{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T05:21:34Z","timestamp":1786684894508,"version":"build-2736575974"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Salmonella enterica serotype Typhimurium is a leading cause of foodborne outbreaks linked to chickens in the United States. To investigate the genomic landscape of this population, 1048 chicken-associated S. Typhimurium genomes collected nationwide were analyzed. Overall, 84.5% of isolates carried at least one antimicrobial resistance (AMR) determinant, and 34.3% displayed multidrug resistance (MDR). Sulfonamide and tetracycline resistance were most prevalent (1.03 and 1.01 AMR determinant per isolate, respectively). AMR gene (ARG) co-occurrence analysis identified strong associations among tet(A), sul1, sul2, aac(3)-VIa, and aadA1, with blaCMY-2 emerging within an expanding co-resistance cluster. ARG-plasmid replicon association analysis indicated significant positive links between sul2 and tet(A) with IncC and ColRNAI. Machine learning-driven association rule mining demonstrated that integron carriage perfectly predicted MDR, and their absence in both non-AMR and AMR but non-MDR isolates underscores their pivotal role as the defining marker of MDR. We observed a pan-genome pattern with 3855 core and 9549 accessory genes, reflecting both genomic conservation and diversity. Whole-genome phylogenetic analysis revealed two major clades, with sequence type 19 comprising 99.0% of the isolates. This research provides a comprehensive genomic characterization of chicken-associated S. Typhimurium in the United States, highlighting key AMR mechanisms relevant for food safety and public health.<\/jats:p>","DOI":"10.1093\/lambio\/ovaf127","type":"journal-article","created":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T13:10:10Z","timestamp":1761916210000},"source":"Crossref","is-referenced-by-count":1,"title":["Comparative genomics reveals antimicrobial resistance and population structure of chicken-associated\n                    <i>Salmonella enterica<\/i>\n                    serotype Typhimurium in the United States"],"prefix":"10.1093","volume":"78","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1784-167X","authenticated-orcid":false,"given":"Zhao","family":"Chen","sequence":"first","affiliation":[{"name":"Joint Institute for Food Safety and Applied Nutrition, and Center for Food Safety and Security Systems, University of Maryland , College Park, MD 20742 ,","place":["United 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