From the Holt lab: “Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants” in Nature Microbiology
In this paper, we set out to define the population structure of aEPEC strains using genomics, and also to investigate variation in the LEE island itself. Our strain set is ~200 newly sequenced aEPEC that were isolated from children with diarrhoea, and from asymptomatic age-matched controls, as part of the Global Enteric Multicenter Study (GEMS) – a massive study into the etiology of childhood diarrhoea across seven sites in Africa and Asia, funded by the Gates Foundation. We also included lots of publicly available genomes from NCBI, which included ~60 additional aEPEC.
So what did we find? Well from a population structure point of view, we confirmed what we suspected from the beginning – that the ~200 aEPEC strains actually represent dozens of distinct lineages or clonal groups within the E. coli whole genome phylogeny. We tried making the core genome tree in a few different ways, including mapping reads to a reference genome vs usingRoary to generate core gene alignments from assemblies; with and without removing recombinant regions identified using ClonalFrameML. The alternative trees all tell the same population structure story, as you can see below. An interactive version of the mapping-based, recombination-filtered tree (which appears in Figure 1 of the paper, panel a below) is available to play with in MicroReact.