Uropathogenic @entity526 (UPEC) are phenotypically and genotypically very diverse. This diversity makes it challenging to understand the evolution of UPEC adaptations responsible for causing @entity293 ( @entity293 ). To gain insight into the relationship between evolutionary divergence and adaptive paths to uropathogenicity, we sequenced at deep coverage (190*) the genomes of 19 @entity526 strains from @entity293 @entity1 from the same geographic area. Our sample consisted of 14 UPEC isolates and 5 non- @entity293 -causing (commensal) rectal @entity526 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 @entity526 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 @entity281 .

Whole-genome sequencing of uropathogenic XXXX reveals long evolutionary history of diversity and virulence.

@entity1 :: ('9606', 'Species') :: ['patients'] @entity281 :: ('MESH:D007239', 'Disease') :: ['infections'] @entity293 :: ('MESH:D014552', 'Disease') :: ['urinary tract infection', 'urinary tract infections', 'UTI'] @entity526 :: ('562', 'Species') :: ['Escherichia coli', 'E. coli']
@entity526 :: (562,Species) :: ['Escherichia coli']
