and antimicrobial resistance of Salmonella from antibiotic-free broilers during organic and conventional processing","volume":"83","author":"Bailey","year":"2020","journal-title":"J. Food Prot."},{"issue":"12","key":"10.1016\/j.psj.2025.104855_bib0006","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.psj.2025.104855_bib0007","doi-asserted-by":"crossref","first-page":"20","DOI":"10.3389\/fsufs.2019.00020","article-title":"Antimicrobial resistant Salmonella enterica Typhimurium colonizing chickens: the impact of plasmids, genotype, bacterial communities, and antibiotic administration on resistance","volume":"3","author":"Bythwood","year":"2019","journal-title":"Front. Sustain. Food Sys."},{"key":"10.1016\/j.psj.2025.104855_bib0008","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinform."},{"issue":"7","key":"10.1016\/j.psj.2025.104855_bib0009","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"PlasmidFinder and pMLST: in silico detection and typing of plasmids","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.psj.2025.104855_bib0010","series-title":"Antimicrobial Resistance. 2019 Antibiotic Resistance Threats Report","year":"2019"},{"key":"10.1016\/j.psj.2025.104855_bib0011","unstructured":"Center for Disease Control and Prevention (CDC). 2024. Salmonella. Accessed September 2024. https:\/\/www.cdc.gov\/salmonella\/index.html."},{"key":"10.1016\/j.psj.2025.104855_bib0012","series-title":"FDA Reports Major Drop in Antibiotics for Food Animals","year":"2018"},{"issue":"1-2","key":"10.1016\/j.psj.2025.104855_bib0013","doi-asserted-by":"crossref","DOI":"10.1016\/j.resmic.2022.103985","article-title":"Biochemical and molecular mechanisms of antibiotic resistance in Salmonella spp","volume":"174","author":"Chaudhari","year":"2023","journal-title":"Res. Microbiol."},{"key":"10.1016\/j.psj.2025.104855_bib0015","series-title":"Performance Standards for Antimicrobial Susceptibility Testing","year":"2024"},{"issue":"3-4","key":"10.1016\/j.psj.2025.104855_bib0016","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1051\/vetres:2001105","article-title":"Mechanisms of quinolone resistance in Salmonella","volume":"32","author":"Cloeckaert","year":"2001","journal-title":"Veterinary Res."},{"issue":"3","key":"10.1016\/j.psj.2025.104855_bib0017","doi-asserted-by":"crossref","first-page":"408","DOI":"10.3382\/japr\/pfv038","article-title":"Salmonella and antimicrobial resistance in broilers: a review","volume":"24","author":"Cosby","year":"2015","journal-title":"J. Appl. Poult. Res."},{"issue":"1","key":"10.1016\/j.psj.2025.104855_bib0018","doi-asserted-by":"crossref","first-page":"40","DOI":"10.4315\/0362-028.JFP-13-251","article-title":"Antibiotic resistance and diversity of Salmonella enterica serovars associated with broiler chickens","volume":"77","author":"Diarra","year":"2014","journal-title":"J. Food Prot."},{"key":"10.1016\/j.psj.2025.104855_bib0020","series-title":"Multi-country outbreak of Salmonella Enteritidis sequence type (ST) 11 infections linked to poultry products in the EU\/EEA and the United Kingdom. Stockholm","year":"2021"},{"key":"10.1016\/j.psj.2025.104855_bib0021","series-title":"2016-2017 NARMS Integrated Summary","year":"2018"},{"key":"10.1016\/j.psj.2025.104855_bib0022","series-title":"Summary Report on Antimicrobials Sold or Distributed for Use in Food-Producing Animals","year":"2022"},{"key":"10.1016\/j.psj.2025.104855_bib0023","series-title":"Salmonella Infections. Diseases of Poultry","first-page":"717","author":"Gast","year":"2020"},{"issue":"10014","key":"10.1016\/j.psj.2025.104855_bib0024","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/S0140-6736(15)00473-0","article-title":"Understanding the mechanisms and drivers of antimicrobial resistance","volume":"387","author":"Holmes","year":"2016","journal-title":"The Lancet"},{"key":"10.1016\/j.psj.2025.104855_bib0025","series-title":"Foodborne illness source attribution estimates for 2015 for Salmonella, Escherichia coli O157, Listeria monocytogenes, and Campylobacter using multi-year outbreak surveillance data, United States","year":"2022"},{"issue":"10","key":"10.1016\/j.psj.2025.104855_bib0026","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1089\/fpd.2017.2283","article-title":"National antimicrobial resistance monitoring system: two decades of advancing public health through integrated surveillance of antimicrobial resistance","volume":"14","author":"Karp","year":"2017","journal-title":"Foodborne Pathog. Dis."