Persisting uropathogenic Escherichia coli lineages show signatures of niche-specific within-host adaptation mediated by mobile genetic elements.

Journal Article (Journal Article)

Large-scale genomic studies have identified within-host adaptation as a hallmark of bacterial infections. However, the impact of physiological, metabolic, and immunological differences between distinct niches on the pathoadaptation of opportunistic pathogens remains elusive. Here, we profile the within-host adaptation and evolutionary trajectories of 976 isolates representing 119 lineages of uropathogenic Escherichia coli (UPEC) sampled longitudinally from both the gastrointestinal and urinary tracts of 123 patients with urinary tract infections. We show that lineages persisting in both niches within a patient exhibit increased allelic diversity. Habitat-specific selection results in niche-specific adaptive mutations and genes, putatively mediating fitness in either environment. Within-lineage inter-habitat genomic plasticity mediated by mobile genetic elements (MGEs) provides the opportunistic pathogen with a mechanism to adapt to the physiological conditions of either habitat, and reduced MGE richness is associated with recurrence in gut-adapted UPEC lineages. Collectively, our results establish niche-specific adaptation as a driver of UPEC within-host evolution.

Full Text

Duke Authors

Cited Authors

  • Thänert, R; Choi, J; Reske, KA; Hink, T; Thänert, A; Wallace, MA; Wang, B; Seiler, S; Cass, C; Bost, MH; Struttmann, EL; Iqbal, ZH; Sax, SR; Fraser, VJ; Baker, AW; Foy, KR; Williams, B; Xu, B; Capocci-Tolomeo, P; Lautenbach, E; Burnham, C-AD; Dubberke, ER; Kwon, JH; Dantas, G; CDC Prevention Epicenters Program,

Published Date

  • July 13, 2022

Published In

Volume / Issue

  • 30 / 7

Start / End Page

  • 1034 - 1047.e6

PubMed ID

  • 35545083

Electronic International Standard Serial Number (EISSN)

  • 1934-6069

Digital Object Identifier (DOI)

  • 10.1016/j.chom.2022.04.008


  • eng

Conference Location

  • United States