Salmonella enterica is one of the most dangerous foodborne pathogens listed by the World Health Organization. In this study, whole-duck samples were collected at wet markets in five districts in Hanoi, Vietnam, in October 2019 to assess their Salmonella infection rates and evaluate the susceptibility of the isolated strains to antibiotics currently used in the prophylaxis and treatment of Salmonella infection. Based on the antibiotic resistance profiles, eight multidrug resistance strains were whole-genome-sequenced, and their antibiotic resistance genes, genotypes, multi-locus sequence-based typing (MLST), virulence factors, and plasmids were analyzed. The results of the antibiotic susceptibility test indicate that phenotypic resistance to tetracycline and cefazolin was the most common (82.4%, 28/34 samples). However, all isolates were susceptible to cefoxitin and meropenem. Among the eight sequenced strains, we identified 43 genes associated with resistance to multiple classes of antibiotics such as aminoglycoside, beta-lactam, chloramphenicol, lincosamide, quinolone, and tetracycline. Notably, all strains carried the bla_CTX-M-55 gene, which confers resistance to third-generation antibiotics including cefotaxime, cefoperazone, ceftizoxime, and ceftazidime, as well as resistance genes of other broad-spectrum antibiotics used in clinical treatment such as gentamicin, tetracycline, chloramphenicol, and ampicillin. Forty-three different antibiotic resistance genes were predicted to be present in the isolated Salmonella strains’ genomes. In addition, three plasmids were predicted in two strains, 43_S11 and 60_S17. The sequenced genomes also indicated that all strains carried SPI-1, SPI-2, and SPI-3. These SPIs are composed of antimicrobial resistance gene clusters and thus represent a potential threat to public health management. Taken together, this study highlights the extent of multidrug-resistant Salmonella contamination in duck meat in Vietnam.

Salmonella enterica is one of the most common agents of foodborne bacterial illness with poultry being an important reservoir. The indiscriminate use of antimicrobial compounds in poultry farming increasingly leads to antimicrobial-resistant (AMR) which threatens the health of both animals and humans. Antimicrobial-resistant Salmonella enterica from the poultry can spread to human through the direct contact with infected poultry or fecal contaminated environments. Antimicrobial-resistant S. enterica, especially fluoroquinolone-resistant nontyphoidal Salmonella is in the list of global health concern stated by the World Health Organization (WHO). Here we report the whole-genome sequencing data and de novo genome assemble of antimicrobial-resistant S. enterica strains S8 and S9 from the C. moschata carcass collected in Vietnam. Genomic DNA of S. enterica were extracted and subjected to whole-genome sequencing using Illumina MiSeq platform. The genome size of antimicrobial-resistant S. enterica strain S8 is 4,707,459 bp with a GC-content of 52.38%, containing 10 antimicrobial resistant genes. The genome size of antimicrobial-resistant Samonella enterica strain S9 is 4,923,944 bp with a GC-content of 52,39%, containing 10 antimicrobial resistance genes. Our data provided the insights on antimicrobial resistant genes of S. enterica isolates from the C. moschata carcass, which help to understand the infection mechanism of antimicrobial-resistant S. enterica in human.