Whole-genome characterization of Salmonella serovars in Cambodia
This study investigates the genetic diversity and antimicrobial resistance characteristics of Salmonella enterica serovars circulating in the Cambodian food chain. Using whole-genome sequencing (WGS), we analyzed 75 isolates recovered from meat, seafood/fish, and fresh vegetables obtained from local markets and farms. Serovar prediction identified 32 distinct serovars, showing clear food-source associations, including S. Corvallis and S. Agona in meat, S. Livingstone and S. Braenderup in seafood, and S. Weltevreden in vegetables.  To characterize antimicrobial resistance, genomes were examined using multiple ARG detection tools, revealing common resistance genes such as tet, qnr, sul, dfr, floR, cml, aac, aph, and blaTEM. Multidrug-resistant determinants were also detected across isolates. Plasmid analysis identified 22 plasmid types, with Col(pHAD28) being most widespread. Although several plasmids were detected, only a minority carried antimicrobial-resistance genes, indicating that most resistance determinants were chromosomally encoded.  Virulence profiling identified a broad set of virulence factors, including genes linked to Type Three Secretion Systems, adherence, macrophage survival, stress tolerance, and magnesium uptake. Twelve Salmonella Pathogenicity Islands (SPIs) were observed across the dataset, with SPI-1, SPI-2, SPI-3, SPI-5, and SPI-9 consistently present in all serovars.  Overall, this study provides comprehensive genomic insights into Salmonella strains circulating in Cambodian food products, highlighting their diversity, resistance profiles, plasmid content, and virulence potential. These findings underscore the need for enhanced surveillance and control strategies within the Cambodian food supply chain and support the importance of WGS-based monitoring to mitigate the spread of antimicrobial-resistant and highly virulent Salmonella.
This study investigates the genetic diversity and antimicrobial resistance characteristics of Salmonella enterica serovars circulating in the Cambodian food chain. Using whole-genome sequencing (WGS), we analyzed 75 isolates recovered from meat, seafood/fish, and fresh vegetables obtained from local markets and farms. Serovar prediction identified 32 distinct serovars, showing clear food-source associations, including S. Corvallis and S. Agona in meat, S. Livingstone and S. Braenderup in seafood, and S. Weltevreden in vegetables.  To characterize antimicrobial resistance, genomes were examined using multiple ARG detection tools, revealing common resistance genes such as tet, qnr, sul, dfr, floR, cml, aac, aph, and blaTEM. Multidrug-resistant determinants were also detected across isolates. Plasmid analysis identified 22 plasmid types, with Col(pHAD28) being most widespread. Although several plasmids were detected, only a minority carried antimicrobial-resistance genes, indicating that most resistance determinants were chromosomally encoded.  Virulence profiling identified a broad set of virulence factors, including genes linked to Type Three Secretion Systems, adherence, macrophage survival, stress tolerance, and magnesium uptake. Twelve Salmonella Pathogenicity Islands (SPIs) were observed across the dataset, with SPI-1, SPI-2, SPI-3, SPI-5, and SPI-9 consistently present in all serovars.  Overall, this study provides comprehensive genomic insights into Salmonella strains circulating in Cambodian food products, highlighting their diversity, resistance profiles, plasmid content, and virulence potential. These findings underscore the need for enhanced surveillance and control strategies within the Cambodian food supply chain and support the importance of WGS-based monitoring to mitigate the spread of antimicrobial-resistant and highly virulent Salmonella.
Laingshun Huoy