Genomic Diversity and Clonal Persistence of Salmonella enterica in Feedlot Cattle and the Pen Environment During a Feeding Trial.

Salmonella enterica, a foodborne pathogen, poses a significant public health risk, particularly multidrug-resistant strains. Because antimicrobial resistance (AMR) is often linked to specific serotypes or clones, factors that shift Salmonella populations in feedlots can indirectly drive resistance. The study aimed to characterize the genomic diversity and clonal composition of Salmonella across cattle and the pen environment from a feedlot trial involving crossbred steers fed a high-starch or control diet combined with erratic or regular feeding management until harvest (168 to 222 days; hereafter 168+). A total of 509 isolates recovered from feces, pen surfaces, hide swabs, and lymph nodes were whole-genome sequenced for in silico prediction of serotype, 7-gene multilocus sequence type (ST), core-genome ST (cgST), AMR genes, and plasmids, as well as single-nucleotide polymorphism-based phylogenetic inference. The population was dominated by four serotypes (Anatum, Montevideo, Kentucky, and Lubbock), each associated with a dominant ST, though Kentucky and Lubbock each comprised two STs. Only two isolates, both from pen surface, carried multiple AMR genes: 1 Montevideo harbored floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, and 1 Anatum carried these plus blaTEM-1A. Serotype populations were clonal within sampling day and pen; no clear treatment-related patterns emerged. Serotype and clonal patterns were assessed through genomic characterization and descriptive visualization. Clonal clustering within pens suggests that environmental persistence and reinoculation from pen surfaces may play a larger role in shaping Salmonella populations than dietary or management factors. The sporadic nature of AMR under limited antibiotic use underscores the need for targeted preharvest interventions focused on the pen environment.