FIG 1.

Unrooted k-mer tree (solid dark gray lines) for all E. coli isolates and individual SNP-based trees (teal boxes) for each subgroup of isolates. The central tree is a neighbor-joining k-mer tree describing the genetic relatedness of the isolates based on the presence of 16-mer motifs throughout the complete chromosomes. The scale indicates Jensen-Shannon divergence length. Neighbor-joining SNP trees were made using complete genome alignments. The number of SNPs separating each node is indicated along the branches. For the tree of ST131 isolates from patient 4, the number of SNPs separating the isolates is indicated at the internal node separating the branches.