Genotypic diversity and zoonotic potential of Salmonella enterica from multiple hosts: implications for One Health

Salmonella enterica is a major zoonotic pathogen with significant impact on human and animal health. In this study, 28 isolates obtained from 20 domestic and wild animals in Brazil were characterized using phenotypic antimicrobial susceptibility testing, epidemiological profiling, and whole-genome sequencing (WGS). The isolates were obtained from a diversity of host species and included globally relevant serotypes such as Newport, Typhimurium, and Dublin, as well as three strains classified as subsp. houtenae, two of which were associated with fatal septicemic disease in dogs. Pangenome, mobilome, and multilocus sequence typing (MLST) analyses revealed pronounced genomic plasticity, with only one-third of genes classified as core and the majority comprising accessory or strain-specific repertoires, reflecting a high adaptive potential. Plasmid analysis identified a diverse set of replicon types, including conjugative elements associated with horizontal gene transfer, indicating a central role of mobile genetic elements in shaping the accessory genome. High levels of resistance to clinically important antimicrobials, notably tetracycline, ciprofloxacin, and ampicillin, were observed, together with a substantial proportion of multidrug-resistant and extensively drug-resistant isolates. Genomic analyses detected 58 resistance-associated genes (including both intrinsic and acquired determinants) and 127 virulence-associated genes, with associations observed between key determinants (e.g., tetA and bla_TEM-1) and corresponding phenotypic resistance, supporting the potential utility of WGS-based resistance prediction. The frequent co-occurrence of resistance and virulence determinants, often linked to mobile genetic elements, may enhanced capacity of these strains to persist, disseminate, and cause disease across different host species. Although limited by sample size and geographic scope, this study provides insights into the genetic diversity and potential epidemiological relevance of S. enterica within the studied context circulating among domestic and wild animals in Brazil. The findings highlight the circulation of genetically diverse and potentially high-risk strains, including non-enterica subspecies associated with severe systemic infection, and emphasize the value of integrated phenotypic and genomic surveillance to support risk assessment and inform prevention and control strategies.