Comparative genomics reveals antimicrobial resistance and population structure of chicken-associated Salmonella enterica serotype Typhimurium in the United States.

Abstract

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.