ArticleCell host & microbe2022
Persisting uropathogenic Escherichia coli lineages show signatures of niche-specific within-host adaptation mediated by mobile genetic elements.
Article in Cell host & microbe, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- UropathogenicAntibiotics (Basel, Switzerland) · 2026Review
- Metabolic strategies of Enterobacteriaceae gut colonization.Nature reviews. Microbiology · 2026Review
- Significant variability in virulence factors and antibiotic resistance of uropathogenic Escherichia coli strains may be counteracted by their susceptibility to lytic bacteriophages.Scientific reports · 2026Article
- Optimized Urine Metagenomic Methods Reveal Longitudinal Microbial Community Dynamics and Predictors of Transition from Asymptomatic Colonization to CAUTI.bioRxiv : the preprint server for biology · 2026Article
- Microbial Conversations Between the Gut and Urinary Tract: Emerging Implications for Kidney and Urinary Tract Diseases.Indian pediatrics · 2026Article
- Loss of O-antigen due toScience advances · 2026Article
- Yad fimbriae are triggered by host cues and enhance extraintestinal pathogenic Escherichia coli tissue colonisation during bloodstream infection.PLoS pathogens · 2026Article
- Unmasking pathogen traits for chronic colonization in neurogenic bladder.Cell reports · 2026Article
- Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli.Nature microbiology · 2026Article
- Integrating Phenotypic and Genomic Data with Machine Learning to Predict Antimicrobial Resistance and Identify Genetic Biomarkers inInternational journal of environmental research and public health · 2026Article
- From colonization to invasion: genomic and phenotypic comparison of faecal and bloodstream isolates from the same patients.Journal of medical microbiology · 2026Article
- Underexplored maternal microbiomes: immune, metabolic, and microbial pathways shaping pregnancy outcomes.Infection and immunity · 2026Review
- Article
- Genomic Characterisation of Pyometra-AssociatedAntibiotics (Basel, Switzerland) · 2026Article
- AreVirulence · 2025Article
- Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection.NPJ biofilms and microbiomes · 2025Article
- Metatranscriptomics-based metabolic modeling of patient-specific urinary microbiome during infection.NPJ biofilms and microbiomes · 2025Article
- Intraspecies associations from strain-rich metagenome samples.Cell reports · 2025Article
- Uropathogenic Escherichia coli (UPEC) that hides its identity: features of LC2 and EC73 strains from recurrent urinary tract infections.BMC microbiology · 2025Article
- Large-scale genomic analysis reveals the distribution and diversity of type VI secretion systems inmSystems · 2025Article
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Abstract
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.
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