Fig. 2

Genome-wide phylogenetic analysis of E. coli and Shigella strains. The maximum likelihood (ML)-based phylogenetic tree based on the concatenated nucleotide sequences of 341 orthologous CDSs was constructed as described previously [35, 37]. Pairwise comparisons of all genome sequences were carried out using NUCmer from the MUMer package [38] and highly similar regions (repeated sequences) were removed from the analysis. Genomes were downloaded from GenBank, including 13 STEC strains, the German outbreak EHAEC strain, 17 other E. coli and 2 Shigella strains