Antimicrobial resistance in non-O157 Shiga-toxin producing Escherichia coli

Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens that cause severe gastrointestinal disease in humans. Monitoring antimicrobial resistance (AMR) in STEC from symptomatic human cases may provide evidence for the extent of transmission of resistant strains and resistance genes from ruminants to humans. The aim of this study was to assess AMR in non-O157 STEC in England and Wales between 2014 and 2016, and to compare phenotypic and Whole Genome Sequencing (WGS) derived AMR profiles.

Six hundred and fifty-three non-O157 STEC isolates were analysed. WGS and bioinformatic analysis were performed on 457 isolates in the top 10 Clonal Complexes (CC) (193 were excluded on the basis of CC) and phenotypic susceptibility typing via breakpoint and minimum inhibitory concentration testing was undertaken on 100 isolates exhibiting resistance to at least one antimicrobial.

Of 457 isolates, 332 lacked identifiable resistance genes and were predicted to be fully susceptible to 11 diverse classes of antimicrobials, 125 were found to carry one or more resistance genes and 83 were multi-drug resistant. Four isolates were identified as extended-spectrum b-lactamase-producers. In total, 46 different genes were detected – which conferred resistance to 8 different antibiotic classes. An overall concordance of 97.5  % was demonstrated between the two methods.

Phenotypic and genome-derived AMR comparisons showed good correlation for non-O157 STEC. This has added to the evidence base to support the use of genotypic approaches for antimicrobial susceptibility typing, to replace phenotypic typing for surveillance purposes, and guide clinical decision making in the more distant future.