Atypical enteropathogenic Escherichia coli (aEPEC) is an important emerging pathogen, which is aetiologically associated with diarrhoea in children in both industrialised and developing countries. Classical approaches to categorise clinical isolates of aEPEC have shown that they are heterogeneous for sequence type (ST), serotype and virulence genes. Associations of aEPEC with diarrhoea are inconsistent, suggesting that the current definition of aEPEC lacks the ability to distinguish between virulent and less virulent isolates.
We have used whole genome sequencing to analyse the genetic variation and evolution of 197 aEPEC isolates from the Global Enteric Multicenter Study. The aEPEC genomes were compared with publicly available Shigella and E. coli genomes including different pathotypes and commensal strains. Phylogenetic analysis revealed the presence of several clonal lineages within the aEPEC isolates. Each clone comprised isolates from countries in Africa and South Asia, indicating these lineages are likely to be of global importance.
Preliminary results indicate that some clones are associated with homologues of known enteropathogenicity genes. Our data indicates that aEPEC comprises several distinct clones that have evolved separately through horizontal acquisition of virulence genes. The epidemiological data from the GEMS study will be used to refine the relationships between genotype and clinical disease phenotypes in humans.