Insights into the Genetic Diversity of Cambodian Salmonella Serovars via Whole-Genome Analysis

Background Antimicrobial resistance (AMR) among Salmonella enterica serovars constitutes a significant challenge for food safety and human health in Cambodia. The aim of this study was to enhance current knowledge about antimicrobial-resistant genes (ARGs) and their associated virulence determinants in Salmonella serovars using whole-genome sequencing (WGS). Methods A total of 32 Salmonella serovars were identified among 75 isolates isolated from vegetables, meat, and seafood/fish obtained from open markets and vegetable farms in Cambodia, using seqSero2. All WGS data were analyzed using multiple antibiotic-resistance gene prediction tools (CARD-RGI, AMRFinderPlus, and ABRicate) to cross-validate ARGs detection, and virulence factor detection tools (PlasmidFinder, VFAnalyzer, ABRicate with VFDB, and SPIFinder). Results The three analysis tools consistently detected several common resistance genes, including tet (48%), qnr (48%), sul and dfr (40%), aac and aph (40%), bla TEM (32%), as well as floR and cml (32%). Twenty-two plasmid types were identified, with the most frequent being Col(pHAD28) (53%), followed by Col440I (17%) and IncFII(S) (14%). A diverse range of virulence genes was observed, with Type Three Secretion System genes detected across all serovars. Additionally, twelve Salmonella Pathogenicity Islands (SPIs) were identified, five of which (SPI-1, SPI-2, SPI-3, SPI-5, and SPI-9) were consistently present in all serovars. Conclusions These results highlight the substantial genetic diversity of Salmonella strains isolated from various food products sold at local markets in Cambodia, which potentially contribute to the spread of AMR within food chains. WGS plays a key role in epidemiological investigations and is essential for ongoing genomic surveillance of Cambodia’s food supply.