ArticlePLoS genetics2023
The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans.
Article in PLoS genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it, 27 citations in OpenAlex.
- Guts of healthy humans, livestock, and pets harbor critical-priority and high-risk Escherichia coli clones.Epidemiology and health · 2025Pooled it
- Contrasting regulation of the ecp common pilus operon in Citrobacter rodentium: essential roles of a distal element and IHF even in the absence of H-NS.Archives of microbiology · 2026Article
- Is Virulence GeneInfectious disease reports · 2026Article
- Genome-based source attribution using a One HealthMicrobial genomics · 2026Article
- Longitudinal source-sink dynamics of fecal litter and farm indoor environmental resistomes in broiler chicken and Cherry Valley ducks.Animal microbiome · 2026Article
- Molecular Epidemiology and Multilevel Drug Resistance Mechanisms ofInfection and drug resistance · 2026Review
- Beyond FimH: Diversity and Relevance of Carbohydrate-Binding Fimbrial Proteins in Escherichia coli.Chembiochem : a European journal of chemical biology · 2025Review
- Large-scale genomic analysis reveals the distribution and diversity of type VI secretion systems inmSystems · 2025Article
- Article
- Whole-genome phenotype prediction with machine learning: open problems in bacterial genomics.Bioinformatics (Oxford, England) · 2025Article
- Variants of β-lactamase-encoding genes are disseminated by multiple genetically distinct lineages of bloodstream Escherichia coli.Communications medicine · 2025Article
- Bloodstream infections: mechanisms of pathogenesis and opportunities for intervention.Nature reviews. Microbiology · 2025Review
- Inferring Staphylococcus aureus host species and cross-species transmission from a genome-based model.BMC genomics · 2025Article
- microGWAS: a computational pipeline to perform large-scale bacterial genome-wide association studies.Microbial genomics · 2025Article
- Genomic and transcriptomic insights into the virulence and adaptation of shock syndrome-causingMicrobiology (Reading, England) · 2025Article
- Major F plasmid clusters are linked with ColV and pUTI89-like marker genes in bloodstream isolates of Escherichia coli.BMC genomics · 2025Article
- Residence-colonization trade-off and niche differentiation enable coexistence of Escherichia coli phylogroups in healthy humans.The ISME journal · 2025Article
- Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series.The ISME journal · 2025Article
- Optimizing Ultrasound Probe Disinfection for Healthcare-Associated Infection Control: A Comparative Analysis of Disinfectant Efficacy.Microorganisms · 2024Review
- Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world.Nature reviews. Microbiology · 2024Review
Corrections and comments
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Authors and funding
14 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Escherichia coli is both a highly prevalent commensal and a major opportunistic pathogen causing bloodstream infections (BSI). A systematic analysis characterizing the genomic determinants of extra-intestinal pathogenic vs. commensal isolates in human populations, which could inform mechanisms of pathogenesis, diagnostic, prevention and treatment is still lacking. We used a collection of 912 BSI and 370 commensal E. coli isolates collected in France over a 17-year period (2000-2017). We compared their pangenomes, genetic backgrounds (phylogroups, STs, O groups), presence of virulence-associated genes (VAGs) and antimicrobial resistance genes, finding significant differences in all comparisons between commensal and BSI isolates. A machine learning linear model trained on all the genetic variants derived from the pangenome and controlling for population structure reveals similar differences in VAGs, discovers new variants associated with pathogenicity (capacity to cause BSI), and accurately classifies BSI vs. commensal strains. Pathogenicity is a highly heritable trait, with up to 69% of the variance explained by bacterial genetic variants. Lastly, complementing our commensal collection with an older collection from 1980, we predict that pathogenicity continuously increased through 1980, 2000, to 2010. Together our findings imply that E. coli exhibit substantial genetic variation contributing to the transition between commensalism and pathogenicity and that this species evolved towards higher pathogenicity.
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Registered trials
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