Whole-Genome Sequencing and Molecular Characterization of Salmonella Isolates in the Meishan Region (2014–2024)

Abstract

To characterize molecular profiles of Salmonella isolates from the Meishan region (2014–2024) via whole-genome sequencing, focusing on serotype distribution, antimicrobial resistance genes (ARGs), virulence genes, and genetic differentiation based on coding-region single nucleotide polymorphisms (cgSNPs), and provide a molecular epidemiological basis for precise prevention, control, and source tracing of Salmonella infections. Sixty Salmonella strains from distinct sources (food surveillance = 2, food poisoning = 7, intestinal surveillance = 23, pathogen surveillance = 17, healthy population surveillance = 2, and other surveillance = 9) (2014–2024), Table 1, were sequenced on Illumina NextSeq 500. Serotypes (SISTR v1.1.0), multilocus sequence typing (MLST v2.0), ARGs/virulence genes (Abricate v1.2.0; CARD v3.2.7, VFDB v202310), and a cgSNP-based phylogenetic tree were constructed using Snippy v4.6.0 with the Salmonella Typhimurium reference genome (GCA_020714865.1). Twelve serotypes were identified; with Salmonella Typhimurium (65.0%, 39/60) as the dominant serotype, widely distributed across clinical, food, and outbreak sources, followed by Salmonella Enteritidis (13.3%, 8/60). Salmonella Typhimurium had prevalent ST34 (59.0%) and ST19 (38.5%); ST34 was confirmed as a locally dominant clone compared to the globally common ST19. All Salmonella Enteritidis were ST11. Five ARG categories (60 types) were detected: aminoglycoside resistance genes (96.7%) were most common, followed by β-lactam (65.0%) and sulfonamide (63.3%) resistance genes. Notably, Salmonella Typhimurium exhibited a high multidrug resistance (MDR) rate of 64.1%, which was significantly higher than that of Salmonella Enteritidis (12.5%). Core virulence genes (e.g., SPI-1, TTSS-1) were ≥95% conserved; serotype-specific genes (e.g., cdtB) were strain-specific. The 60 strains were divided into 14 clusters, with 76.7% (46 strains) assigned to 3 major clusters, confirming epidemiological links between outbreaks and sources. Salmonella Typhimurium ST34/ST19 with a high MDR rate is the dominant epidemic clone in the Meishan region, posing significant public health risks. cgSNPs are useful for source tracing. Targeted surveillance of dominant clones and stricter antibiotic regulation are imperative.