Bacterial isolates

The bacterial isolates analysed in this study, and the details of each of the genomes sequenced, are listed in Table 1 and also described in a companion study³⁴. The EPEC (LEE+/bfpA+/stx−) isolates analysed in this study were obtained from GEMS as previously described^2,23. A total of 24 tEPEC isolates from lethal cases (LI) were obtained, representing all tEPEC isolates associated with a lethal outcome in GEMS^2,23. The isolates from lethal outcomes were from only five sites of the seven in GEMS (The Gambia, Mail, Mozambique, Kenya and Pakistan), so there is an over-representation of isolates from Africa. A matching scheme using geography and clinical parameters of the subject was used to select one EPEC isolate from a non-lethal symptomatic case (NSI) and one EPEC isolate from an asymptomatic case (AI) representing controls for each tEPEC from a lethal case as previously described³⁴. One NSI case and one AI case served as controls for two different LI cases, resulting in 23 EPEC from NSI cases and 23 EPEC from AI cases. A tEPEC isolate (bfpA+) was obtained from 20 of the NSI cases and 17 of the AI cases, with the remaining EPEC cases containing an aEPEC (bfpA−). The recent publication by Donnenberg et al.³⁴ describes the case-control aspect of this study and the comparison of the isolates that were directly matched based on patient and clinical parameters. In the current study we delve into the phylogenomic content of the isolates, irrespective of matching criteria and only consider the genotypic presentation of EPEC and the outcome of the infection.