Genomic architecture of antimicrobial resistance and mobile genetic elements in Salmonella enterica isolated from necropsied cattle in central Kentucky.

UNLABELLED: Non-typhoidal Salmonella remains a leading global cause of foodborne disease and an important contributor to the global burden of antimicrobial resistance (AMR) within the One Health framework. Cattle serve as an important reservoir, facilitating the dissemination of antimicrobial-resistant Salmonella through the food chain and the environment. In this study, we analyzed the genomes of 27 Salmonella enterica isolates recovered from necropsied cattle in central Kentucky to characterize their genomic AMR, virulence, and mobile genetic element profiles. Multilocus sequence typing (MLST) identified 12 sequence types (STs), with ST10 (S. Dublin) representing the dominant lineage (25.9%). Genomic screening revealed 4,618 virulence gene occurrences, including conserved factors associated with secretion and adhesion, as well as variable toxin and immune evasion genes. Antimicrobial resistance genes (ARGs) were detected across the isolate collection, with resistance primarily associated with efflux systems (62.1%) and genes conferring resistance to aminoglycosides, tetracyclines, sulfonamides, phenicols, and β-lactams. Plasmids were detected in 77.8% of isolates, integrons were identified in 11.1% of isolates, and prophages and insertion sequence (IS) elements were widely distributed. While most resistance loci were chromosomal (63.5%), plasmid-associated ARGs (11.7%) demonstrated significantly greater proximity to IS elements, suggesting an increased potential for mobilization. Pan-genome analysis revealed an open pan-genome structure with a limited core (19.9%) and a dominant accessory genome (77.6%). Core-genome phylogenetic analysis incorporating 97 publicly available genomes demonstrated close clustering of cattle-associated isolates with isolates from food, human, and environmental sources, suggesting the presence of shared or closely related lineages across interconnected One Health compartments. These findings characterize the genomic architecture of AMR in cattle-associated Salmonella and highlight the potential contribution of mobile genetic elements to shaping AMR evolution and dissemination across interconnected One Health systems. IMPORTANCE: This study reveals that multidrug-resistant Salmonella enterica in cattle is sustained by a dual genomic architecture in which resistance determinants are both chromosomally embedded and mobilized through plasmids, prophages, and insertion sequence (IS) elements. The presence of plasmid-borne resistance genes and IS elements suggests their potential involvement in transposition-mediated dissemination. The predominance of chromosomal resistance may indicate greater persistence of resistance determinants within bacterial lineages. The dominance of the ST10 (S. Dublin) lineage and its close genomic relatedness to food-associated isolates, together with an open pan-genome structure, suggest ongoing circulation and genomic diversification of high-risk lineages across interconnected animal, food, and environmental systems.