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

Emmanuel W. Bumunang, Rahat Zaheer, Kim Stanford, Chad Laing, Dongyan Niu, Le Luo Guan, Linda Chui, Gillian A.M. Tarr, Tim A. McAllister

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


Shiga toxin (stx) is the principal virulence factor of the foodborne pathogen, Shiga toxin-producing Escherichia coli (STEC) O157:H7 and is associated with various lambdoid bacterio (phages). A comparative genomic analysis was performed on STEC O157 isolates from cattle (n = 125) and clinical (n = 127) samples to characterize virulence genes, stx-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 stx1a and stx2a. Most cattle (76.0%) and clinical (76.4%) isolates carried the virulence gene combination of stx1, stx2, eae and hlyA. Characterization of stx1 and stx2-carrying phages in assembled contigs revealed that they were associated with mlrA and wrbA insertion sites, respectively. In cattle isolates, mlrA and wrbA 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, n = 8 and clinical, n = 6) with streptomycin (aadA1, aadA2, ant(3’’)-Ia and aph(3’’)-Ib) being the most prevalent gene in ARCs. The profound disparity between the cattle and clinical strains in occupancy of the wrbA locus suggests that this trait may serve to differentiate cattle from human clinical STEC O157:H7. These findings are important for stx screening and stx-phage insertion site genotyping as well as monitoring ARGs in isolates from cattle and clinical samples.

Original languageEnglish (US)
Article number603
Issue number9
StatePublished - Sep 2022

Bibliographical note

Funding Information:
This work was supported by Agriculture Funding Consortium, project #2019R048R and the Beef Cattle Research Council (BCRC) #FOS.01.18.

Publisher Copyright:
© 2022 by the authors.


  • Escherichia coli O157
  • Shiga toxins
  • antimicrobial resistance
  • insertion sites
  • stx-carrying phages

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't


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