Whole genome sequencing of Salmonella serovars isolated from organic and non-organic whole broiler carcasses on the eastern shore of Maryland, USA

Multidrug-resistant Salmonella is becoming a public health hazard. This study aimed to investigate the genomic diversity of the selected Salmonella serovars isolated from organic and non-organic chickens using whole-genome sequencing (WGS). A total of 94 Salmonella isolates [Infantis (n = 71), Enteritidis (n = 13), Typhimurium (n = 10)] recovered from organic and non-organic retail chickens were subjected to WGS using Illumina MiSeq. All Salmonella isolates contained at least one antibiotic resistance (AR) gene (ARG). All S. Typhimurium and S. Enteritidis isolates, and 98.6 % of S. Infantis isolates possessed aac(6')-Iaa which predicted resistant to aminoglycosides. Most isolates harbored ARGs for sulfonamides, β-lactamase inhibitors, tetracyclines, and fluoroquinolone/quinolone resistance regardless of chicken types. Fisher's exact test indicated a significantly higher prevalence of ARGs in Salmonella isolated from organic chickens. The virulence genes that stimulate Salmonella pathogenicity island 1 (SPI1) encoding, type three secretion system 1 (TTSS-1) translocated effectors, SPI2 encoding, TTSS-2 translocated effectors, fimbrial adherence determinants, serum resistance, stress adaptation and Mg²⁺ uptake were observed in every serovar regardless of chicken types. Seven plasmids were detected in Salmonella isolates from non-organic chicken, including IncFIB(pN55391), IncFIB(S), Col(BS512), IncFII(S), IncX1, IncC, and ColpVC, whereas Salmonella isolates from organic chicken carried only three plasmids [IncFIB(pN55391), Col(BS512), and IncC]. Phylogenetic analysis confirmed that a significant portion of the isolates had single nucleotide polymorphism (SNP) distances greater than the threshold (SNP ≤ 20), indicating genetic distance among them. These results suggest that the Salmonella isolates from organic and non-organic chickens possessed various AR and virulence genes and thus have the potential to cause salmonellosis.