Genomic profiling of enterotoxigenic Escherichia coli toxins and adhesins in livestock isolates from Kenya

Enterotoxigenic <i>Escherichia coli</i> (ETEC) is a significant cause of diarrhoea in livestock and humans. The epidemiology of ETEC in animals remains understudied, prompting an investigation into the virulence factors and associated adhesins of ETEC in livestock from Western Kenya. Also, there is limited evidence supporting the role of livestock as possible zoonotic reservoirs for ETEC. ETEC strains harbour colonization factors/adhesins and enterotoxins, with animal ETECs exhibiting various adhesins (F4, F5, F6, F17, F18 and F41). Enterotoxins include heat-labile (LT) and heat-stable (ST) toxins and are further divided into LT-I and LT-II and STa and STb, respectively. Additional toxin combinations occur, with ETEC and Shiga toxin-producing <i>E. coli</i> (STEC) hybrids garnering public health significance. Here, we analysed faecal and mesenteric lymph node samples from diverse livestock across three Western Kenyan counties (Busia, Bungoma and Kakamega), using whole-genome sequencing. <i>In silico</i> screening determined the presence of AB₅ and A₂B₅-like toxin genes, including cytolethal distending toxin (<i>cdt</i>ABC) along with associated adhesins. To broaden the screening panel, adhesin genes identified were further characterized to identify both known and novel alleles, particularly focusing on human-ETEC colonization factors. Two <i>estA</i> alleles (<i>estA-</i>4-06, <i>estA-</i>6-02) and six <i>eltAB</i>-II toxin alleles (<i>eltAB</i>-II-a2-01, <i>eltAB</i>-II-a3-01, <i>eltAB</i>-II-c1-02, <i>eltAB</i>-II-c6-03, <i>eltAB</i>-II-c6-04 and <i>eltAB</i>-II-c7-02) were identified in livestock. Hybrid ETECs identified were ETEC/STEC present in 6.7% (4/60) of ETEC strains and ETEC with <i>cdtABC</i> type I. An A₂B₅-like tripartite toxin, potentially resembling the typhoid toxin, was detected in 8.7% (4/46) of the <i>eltAB</i>-II-positive strains. It may have unique effects on enterocytes distinct from known toxins. These findings expand our understanding of ETEC pathogenicity and genetic diversity in animal reservoirs, while also highlighting potential zoonotic risks. They broaden the toxin repertoire, offer adhesin-based vaccine candidates for livestock and provide valuable insights for future vaccine development and public health strategies in the Lake Victoria Crescent ecosystem and beyond.