Genome-based assessment of antimicrobial resistance, virulence-associated genes, and prophage diversity across clinical Salmonella Typhimurium isolates in the south of Tunisia

Abstract

Salmonella Typhimurium is a significant foodborne pathogen and a leading cause of gastroenteritis in humans and animals. Among its various lineages, the DT104 strain is particularly notable for its high level of antimicrobial resistance, making it a significant global concern. Here, we used whole-genome sequencing to investigate the antimicrobial resistance and virulence-associated genomic features of clinical S. Typhimurium DT104, and we compared them to non-DT104 strains recovered from southern Tunisia between 2000 and 2013. Among 88 S. Typhimurium isolates, 39.8 % were definitive type DT104. Antimicrobial resistome analysis revealed clinically significant genes including bla_CARB-2, bla_TEM-1B, aadA2, sul1, sul2, tet(G), floR, dfrA5, and biocide resistance gene qacEΔ1. β-lactams resistance in DT104 and non-DT104 strains was associated with bla_CARB-2 (91 %) and bla_TEM-1 (34 %) genes, respectively. Resistance mutations in GyrA (D87N or S83R) were identified in three isolates with reduced susceptibility to nalidixic acid. Among 10 intact prophages, the main prophages detected were Gifsy_1 (96.6 %), and Gifsy_2 (95.5 %). Virulence gene screening suggested that DT104 is not more pathogenic than non-DT104 isolates. Furthermore, virulence plasmid genes were identified in approximately 95 % of isolates. Ten Salmonella pathogenicity islands (SPIs) encoding virulence factors were detected in all isolates except SPI-14 and CS54_island. SNP analysis revealed clade-specific missense mutations within plasmid virulence, SPI-1, SPI-2, and fimbriae genes. Genomic characterization sheds light on the diversity of genetic elements contributing to clinical S. Typhimurium strains' pathogenicity and antibiotic resistance from Tunisia. Therefore, continuous genomic surveillance is an important tool for preserving human health.