ArticleApplied and environmental microbiology2022
The Population Genomics of Increased Virulence and Antibiotic Resistance in Human Commensal Escherichia coli over 30 Years in France.
Article in Applied and environmental microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 45 citations in OpenAlex.
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- Fluoroquinolone resistance without fluoroquinolone use; the genie is truly out of the bottle.Frontiers in microbiology · 2026Review
- Basic reproduction number varies markedly between closely related pandemic Escherichia coli clones.Nature communications · 2025Article
- Overstory plant canopy and plant organ-age enhance the survival capacity and the medicinal properties of Tephrosia apollinea in Fujairah.Scientific reports · 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
- Diversity, distribution, and population structure of Escherichia coli in the lower gastrointestinal tract of humans.PloS one · 2025Article
- Extraintestinal traits of pathogenicity and sequence type lineages in commensalFrontiers in microbiology · 2025Article
- Genomic evidence ofmSphere · 2024Article
- A microbiological and genomic perspective of globally collected Escherichia coli from adults hospitalized with invasive E. coli disease.The Journal of antimicrobial chemotherapy · 2024Observational
- Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan.Nature communications · 2024Article
- Review
- Genomic surveillance for antimicrobial resistance - a One Health perspective.Nature reviews. Genetics · 2024Review
- The Scr and Csc pathways for sucrose utilization co-exist inFrontiers in microbiology · 2024Article
- Genome-Based Molecular Diversity of Extended-SpectrumTransboundary and emerging diseases · 2024Article
- Article
- Comparison of phylogenetic and virulence factors betweenHeliyon · 2023Article
- Community carriage of ESBL-producingmSphere · 2023Article
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Escherichia coli is a commensal species of the lower intestine but is also a major pathogen causing intestinal and extraintestinal infections that is increasingly prevalent and resistant to antibiotics. Most studies on genomic evolution of E. coli used isolates from infections. Here, instead, we whole-genome sequenced a collection of 403 commensal E. coli isolates from fecal samples of healthy adult volunteers in France (1980 to 2010). These isolates were distributed mainly in phylogroups A and B2 (30% each) and belonged to 152 sequence types (STs), the five most frequent being ST10 (phylogroup A; 16.3%), ST73 and ST95 (phylogroup B2; 6.3 and 5.0%, respectively), ST69 (phylogroup D; 4.2%), and ST59 (phylogroup F; 3.9%), and 224 O:H serotypes. ST and serotype diversity increased over time. The O1, O2, O6, and O25 groups used in bioconjugate O-antigen vaccine against extraintestinal infections were found in 23% of the strains of our collection. The increase in frequency of virulence-associated genes and antibiotic resistance was driven by two evolutionary mechanisms. Evolution of virulence gene frequency was driven by both clonal expansion of STs with more virulence genes ("ST-driven") and increases in gene frequency within STs independent of changes in ST frequencies ("gene-driven"). In contrast, the evolution of resistance was dominated by increases in frequency within STs ("gene-driven"). This study provides a unique picture of the phylogenomic evolution of E. coli in its human commensal habitat over 30 years and will have implications for the development of preventive strategies.
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