Cross-species genomic analysis of Salmonella enterica subspecies enterica serovar Dublin isolated from dairy cattle, dogs, and humans in Florida from 2019 to 2024.

Salmonella enterica serovar Dublin (S. Dublin) is a cattle-adapted pathogen that can cause severe systemic infections in humans and animals. Understanding genomic relatedness across host species is essential for assessing the zoonotic potential and dissemination of antimicrobial resistance (AMR). In this study, 78 clinical S. Dublin strains, isolated in Florida between 2019 and 2024, were subjected to comparative genomic analysis. These included 19 animal-derived isolates (17 from dairy cattle and two from dogs) and 59 human-derived isolates. AMR gene profiling revealed widespread multidrug resistance, with genes conferring resistance to aminoglycoside (aac(6')-Iaa, aph(6)-Id), tetracycline (tetA), and sulfonamide (sul2) detected in all isolates. Beta-lactamase genes, particularly bla TEM variants, were detected more frequently in human- and dog-derived isolates than in cattle-derived isolates. In contrast, rare bla CMY variants (bla CMY-61, bla CMY-130, bla CMY-153, and bla CMY-2b) were detected in only one cattle isolate. Plasmid analysis revealed that IncX1, IncFII(S), and IncC replicons were common among the isolates, highlighting their potential role in facilitating AMR dissemination via horizontal gene transfer. Virulence gene profiling revealed conserved Salmonella pathogenicity islands, type III and type VI secretion systems, and the spv operon across S. Dublin isolates from all host species. Multilocus sequence typing (MLST) confirmed that all isolates belonged to sequence type (ST) 10, and most harbored the Gifsy-2 prophage. The SNP-based phylogeny revealed distinct host-associated clades as well as mixed-host clusters, demonstrating close genomic relatedness among isolates from different host species and suggesting possible cross-species transmission, exposure to shared sources, or circulation of closely related lineages. These findings illustrate the interconnectedness of animal and human S. Dublin infections, emphasize the importance of responsible antimicrobial use, and highlight the value of genomic surveillance for detecting and controlling S. Dublin infections. Collectively, this study provides a genomic framework for assessing cross-species relatedness, virulence characteristics, and AMR patterns of S. Dublin.