Distribution and Genome Epidemiological Characteristics of Salmonella Isolates in Low Water Activity Foods

Abstract

Salmonella remains a leading global foodborne pathogen, whereas low-water-activity foods are often underestimated as transmission vehicles. Here, whole-genome sequencing and bioinformatic analyses were performed on 59 Salmonella strains isolated from low-water-activity foods (2017–2025) to investigate their genomic traits, antimicrobial resistance profiles, virulence genes, and mobile genetic elements. The isolates were mainly recovered from dried meat (44.07%) and dried soybean products (33.90%), covering 33 serovars and 36 sequence types. Salmonella Agona (ST13), S. Senftenberg (ST14), and S. Idikan (ST1561) predominated. Forty antimicrobial resistance genes across ten categories were detected. Notably, one S. Schwarzengrund isolate harbored the IncHI2 plasmid pWW013_mcr-9.2 carrying the mcr-9.2 gene, as well as various antibiotic resistance genes and heavy metal resistance operons. Comparative genomics revealed a conserved plasmid backbone and a distinctive resistance island. This study documents the first detection of an mcr-9.2-carrying Salmonella in low-water-activity foods in Beijing. Our findings demonstrate high genomic diversity, widespread resistance determinants, and the emergence of an mcr-9.2-carrying plasmid, supplying key genomic evidence for risk assessment and targeted control of Salmonella in low-water-activity foods.