Enterotoxigenic Escherichia coli (ETEC) are a member of the Enterobacteriacea family that mediate disease in mammals via the production of host-specific enterotoxins. These pathogens often display antimicrobial resistance and are usually responsible for sporadic or endemic diarrhoeal disease within pig production systems, observed on a global scale. This study involved the Australia-first whole genome characterisation of 50 porcine-sourced E. coli isolates through molecular and combinational whole genome sequencing and bioinformatic analyses. These isolates include several highly pathogenic representatives of ETEC found in NSW, Australia, and isolates derived from both diseased and healthy weaner piglets both pre- and post-antibiotic treatment from a single farm. Initial studies showed many of these isolates were multi-drug resistant with a high prevalence of class 1 integrons, and carried a diverse array of virulence genes, including those encoding adhesins (faeG, eaeA), haemolysins (ehxA, hlyA) and enterotoxins (STa, STb and LT).
Phylogenetics performed through in silico sequence typing and PhyloSift analysis identified 19 sequence types, clustered into three large clades. Additionally, subclades in this analysis clustered by sequence type, helping validate the methods. High throughput BLASTn analysis was used to screen the collection for over 60 known ETEC virulence factors, and identified a diverse array of virulence profiles involving the ETEC toxins, adhesins, and interestingly some clustered iron acquisition genes; iutA/iucD/sitD and fyuA/irp2. An extremely high prevalence of the insertion sequence IS26 was observed in the collection, including examples where IS26 was located in close proximity to the class 1 integrase. Our screens indicated that Tn6026/6029, a pair of transposons flanked by direct copies ofIS26, are not present, suggesting that different transposons may be mobilising antimicrobial resistance genes within these isolates.
This analysis is improving our understanding of genetic variability and mobility in both pathogenic and commensal E. coli isolates derived from young pigs.