Novel genetic features associated with the recently emerged MDR clade of Salmonella Dublin linked to human clinical cases.

Salmonella Dublin is an enteric pathogen that has adapted to cattle as its primary host. It rarely causes foodborne outbreaks but is frequently associated with invasive and severe infections in humans. However, the underlying mechanisms responsible for its enhanced virulence in humans remain unknown. In this study, we conducted comparative genomic analyses and an oxidative stress assay focusing on Salmonella Dublin isolates classified, in a previous study, as human-associated (HA) or non-human-associated (NHA). We found that 82.5% and 20% of the isolates in the NHA group harbor premature stop codons (PMSCs) in pgtC and sadA, respectively, with disrupted sadA possibly contributing to attenuated virulence in these isolates. PMSCs in yahO and ratB were found in 100% of isolates in the HA group and in 62.5% and 60% of isolates in the NHA group, respectively. In addition, 100% and 42.5% of isolates in the HA group harbor PMSCs in gsiB and zirT, respectively, with disrupted zirT possibly contributing to an enhanced virulence in these isolates. Moreover, a multidrug resistance plasmid (pVPS18S0911-1-like) was strongly associated with HA isolates, which may allow these isolates to cause prolonged infections leading to increased clinical severity. While an IS1 transposon inserted within panE, located between two genes putatively involved in oxidative stress, was observed exclusively among HA isolates, these isolates did not show a significantly different oxidative stress survival to H(2)O(2) as compared to NHA isolates. Finally, the presence of the Salmonella virulence plasmid and the Vi antigen was not associated with the HA isolates.IMPORTANCESalmonella Dublin causes a severe extra-intestinal infection in 64% of human cases with a 3% fatality rate. In this study, we compared the genomes of human-associated (HA) Salmonella Dublin isolates to non-human-associated (NHA) isolates and identified genetic features associated with the HA or NHA groups, such as single nucleotide polymorphisms in genes putatively involved in virulence, presence of antimicrobial resistance genes in an HA-associated plasmid, and an insertion element between two genes putatively involved in oxidative stress. HA and NHA isolates showed, however, no differences in an oxidative stress survival assay. Overall, this study identified novel genetic features putatively involved in the virulence diversity within Salmonella Dublin throughout a combination of phylogenetic analysis, genome-wide association study, and phenotypic assessment, providing insights for future studies to elucidate the mechanisms leading to the severe human infections typically caused by Salmonella Dublin.