Evidence for Horizontal Transmission and Recirculation of Shiga Toxin-Producing Escherichia coli in the Beef Production Chain in South Africa Using Whole Genome Sequencing

We used whole genome sequencing (WGS) as an epidemiologic surveillance tool to elucidate the transmission dynamics of Shiga toxin-producing <i>Escherichia coli</i> (STEC) strains along the beef production chain in South Africa. Isolates were obtained from a cattle farm, abattoirs and retail outlets. Isolates were analysed using WGS on a MiSeq platform (Illumina, San Diego, CA, USA) and phylogenetic analysis was carried out. Of the 85 isolates, 39% (33) carried the <i>stx</i> gene and 61% (52) had lost the <i>stx</i> gene. The prevalence of <i>stx</i> subtypes was as follows; <i>stx</i>_1<i>a</i> 55% (18/33), <i>stx</i>_1<i>b</i> 52% (17/33), <i>stx</i>_2<i>a</i> 55% (18/33), <i>stx</i>_2<i>b</i> 27% (9/33), <i>stx</i>_2<i>dB</i> 30% (10/33) and <i>stx</i>_{2<i>d</i>1<i>A</i>} 15% (5/33). Thirty-five different serogenotypes were detected, of which 65% (56) were flagellar H-antigens and 34% (29) were both O-antigens and flagellar H-antigens. We identified 50 different sequence types (STs), and only nine of the isolates were assigned to three different clonal complexes. Core genome phylogenetic analysis revealed genetic relatedness, and isolates clustered mainly according to their STs and serogenotypes regardless of <i>stx</i> subtypes. This study provides evidence of horizontal transmission and recirculation of STEC strains in Gauteng province and demonstrates that every stage of the beef production chain plays a significant role in STEC entry into the food chain.