Core-gene tree. The E. coli tree was created from the alignment of 1,278 core-genes from the 186 E. coli genomes. MLST types are annotated to the far right of each genome name. The Escherichia genus tree was created from 297 core-genes. The phylotypes, as determined by the in silico Clermont  method, are marked with the colors blue (A), red (B1), purple (B2), green (D), and the Shigella genomes are marked with the color brown. At each node a black circle indicates a bootstrap value of 1, a grey circle a bootstrap value between 1 and 0.7 and a red number indicate an actual bootstrap value below 0.7. The dashed line in the figure represents a branch, which has been manually shortened by the authors to fit the figure on a printed page. The original tree with all bootstrap values can be seen in Additional file 2. Both trees are unrooted, but the E. coli tree has been visually rooted on the node leading to Clade I.