Phylogenic analysis of Shigella strains. Data were compiled from this study, and . Details on tree generation are described in Materials and Methods. Phylogenetic tree generated by the neighbor-joining method for the combined data of 66 strains (Table 1 and additional file 5). For Shigella strains used in our study, S. dysenteriae, S. flexneri, S. boydii and S. sonnei are abbreviated to D, F, B, and SS respectively, followed by the serotype number. E. coli k-12 MG1655 is abbreviated to MG1655. For pathogenic E. coli and Shigella strains used in previous study, the strains' abbreviations are according to the additional file 5. Bootstrap values greater than 50% are indicated at the nodes. The three major clusters of Shigella were indicated by vertical dashed lines in the right.