ArticleNature microbiology2022
Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects.
Article in Nature microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
24 citing papers in PubMed.
- Review
- Metabolic strategies of Enterobacteriaceae gut colonization.Nature reviews. Microbiology · 2026Review
- Microbiome features associated with persistent intestinal carriages of Escherichia coli ST131 in a Southeast Asian cohort study.Nature communications · 2026Article
- The Human Exposome: Integrating the Environment, Human Health, and Society for the Next 60 years.Environmental science & technology · 2026Review
- Gut microbiome features associated with Bifidobacterium colonization predict personalized probiotic persistence patterns.Nature communications · 2026Article
- Uniform bacterial genetic diversity along the gut.Nature communications · 2026Article
- Microbiome-mediated colonization resistance to and countermeasures of Klebsiella pneumoniae.Nature communications · 2026Article
- Eco-evolutionary responses to plasmid-dependent phage constrain the spread of multidrug-resistance plasmids.The ISME journal · 2026Article
- Differential gut transmission of IncP plasmid clades involving hypervirulent Klebsiella pneumoniae reveals plasmid-specific ecological adaptation.Nature communications · 2025Article
- Quantifying compositional variability in microbial communities with FAVA.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations.Nature microbiology · 2025Article
- The potential of the microbiome as a target for prevention and treatment of carbapenem-resistant Enterobacteriaceae infections.Frontiers in cellular and infection microbiology · 2025Review
- Eosinophilic gastrointestinal diseases with overall gastrointestinal tract causing liver abscess in an older patient: a case report and literature review.BMC geriatrics · 2024Review
- Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes.Nature communications · 2024Article
- Gut community structure as a risk factor for infection inmSystems · 2024Article
- The Effect of Antibiotics on the Eradication of Multidrug-Resistant Organisms in Intestinal Carriers-A Systematic Review with Meta-Analysis.Antibiotics (Basel, Switzerland) · 2024Review
- Quantifying compositional variability in microbial communities with FAVA.bioRxiv : the preprint server for biology · 2024Article
- Article
- Antibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites.Nature communications · 2023Article
- Antimicrobial Resistance in the Global Health Network: Known Unknowns and Challenges for Efficient Responses in the 21st Century.Microorganisms · 2023Review
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Long-term colonization of the gut microbiome by carbapenemase-producing Enterobacteriaceae (CPE) is a growing area of public health concern as it can lead to community transmission and rapid increase in cases of life-threatening CPE infections. Here, leveraging the observation that many subjects are decolonized without interventions within a year, we used longitudinal shotgun metagenomics (up to 12 timepoints) for detailed characterization of ecological and evolutionary dynamics in the gut microbiome of a cohort of CPE-colonized subjects and family members (n = 46; 361 samples). Subjects who underwent decolonization exhibited a distinct ecological shift marked by recovery of microbial diversity, key commensals and anti-inflammatory pathways. In addition, colonization was marked by elevated but unstable Enterobacteriaceae abundances, which exhibited distinct strain-level dynamics for different species (Escherichia coli and Klebsiella pneumoniae). Finally, comparative analysis with whole-genome sequencing data from CPE isolates (n = 159) helped identify substrain variation in key functional genes and the presence of highly similar E. coli and K. pneumoniae strains with variable resistance profiles and plasmid sharing. These results provide an enhanced view into how colonization by multi-drug-resistant bacteria associates with altered gut ecology and can enable transfer of resistance genes, even in the absence of overt infection and antibiotic usage.
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