Genomic Analysis of Shiga Toxin-Producing O157 Cattle and Clinical Isolates from Alberta, Canada.

Shiga toxin () is the principal virulence factor of the foodborne pathogen, Shiga toxin-producing (STEC) O157:H7 and is associated with various lambdoid bacterio (phages). A comparative genomic analysis was performed on STEC O157 isolates from cattle ( = 125) and clinical ( = 127) samples to characterize virulence genes, -phage insertion sites and antimicrobial resistance genes that may segregate strains circulating in the same geographic region. In silico analyses revealed that O157 isolates harboured the toxin subtypes and Most cattle (76.0%) and clinical (76.4%) isolates carried the virulence gene combination of , , and . Characterization of and -carrying phages in assembled contigs revealed that they were associated with and insertion sites, respectively. In cattle isolates, and insertion sites were occupied more often (77% and 79% isolates respectively) than in clinical isolates (38% and 1.6% isolates, respectively). Profiling of antimicrobial resistance genes (ARGs) in the assembled contigs revealed that 8.8% of cattle (11/125) and 8.7% of clinical (11/127) isolates harboured ARGs. Eight antimicrobial resistance genes cassettes (ARCs) were identified in 14 isolates (cattle, = 8 and clinical, = 6) with streptomycin (, , and -) being the most prevalent gene in ARCs. The profound disparity between the cattle and clinical strains in occupancy of the locus suggests that this trait may serve to differentiate cattle from human clinical STEC O157:H7. These findings are important for screening and -phage insertion site genotyping as well as monitoring ARGs in isolates from cattle and clinical samples.