Whole-genome sequencing of uropathogenic Escherichia coli reveals long evolutionary history of diversity and virulence

Abstract

Uropathogenic Escherichia coli (UPEC) are phenotypically and genotypically very diverse. This diversity makes it challenging to understand the evolution of UPEC adaptations responsible for causing urinary tract infections (UTI). To gain insight into the relationship between evolutionary divergence and adaptive paths to uropathogenicity, we sequenced at deep coverage (190×) the genomes of 19 E. coli strains from urinary tract infection patients from the same geographic area. Our sample consisted of 14 UPEC isolates and 5 non-UTI-causing (commensal) rectal E. coli isolates. After identifying strain variants using de novo assembly-based methods, we clustered the strains based on pairwise sequence differences using a neighbor-joining algorithm. We examined evolutionary signals on the whole-genome phylogeny and contrasted these signals with those found on gene trees constructed based on specific uropathogenic virulence factors. The whole-genome phylogeny showed that the divergence between UPEC and commensal E. coli strains without known UPEC virulence factors happened over 32 million generations ago. Pairwise diversity between any two strains was also high, suggesting multiple genetic origins of uropathogenic strains in a small geographic region. Contrasting the whole-genome phylogeny with three gene trees constructed from common uropathogenic virulence factors, we detected no selective advantage of these virulence genes over other genomic regions. These results suggest that UPEC acquired uropathogenicity long time ago and used it opportunistically to cause extraintestinal infections.

Keywords: Next-generation sequencing; Phylogeny; Uropathogen.

Figure 1. Phylogeny constructed from whole-genome assembly-based variants

The phylogeny is rooted by E. fergusonii (long branch not shown). Nodes are labeled by the sample codes as listed in Table 2. All strains are of phylogroup B2. Branches with circles represent bootstrap values, and branches with triangles represent bootstrap values. All unmarked branches have bootstrap value. Scale shows length on branches representing 500 pairwise sequence differences.

Figure 2. Unrooted trees derived from three selected virulence factors: (a) aer, (b) hly, and (c) kpsMT for uropathogenic and commensal E. coli

Each gene tree consists of a different number of tree leaves, as not all virulence factors occurred on all strains. Scale shows length on branches representing 5 pairwise sequence differences.

Figure 2. Unrooted trees derived from three selected virulence factors: (a) aer, (b) hly, and (c) kpsMT for uropathogenic and commensal E. coli

Each gene tree consists of a different number of tree leaves, as not all virulence factors occurred on all strains. Scale shows length on branches representing 5 pairwise sequence differences.

Figure 2. Unrooted trees derived from three selected virulence factors: (a) aer, (b) hly, and (c) kpsMT for uropathogenic and commensal E. coli

Each gene tree consists of a different number of tree leaves, as not all virulence factors occurred on all strains. Scale shows length on branches representing 5 pairwise sequence differences.