Niche-specific evolution and gene exchange of Salmonella in retail pork and chicken

[Display omitted] •Industry modernization drives Salmonella diversity and resistance in retail meats.•Pork Salmonella diversity trails chicken, correlating with higher resistance.•Resistance genes and co-selection in Salmonella shape ecological adaptation. Salmonella exhibits extensive genetic diversity, facilitated by horizontal gene transfer occurring within and between species, playing a pivotal role in this diversification. Nevertheless, most studies focus on clinical and farm animal isolates, and research on the pangenome dynamics of Salmonella isolates from retail stage of the animal food supply chain is limited. Here, we investigated the genomes of 950 Salmonella isolates recovered from retail chicken and pork meats in seven provinces and one municipality of China in 2018. We observed a strong correlation between Salmonella sublineage diversity and the accessory genome with meat type, revealing reduced diversity associated with increased resistance. Importantly, genes associated with antibiotic, biocide, and heavy metal resistance were unevenly distributed in Salmonella from retail chicken and pork. Pork Salmonella isolates showed a higher prevalence of copper and silver resistance genes, while chicken Salmonella isolates displayed a significant predominance of genetic determinants associated with cephalosporin and ciprofloxacin resistance. Moreover, co-occurrence patterns of resistance determinants and their interaction with mobile genetic elements also correlated with meat type. In summary, our findings shed light on how Salmonella achieves their ecological niche success driven by evolution and gene changes in the retail stage of the animal food supply chain.