Genomic Diversity, Antimicrobial Resistance, Plasmidome, and Virulence Profiles of Salmonella Isolated from Small Specialty Crop Farms Revealed by Whole-Genome Sequencing

Abstract

<i>Salmonella</i> is the leading cause of death associated with foodborne illnesses in the USA. Difficulty in treating human salmonellosis is attributed to the development of antimicrobial resistance and the pathogenicity of <i>Salmonella</i> strains. Therefore, it is important to study the genetic landscape of <i>Salmonella</i>, such as the diversity, plasmids, and presence antimicrobial resistance genes (AMRs) and virulence genes. To this end, we isolated <i>Salmonella</i> from environmental samples from small specialty crop farms (SSCFs) in Northeast Ohio from 2016 to 2021; 80 <i>Salmonella</i> isolates from 29 <i>Salmonella</i>-positive samples were subjected to whole-genome sequencing (WGS). In silico serotyping revealed the presence of 15 serotypes. AMR genes were detected in 15% of the samples, with 75% exhibiting phenotypic and genotypic multidrug resistance (MDR). Plasmid analysis demonstrated the presence of nine different types of plasmids, and 75% of AMR genes were located on plasmids. Interestingly, five <i>Salmonella</i> Newport isolates and one <i>Salmonella</i> Dublin isolate carried the ACSSuT gene cassette on a plasmid, which confers resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide, and tetracycline. Overall, our results show that SSCFs are a potential reservoir of <i>Salmonella</i> with MDR genes. Thus, regular monitoring is needed to prevent the transmission of MDR <i>Salmonella</i> from SSCFs to humans.