High-resolution genomic comparisons within Salmonella enterica serotypes derived from beef feedlot cattle: parsing the roles of cattle source, pen, animal, sample type and production period

is a major foodborne pathogen, and contaminated beef products have been identified as one of the primary sources of -related outbreaks. Pathogenicity and antibiotic resistance of are highly serotype- and subpopulation-specific, which makes it essential to understand high-resolution population dynamics in cattle. Time of year, source of cattle, pen, and sample type(i.e., feces, hide or lymph nodes) have previously been identified as important factors influencing the serotype distribution of (e.g., Anatum, Lubbock, Cerro, Montevideo, Kentucky, Newport, and Norwich) that were isolated from a longitudinal sampling design in a research feedlot. In this study, we performed high-resolution genomic comparisons of isolates within each serotype using both single-nucleotide polymorphism (SNP)-based maximum likelihood phylogeny and hierarchical clustering of core-genome multi-locus sequence typing. The importance of the aforementioned features on clonal expansion was further explored using a supervised machine learning algorithm. In addition, we identified and compared the resistance genes, plasmids, and pathogenicity island profiles of the isolates within each sub-population. Our findings indicate that clonal expansion of strains in cattle was mainly influenced by the randomization of block and pen, as well as the origin/source of the cattle; that is, regardless of sampling time and sample type (i.e., feces, lymph node or hide). Further research is needed concerning the role of the feedlot pen environment prior to cattle placement to better understand carry-over contributions of existing strains of and their bacteriophages. serotypes isolated from outbreaks in humans can also be found in beef cattle and feedlots. Virulence factors and antibiotic resistance are among the primary defense mechanisms of , and are often associated with clonal expansion. This makes understanding the subpopulation dynamics of in cattle critical for effective mitigation. There remains a gap in the literature concerning subpopulation dynamics within serotypes in feedlot cattle from the beginning of feeding up until slaughter. Here, we explore population dynamics within each serotype using core genome phylogeny and hierarchical classifications. We used machine-learning to quantitatively parse the relative importance of both hierarchical and longitudinal clustering among cattle host samples. Our results reveal that populations in cattle are highly clonal over a 6-month study period, and that cl