Phylogenetic relationship among genome-sequenced E. coli and Shigella strains. The phylogenetic tree was generated by PhyML with amino-acid sequences of 1,273 core genes from completely sequenced E. coli and Shigella strains. Each color indicates the phylogenetic group of E. coli (red, A; yellow, B1; black, Shigella; blue, E; purple, D; green, B2). Bootstrap values (percentages of 1,000 replications) greater than 50% are shown at each node. Escherichia fergusonii ATCC 35469 were used for the out-group. The scale bar represents 0.001 nucleotide substitutions per site.