Genomic and epidemiologic evidence for attenuated virulence in Salmonella Montevideo associated with cattle and beef products in the United States

Salmonella enterica serovar Montevideo ( S . Montevideo) is frequently isolated from cattle, their products, and related environments, yet rarely causes human illness through these sources, suggesting variation in human virulence and niche adaptation among its lineages. Building on our previous identification of a predominant S . Montevideo phylogenetic group comprising 12 clades with distinct ecological associations, we conducted comparative genomic and evolutionary analyses to characterize clades differing in human association and source adaptation. We identified one non-human-associated (NHA) clade (clade 10, cattle-adapted) and three human-associated (HA) clades (clade 7, non-animal-environment-adapted; clades 3 and 6, lacking source specificity), all four of which exhibited open pan-genomes, indicating ongoing genetic exchange. Of the genes significantly overrepresented in the HA clades relative to the NHA clade, 35%−66% were carried on mobile genetic elements. In contrast, all five virulence factors enriched in HA clades were chromosomally encoded. Compared to HA clades, the NHA clade showed a 7–19-fold enrichment in premature stop codons in genes encoding virulence factors, including genes involved in epithelial invasion and systemic infection, suggesting functional loss linked to host adaptation and reduced virulence. Finally, evolutionary reconstruction revealed that clade 10 emerged most recently and evolved the fastest, reflecting rapid host adaptation, whereas clade 7 is ancient and demonstrated genomic stability indicative of long-term environmental persistence. Clades 3 and 6 displayed intermediate evolutionary rates, with clade 3 encompassing two recently emerged sub-clades exhibiting signatures of clonal expansion. Hence, our study underscores the need for a risk-based approach to control for Salmonella in agricultural animals and their derived food products to generate a more efficient and significant public health impact.