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

Details

• Alternative Title:
  Cell Host Microbe
• Personal Author:
  Thänert, Robert ; Choi, JooHee ; Reske, Kimberly A. ; Hink, Tiffany ; Thänert, Anna ; Wallace, Meghan A. ; Wang, Bin ; Seiler, Sondra ; Cass, Candice ; Bost, Margaret H. ; Struttmann, Emily L. ; Iqbal, Zainab Hassan ; Sax, Steven R. ; Fraser, Victoria J. ; Baker, Arthur W. ; Foy, Katherine R. ; Williams, Brett ; Xu, Ben ; Capocci-Tolomeo, Pam ; Lautenbach, Ebbing ; Burnham, Carey-Ann D. ; Dubberke, Erik R. ; Kwon, Jennie H. ; Dantas, Gautam
• Corporate Authors:
  CDC Prevention Epicenter Program
• Description:
  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.
• Subjects:
  Escherichia Coli Infections Escherichia Coli Proteins Host Adaptation Humans Interspersed Repetitive Sequences Urinary Tract Infections
• Source:
  Cell Host Microbe. 30(7):1034-1047.e6
• Pubmed ID:
  35545083
• Pubmed Central ID:
  PMC10365138
• Document Type:
  Journal Article
• Funding:
  U54CK000482/ACL/ACL HHSUnited States/ ; K23 AI137321/AI/NIAID NIH HHSUnited States/ ; R01 AI123394/AI/NIAID NIH HHSUnited States/ ; KL2 TR002346/TR/NCATS NIH HHSUnited States/ ; R01 HD092414/HD/NICHD NIH HHSUnited States/ ; U54 CK000482/CK/NCEZID CDC HHSUnited States/ ; UL1 TR002345/TR/NCATS NIH HHSUnited States/
• Volume:
  30
• Issue:
  7
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:30b30b2a27c98a4d4ab329f4d95d7c9357cf9ebe67a80d771b9b429e56836fb3
• Download URL:
  https://stacks.cdc.gov/view/cdc/131267/cdc_131267_DS1.pdf
• File Type:
  [PDF - 2.48 MB ]