title: 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.
authors.affiliation: Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: yancylo@umich.edu.
authors.forename: Yancy
authors.initials: Y
authors.lastname: Lo
authors.affiliation: Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
authors.forename: Lixin
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of Epidemiology, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Betsy
authors.initials: B
authors.lastname: Foxman
authors.affiliation: Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Zöllner
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics; D004927:Escherichia coli Infections / Q000382:microbiology*; D029968:Escherichia coli Proteins / Q000235:genetics; D019143:Evolution, Molecular; D005260:Female; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D014552:Urinary Tract Infections / Q000382:microbiology*; D056689:Uropathogenic Escherichia coli / Q000235:genetics*; D014774:Virulence; D037521:Virulence Factors / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D037521:Virulence Factors
keywords: Next-generation sequencing; Phylogeny; Uropathogen