Enteropathogenic Escherichia coli revisited – New insights into old EPEC isolates using whole genome sequencing

Abstract

Enteropathogenic E. coli (EPEC) cause severe diarrhoeal disease in children under the age of three in low- and middle-income countries. Upon ingestion of contaminated food or water, the bacteria colonise the small intestine. EPEC are grouped into typical and atypical isolates based on the presence or absence of the genes encoding the bundle-forming pilus (Bfp), with tEPEC (Bfp⁺) adhering to cells in microcolonies, whereas aEPEC show a more diffuse adherence phenotype. All EPEC express a type III secretion system (T3SS) encoded on the locus of enterocyte effacement (LEE) pathogenicity island, which is required for the translocation of effector proteins into the host cell, aiding bacterial adhesion and survival. Historically classified as EPEC by serogroups according to WHO guidelines, current practice identifies EPEC by PCR for characteristic virulence genes eae (intimin) and bfp. Here, we analysed a collection of 41 older clinical isolates initially grouped as EPEC using whole genome sequencing (WGS) combined with phenotypic characterisation including biofilm formation, adherence type, and pedestal formation. This allowed us to correctly define isolate pathotypes in addition to determining the integration site of the LEE and identifying three potential new T3SS effectors. Uniting phenotypic characterisation with genetic information, we were able to identify the molecular mediators of observed phenotypes. This suggests that, while non-WGS-based isolate profiling is important to decide immediate treatment options, only detailed knowledge of the isolates can provide in-depth information on the potential disease development and severity.