The whole-genome assemblies were aligned using Mugsy44 as previously described18. The regions of sequence that aligned in all genomes were concatenated into a single 820,355-bp sequence for each genome, and the concatenated sequences were used to generate a maximum-likelihood phylogeny with 100 bootstrap replications, which was constructed using RAxML v.7.2.845, and visualized using FigTree v.1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/). Bootstrap values of ≥80 are designated on the tree by a filled circle. Genomes examined in this study that were obtained from lethal cases (LI) are indicated in orange, those from non-lethal symptomatic (NSI) cases are indicated in green and isolates from asymptomatic (AI) cases in blue. The presence of bfpA is indicated by a star symbol. The four novel EPEC phylogenomic lineages identified in this study are indicated by an asterisk.