ArticleNature communications2023
Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed, 1 synthesis or guideline pooled it, 52 citations in OpenAlex.
- Guts of healthy humans, livestock, and pets harbor critical-priority and high-risk Escherichia coli clones.Epidemiology and health · 2025Pooled it
- A network dynamical simulation model for the study of antibiotic resistance in microbial communities.Gut microbes · 2026Article
- Pre-existing β-lactamase gene diversity is associated with lower risk of ESBL-producing Enterobacterales colonization in patients exposed to ceftriaxone.Gut microbes · 2026Article
- Exploring Gut Microbiota Composition and Occurrence of Selected Antimicrobial Resistance Genes in Domestic Pigs and Urban and Sylvatic Wild Boars from Sicily.Animals : an open access journal from MDPI · 2026Article
- Gene Exchange Mechanisms in Natural and Engineered Probiotics Within the Human Gut Implications for Antibiotic Resistance and Metabolic Modulation.Probiotics and antimicrobial proteins · 2026Review
- Farming practices exert selection pressures on the resistome of natural populations of house mice.Nature communications · 2026Article
- Profiling the gut resistome to unlock antimicrobial resistance biology and inform clinical risk.Nature communications · 2026Review
- Antibiotic-Driven Gut Microbiome Dysbiosis: Resistome Dynamics, Metabolic Disruption, and Paths to Restoration.Antibiotics (Basel, Switzerland) · 2026Review
- Long-read metagenomics and methylation-based binning support the discovery of antibiotic resistance gene-host associations in complex communities.Genome biology · 2026Article
- Modelling the role of the microbiome in antimicrobial resistance across scales.Nature microbiology · 2026Review
- Antibiotic-induced gut microbiome dysbiosis: risks and strategies for mitigation.The EMBO journal · 2026Review
- The gut commensal Bacteroides thetaiotaomicron harbors prevalent class A and D β-lactamases with cross-taxa dissemination potential.NPJ biofilms and microbiomes · 2026Article
- Metabolic reprogramming of the infant gut by bifidobacteria-based probiotics drives exclusion of antibiotic-resistant pathobionts.Cell reports. Medicine · 2026Article
- Review
- Highly Resolved Community Sewage Metagenomics Unveiling Landscape and Transmission Patterns of Antibiotic Resistome in Hong Kong Populations.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Assessing the Ecological Roles of Resistomes within Microbial Communities in Antibiotic-contaminated Ecosystems.Microbial ecology · 2026Review
- Lifestyle associates with unique resistome and microbiome signatures in children.BMC microbiology · 2026Article
- Molecular Insights into Carbapenem Resistance inInternational journal of molecular sciences · 2026Review
- Global landscape of antibiotic resistance genes in the human gut microbiome metagenome-assembled genomes.BMC microbiology · 2025Article
- Use of proximity ligation shotgun metagenomics to investigate the dynamics of plasmids and bacteriophages in the gut microbiome following fecal microbiota transplantation.Gut microbes · 2025Article
Corrections and comments
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Authors and funding
15 authors at 6 institutions in 5 countries.
Funding
Abstract
The acquisition of antimicrobial resistance (AR) genes has rendered important pathogens nearly or fully unresponsive to antibiotics. It has been suggested that pathogens acquire AR traits from the gut microbiota, which collectively serve as a global reservoir for AR genes conferring resistance to all classes of antibiotics. However, only a subset of AR genes confers resistance to clinically relevant antibiotics, and, although these AR gene profiles are well-characterized for common pathogens, less is known about their taxonomic associations and transfer potential within diverse members of the gut microbiota. We examined a collection of 14,850 human metagenomes and 1666 environmental metagenomes from 33 countries, in addition to nearly 600,000 isolate genomes, to gain insight into the global prevalence and taxonomic range of clinically relevant AR genes. We find that several of the most concerning AR genes, such as those encoding the cephalosporinase CTX-M and carbapenemases KPC, IMP, NDM, and VIM, remain taxonomically restricted to Proteobacteria. Even cfiA, the most common carbapenemase gene within the human gut microbiome, remains tightly restricted to Bacteroides, despite being found on a mobilizable plasmid. We confirmed these findings in gut microbiome samples from India, Honduras, Pakistan, and Vietnam, using a high-sensitivity single-cell fusion PCR approach. Focusing on a set of genes encoding carbapenemases and cephalosporinases, thus far restricted to Bacteroides species, we find that few mutations are required for efficacy in a different phylum, raising the question of why these genes have not spread more widely. Overall, these data suggest that globally prevalent, clinically relevant AR genes have not yet established themselves across diverse commensal gut microbiota.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.