Phylogenetic tree of ST131 <i>E. coli</i>.

<p>The tree is based on a 3,629,034 bp core genome (3,734 orthologous genes: 90% identity and 90% coverage) and 100 bootstrapping replicates. ST131 clades are named according to <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004766#pgen.1004766-Petty1" target="_blank">[16]</a> and further subdivided and colored according to virotypes <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004766#pgen.1004766-Blanco2" target="_blank">[36]</a>: virotype A (blue), virotype B (yellow), virotype C (pink), virotype D (green). Virotype classification is based on the presence/absence of four putative virulence factors: <i>afaFM955459</i> (encoding an Afa/Dr adhesin), <i>sat</i> (secreted autotransporter toxin, present in PAI-CFT073-pheV), <i>ibeA</i> (invasion of brain endothelium) and <i>iroN</i> (salmochelin siderophore receptor). The commensal ST131 strain SE15 was used to root the tree (virotype non typable; serotype O150 in the original publication <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004766#pgen.1004766-Toh1" target="_blank">[91]</a> but lying within the H41 cluster in the phylogenomic study of <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004766#pgen.1004766-Petty1" target="_blank">[16]</a>). Given SNP numbers are approximate averages of individual comparisons.