Alternate antimicrobial resistance genes in multidrug resistant Salmonella spp. isolated from retail meats in Vietnam using RNA‐sequencing analysis

Abstract The aim of this study was to examine the resistome characteristics of Salmonella spp. Contamination found in raw retail beef, pork, and chicken samples collected in Hanoi, Vietnam. Approximately 28% (25/90) of samples tested carried Salmonella bacteria. A total of 13/25 (52%) of these Salmonella bacteria were resistant to at least one antibiotic and 9/25 (36%) of the isolates were found to be multidrug resistant. RNA‐seq analysis detected the expression of 107 antibiotic resistance genes (e.g., 22 β‐lactam, 46 aminoglycosides, 8 quinolones, 7 chloramphenicol, 6 tetracycline, and 6 sulfonamide‐trimethoprim resistance genes, and 12 other antimicrobial resistance genes). The parC (S80R and novel mutations A628S) and gyrA (S83F and D87G) mutations contributed to ciprofloxacin resistance in Salmonella Indiana. The findings illustrate the significant potential for multiple‐antibiotic resistant Salmonella in raw retail meats from Hanoi markets, and also provide abundant data to better understand the multidrug resistant Salmonella resistome. Practical Applications Studying the antibiotic resistance characteristics of Salmonella will provide important information for the prevention, control of diseases as well as food contamination control and regulations on the use of antibiotics in treatment and animal husbandry in order to limit antibiotic resistance of bacteria. Studying the expression genome of Salmonella, especially antibiotic resistance genes in multi‐antibiotic resistant Salmonella isolates, provides insight into the molecular epidemiology of antibiotic resistance genes. More importantly, it is possible to detect new mutations in antibiotic resistance genes that cause antibiotic resistance in Salmonella. In addition, studying the expression genome could help to identify new gene groups that can cause antibiotic resistance in this bacterium.