Abstract
Salmonella enterica subsp. enterica serotype Enteritidis (SE) is recognized as a major cause of human salmonellosis worldwide, and most human salmonellosis is due to the consumption of contaminated poultry meats and poultry byproducts. Whole-genome sequencing (data were obtained from 96 SE isolates from poultry sources, including an integrated broiler supply chain, farms, slaughterhouses, chicken transporting trucks, and retail chicken meats in South Korea during 2010–2017. Antimicrobial resistance and virulence genes were investigated using WGS data, and the phylogenetic relationship of the isolates was analyzed using single-nucleotide polymorphism (SNP) typing and core genome multilocus sequence typing (cgMLST). All isolates carried aminoglycoside resistance genes, aac(6’)-Iaa, and 56 isolates carried multiple antimicrobial resistance genes. The most frequent virulence gene profile, pef-fim-sop-inv.-org-sip-spa-sif-fli-flg-hil-ssa-sse-prg-pag-spv, was found in 90 isolates. The SNP analysis provided a higher resolution than the cgMLST analysis, but the cgMLST analysis was highly congruent with the SNP analysis. The phylogenetic results suggested the presence of resident SE within the facility of processing plants, environments of slaughterhouses, and the integrated broiler supply chain, and the phylogenetically related isolates were found in retail meats. In addition, the SE isolates from different origins showed close genetic relationships indicating that these strains may have originated from a common source. This study could be valuable reference data for future traceback investigations in South Korea.
Highlights
Nontyphoidal Salmonella enterica (S. enterica) is one of the most prevalent foodborne pathogens in the world [1,2]
The SNP analysis provided a higher resolution than the Core genome MLST (cgMLST) analysis, but the cgMLST analysis was highly congruent with the SNP analysis
The whole-genome sequencing (WGS) data were used to detect the presence of antimicrobial resistance genes in the 96 isolates, and a total of 12 antimicrobial resistance patterns were observed (Table 1 and Supplementary Table S1)
Summary
Nontyphoidal Salmonella enterica (S. enterica) is one of the most prevalent foodborne pathogens in the world [1,2]. In South Korea, S. enterica was the second most common pathogen associated with foodborne illnesses over the past 15 years, according to the foodborne outbreak surveillance system of Korea’s Food and Drug Administration (https: //www.foodsafetykorea.go.kr/portal/healthyfoodlife/foodPoisoningStat.do). Whole-genome sequencing (WGS) has been frequently implemented in routine surveillance of foodborne pathogens as well as foodborne disease outbreak investigation [2,7,8,9,10,11]. Only a few studies using WGS analysis for Salmonella spp. in South Korea have been reported [21,22,23], and WGS is not yet routinely used as a tool for genetic characterization of SE in the food supply chain in South Korea
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