Virulence Gene Profile, Antimicrobial Resistance and Multilocus Sequence Typing of Salmonella enterica Subsp. enterica Serovar Enteritidis from Chickens and Chicken Products

Simple Summary We investigated the pathogenicity, antimicrobial resistance and multilocus sequence types of Salmonella enterica subspecies enterica serovar Enteritidis isolated from fresh chicken meat, ready-to-eat chicken meat as well as from cloacal swabs of live chickens in some selected locations within the central region of peninsular Malaysia. After culture and serotype confirmation of the Salmonella isolates, the genomic DNA was extracted and whole-genome sequencing was conducted using the NextSeq 550 System (Illumina, San Diego, CA, USA). In silico serotypes were determined with the aid of SeqSero WGS in silico software version 2, while multilocus sequence types, as well as virulence and antimicrobial resistance determinants, were all determined using the BioEasy Epinod pipeline. The S. Enteritidis isolates were found to harbour several virulence genes, with multidrug-resistance characteristics. The results of this investigation indicate the potential risks both humans and livestock are exposed to due to this foodborne pathogen. This study was undertaken to determine the virulence, antimicrobial resistance and molecular subtypes of Salmonella in the Central Region of Peninsular Malaysia. A total of 45 Salmonella Enteritidis were detected from live chicken (cloacal swab), and chicken products (fresh and ready-to-eat meat) samples upon cultural isolation and serotyping. Similarly, an antimicrobial susceptibility test based on the Kirby Bauer disk diffusion method as well as antimicrobial resistance AMR genes, virulence determinants and multilocus sequence typing (MLST) typing were conducted after the Whole Genome Sequencing and analysis of the isolates. The results indicate that sequence types ST1925 (63.7%), and ST11 (26.5%) were the predominant out of the seven sequence types identified (ST292, ST329, ST365, ST423 and ST2132). The phenotypic antimicrobial profile corresponds to the genotypic characterization in that the majority of the isolates that exhibited tetracycline, gentamycin and aminoglycoside resistance; they also possessed the tetC and blaTEM beta-Lactam resistance genes. However, isolates from cloacal swabs showed the highest number of resistance genes compared to the chicken products (fresh and ready-to-eat meat) samples. Furthermore, most of the virulence genes were found to cluster in the Salmonella pathogenicity island (SPI). In this study, all the isolates were found to possess SPI-1, which codes for the type III secretion system, which functions as actin-binding proteins (SptP and SopE). The virulence plasmid (VP) genes (spvB, spvC) were present in all genotypes except ST365. The findings of this study, particularly with regard to the molecular subtypes and AMR profiles of the Salmonella Enteritidis serotype shows multidrug-resistance features as well as genetic characteristics indicative of high pathogenicity.