FIG 1 .

Phylogenomic analysis of representative EPEC isolates. The genome sequences of representative EPEC isolates were compared with those of a reference collection of diverse E. coli and Shigella isolates that had been sequenced previously and are available in the public domain. The genomes were aligned using Mugsy (95) as previously described (31, 94). A 1.9-Mb aligned region was used to generate a maximum-likelihood phylogeny with 100 bootstrap replicates using RAxML v.7.2.8 (97), and the results were visualized using FigTree v.1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/). The representative EPEC isolates that were analyzed using RNA-Seq are indicated in bold.