Global and group-by-group phylogenetic analysis of the genomes. (a) Phylogeny of all 486 genomes from included CDI cases. Clades corresponding to STs are shown as triangles, the height of which represents the diversity of each ST. Numbers in parentheses indicate the number of genomes belonging to each ST sequenced. The 15 STs or groups of closely related STs analyzed in detail are shaded, and indexed from 1 to 15. (b) Detailed phylogeny for samples in group 9. The ten genomes of ST54 are labeled from A to J and the five genomes of ST63 are labeled from K to O. The × co-ordinate of each genome indicates time of isolation. For each internal node of the tree (corresponding to a common ancestor), the mean inferred age is shown on the tree with the 95% credibility interval around this mean shown as a blue bar.