The phylogenetic structure of Escherichia coli. The phylogenetic relationship between 1581 sequenced E. coli genomes based on the concatenated sequence of 159 core genes as estimated by maximum likelihood, and the distribution of an intestinal (blue) versus extra-intestinal (red) source of isolation. Isolates coloured grey in both channels have either been isolated from a non-intestinal or extra-intestinal source, or no data is available for their source of isolation. The position of MS499 in the dendrogram is marked with an asterisk. A bootstrapped tree using a subset of these isolates is included in Additional file 3.