},{"issue":"6","key":"10.1016\/j.psj.2025.104855_bib0027","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1089\/fpd.2015.2102","article-title":"Antimicrobial susceptibility and plasmid replicon typing of Salmonella enterica serovar Kentucky isolates recovered from broilers","volume":"13","author":"Ladely","year":"2016","journal-title":"Foodborne Pathog. Dis."},{"issue":"4","key":"10.1016\/j.psj.2025.104855_bib0028","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1128\/JCM.06094-11","article-title":"Multilocus sequence typing of total-genome-sequenced bacteria","volume":"50","author":"Larsen","year":"2012","journal-title":"J. Clin. Microbiol."},{"issue":"W1","key":"10.1016\/j.psj.2025.104855_bib0029","doi-asserted-by":"crossref","first-page":"W256","DOI":"10.1093\/nar\/gkz239","article-title":"Interactive Tree of Life (iTOL) v4: recent updates and new developments","volume":"47","author":"Letunic","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.psj.2025.104855_bib0030","doi-asserted-by":"crossref","DOI":"10.3389\/fvets.2017.00096","article-title":"Diversity of antimicrobial resistance phenotypes in Salmonella isolated from commercial poultry farms","volume":"4","author":"Liljebjelke","year":"2017","journal-title":"Front. Vet. Sci."},{"issue":"9","key":"10.1016\/j.psj.2025.104855_bib0031","doi-asserted-by":"crossref","first-page":"5515","DOI":"10.1128\/AAC.01030-16","article-title":"Whole-genome sequencing for detecting antimicrobial resistance in nontyphoidal Salmonella","volume":"60","author":"McDermott","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.psj.2025.104855_bib0032","series-title":"FSIS NARMS multi-year Report \u20132014-2019","year":"2023"},{"issue":"4","key":"10.1016\/j.psj.2025.104855_bib0033","doi-asserted-by":"crossref","DOI":"10.1128\/aem.02035-22","article-title":"Combined quantification and deep serotyping for Salmonella risk profiling in broiler flocks","volume":"89","author":"Obe","year":"2023","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.psj.2025.104855_bib0034","doi-asserted-by":"crossref","DOI":"10.1128\/aem.02297-23","article-title":"Accumulation of resistance genes in Salmonella Typhimurium transmitted between poultry and dairy farms increases the risk to public health","author":"Perry","year":"2024","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.psj.2025.104855_bib0035","series-title":"No-antibiotics-ever production slips, but U. S. producers remain committed to reducing antibiotic use. The Poultry Site","year":"2021"},{"key":"10.1016\/j.psj.2025.104855_bib0036","article-title":"Prevalence and antimicrobial resistance of Salmonella in conventional and no antibiotics ever broiler farms in the United States","volume":"135","author":"Rama","year":"2022","journal-title":"Food control"},{"issue":"10","key":"10.1016\/j.psj.2025.104855_bib0037","doi-asserted-by":"crossref","first-page":"1793","DOI":"10.4315\/0362-028X.JFP-19-056","article-title":"Phenotypic and genotypic characterization of antimicrobial resistance in Salmonella strains isolated from chicken carcasses and parts collected at different stages during processing","volume":"82","author":"Ramirez-Hernandez","year":"2019","journal-title":"J. Food Prot."},{"issue":"14","key":"10.1016\/j.psj.2025.104855_bib0038","doi-asserted-by":"crossref","first-page":"2989","DOI":"10.1017\/S0950268816001515","article-title":"Prevalence and molecular characterization of Salmonella enterica isolates throughout an integrated broiler supply chain in China","volume":"144","author":"Ren","year":"2016","journal-title":"Epi. Inf."},{"issue":"1","key":"10.1016\/j.psj.2025.104855_bib0039","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.vetmic.2005.10.030","article-title":"Distribution and function of plasmids in Salmonella enterica","volume":"112","author":"Rychlik","year":"2006","journal-title":"Vet. Microbiol."