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

•We sequenced 14 uropathogenic E. coli and 5 commensals at >190×.•We found deep split between uropathogenic and commensal E. coli (>32 million generations).•High between-strain diversity showed no signal of epidemics in the sampled area.•High diversity in each ST and pathotype suggested multiple origins of pathogenicity.•We detected no selective advantage of virulence factors over other genomic regions.