Genomic evidence of IS26-mediated structural variation in a lettuce-derived pESI-positive Salmonella Infantis identified through non-poultry food surveillance.

Non-typhoidal Salmonella is a leading cause of salmonellosis in humans. In this study, we investigated the occurrence and characteristics of Salmonella spp. recovered from non-poultry food sources in Korea. A total of 3328 samples were collected from pig and cattle farms, slaughterhouses, retail meat products, fresh produce, and seafood. Although the overall detection frequency was low (0.5%), Salmonella was recovered from cattle slaughterhouse environments, domestic pork, imported pork, and lettuce, yielding diverse serotypes and sequence types (STs), including S. Typhimurium ST34, S. Derby ST682, S. Brandenburg ST65, S. Rissen ST469, and S. Give ST516. Several isolates, particularly S. Typhimurium ST34, exhibited multidrug-resistant (MDR) phenotypes. An MDR S. Infantis isolate was detected in lettuce. Whole-genome sequencing revealed that the lettuce-derived S. Infantis carried a pESI-like megaplasmid encoding multiple antimicrobial resistance and virulence-associated genes. Phylogenetic analysis revealed that the lettuce isolate was closely related to poultry-derived pESI-positive S. Infantis lineages, with a highly similar pESI-like plasmid. Comparative plasmid structure analysis identified an IS26-flanked ∼9-kb deletion in the lettuce isolate, resulting in the loss of two resistance genes and several mobility-associated loci, indicating a localized structural variation within the plasmid. These findings indicate genomic relatedness and a possible shared epidemiological background between the lettuce-derived isolate and poultry-associated pESI-positive S. Infantis lineages; however, no direct source attribution, transmission pathway, or directionality can be established. This study highlights the importance of continued surveillance of non-poultry food sources within a One Health framework to monitor the dissemination of this high-risk lineage across the food production continuum.