FIG 1.

Phylogenetic relationships among Escherichia coli (A) and Enterococcus faecalis (B) strains identified using whole-genome sequencing of purified single isolates (labeled with sample numbers followed by “_i”) and direct sequencing of urine samples (labeled with sample numbers followed by “_d”). SNP trees were constructed using an online application (21). Data were obtained from single isolates and directly from samples clustered together, and it was also possible to place data in a phylogenetic context when it was not possible to culture single isolates. Branch length in the snpTree output indicates number of substitutions per site.