},{"key":"10.1016\/j.psj.2025.104855_bib0040","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.anifeedsci.2018.04.027","article-title":"Broiler production without antibiotics: United States field perspectives","volume":"250","author":"Smith","year":"2019","journal-title":"Animal Feed Sci. Technol."},{"key":"10.1016\/j.psj.2025.104855_bib0041","doi-asserted-by":"crossref","DOI":"10.3389\/fsufs.2021.695368","article-title":"High-resolution comparative genomics of Salmonella Kentucky aids source tracing and detection of ST198 and ST152 lineage-specific mutations","volume":"5","author":"Soltys","year":"2021","journal-title":"Front. Sustain. Food Syst."},{"issue":"8","key":"10.1016\/j.psj.2025.104855_bib0042","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1089\/fpd.2022.0005","article-title":"Genomic diversity, antimicrobial resistance, and virulence gene profiles of Salmonella serovar Kentucky isolated from humans, food, and animal ceca content sources in the United States","volume":"19","author":"Tate","year":"2022","journal-title":"Foodborne Pathog. Dis."},{"key":"10.1016\/j.psj.2025.104855_bib0043","first-page":"879","article-title":"RStudio: integrated development for R.R Studio","volume":"700","author":"Team","year":"2015","journal-title":"Inc. Boston MA"},{"key":"10.1016\/j.psj.2025.104855_bib0044","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1093\/jac\/46.1.7","article-title":"Epidemic Salmonella typhimurium DT 104T \u2013 a truly international multi-resistant clone","volume":"46","author":"Threlfall","year":"2000","journal-title":"J. Antimicrobial. Chemotherap."},{"key":"10.1016\/j.psj.2025.104855_bib0045","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-014-0524-x","article-title":"The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes","volume":"15","author":"Treangen","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.psj.2025.104855_bib0047","doi-asserted-by":"crossref","first-page":"2144","DOI":"10.3382\/ps\/pex449","article-title":"Prevalence and antimicrobial resistance patterns of Salmonella isolated from poultry farms in southeastern United States","volume":"97","author":"Velasquez","year":"2018","journal-title":"Poult. Sci."},{"key":"10.1016\/j.psj.2025.104855_bib0048","series-title":"WHO bacterial priority pathogens list, 2024","year":"2024"},{"key":"10.1016\/j.psj.2025.104855_bib0049","doi-asserted-by":"crossref","DOI":"10.3389\/fvets.2023.1292401","article-title":"Antimicrobial resistance and genomic characteristics of Salmonella from broilers in Shandong Province","volume":"10","author":"Zhao","year":"2023","journal-title":"Front. Vet. Sci."},{"key":"10.1016\/j.psj.2025.104855_bib0050","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1016\/j.watres.2018.12.034","article-title":"Deciphering of microbial community and antibiotic resistance genes in activated sludge reactors under high selective pressure of different antibiotics","volume":"151","author":"Zhao","year":"2019","journal-title":"Water Res."}],"container-title":["Poultry Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0032579125000926?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0032579125000926?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,3,17]],"date-time":"2025-03-17T03:12:33Z","timestamp":1742181153000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0032579125000926"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3]]},"references-count":47,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,3]]}},"alternative-id":["S0032579125000926"],"URL":"https:\/\/doi.org\/10.1016\/j.psj.2025.104855","relation":{},"ISSN":["0032-5791"],"issn-type":[{"value":"0032-5791","type":"print"}],"subject":[],"published":{"date-parts":[[2025,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Genotypic and phenotypic characterization of antimicrobial resistance in Salmonella strains isolated from both No-Antibiotics-Ever (NAE) and conventional broiler complexes","name":"articletitle","label":"Article Title"},{"value":"Poultry Science","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.psj.2025.104855","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc. on behalf of Poultry Science Association Inc.","name":"copyright","label":"Copyright"}],"article-number":"104855"}}