ArticleNature microbiology2023
Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains.
Article in Nature microbiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed, 1 synthesis or guideline pooled it, 28 citations in OpenAlex.
- A systematic review of antimicrobial therapy in children with tracheostomies.Pediatric pulmonology · 2024Pooled it
- Predicting resistance evolution to guide antibiotic development.Nature reviews. Microbiology · 2026Review
- Firewalled synthetic commensal blocks horizontal gene transfer in the gut.bioRxiv : the preprint server for biology · 2026Article
- Exploring the Oral Resistome: From Metagenomics to Precision Oral Health.Microorganisms · 2026Review
- Profiling the gut resistome to unlock antimicrobial resistance biology and inform clinical risk.Nature communications · 2026Review
- Organosulfur compounds as dual-action agents: a critical review of antimicrobial and immunomodulatory potentials, and translational barriers.Frontiers in pharmacology · 2026Review
- Fosfomycin Resistance: An Update on the Anthropogenic Impact Through Agriculture.Pathogens (Basel, Switzerland) · 2025Review
- Article
- Combating Antimicrobial Resistance: Role of Key Stakeholders with Focus on the Pharmaceutical Sector.Pharmaceutical medicine · 2025Review
- Synthetic and Functional Engineering of Bacteriophages: Approaches for Tailored Bactericidal, Diagnostic, and Delivery Platforms.Molecules (Basel, Switzerland) · 2025Review
- Fighting Antibiotic Resistance: Insights Into Human Barriers and New Opportunities: Antibiotic Resistance Constantly Rises With the Development of Human Activities. We discuss Barriers and Opportunities to Get It Under Control.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Exploring the principles behind antibiotics with limited resistance.Nature communications · 2025Article
- ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro.Nature microbiology · 2025Article
- Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance.Nature communications · 2024Article
- Systematic interrogation of CRISPR antimicrobials in Klebsiella pneumoniae reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity.Nucleic acids research · 2024Article
- Intraspecific variation in antibiotic resistance potential withinMicrobiology spectrum · 2024Article
- Phage-layer interferometry: a companion diagnostic for phage therapy and a bacterial testing platform.Scientific reports · 2024Article
- ContScout: sensitive detection and removal of contamination from annotated genomes.Nature communications · 2024Article
- Prospects and Challenges of Bacteriophage Substitution for Antibiotics in Livestock and Poultry Production.Biology · 2024Review
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
30 authors at 6 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Functional metagenomics is a powerful experimental tool to identify antibiotic resistance genes (ARGs) in the environment, but the range of suitable host bacterial species is limited. This limitation affects both the scope of the identified ARGs and the interpretation of their clinical relevance. Here we present a functional metagenomics pipeline called Reprogrammed Bacteriophage Particle Assisted Multi-species Functional Metagenomics (DEEPMINE). This approach combines and improves the use of T7 bacteriophage with exchanged tail fibres and targeted mutagenesis to expand phage host-specificity and efficiency for functional metagenomics. These modified phage particles were used to introduce large metagenomic plasmid libraries into clinically relevant bacterial pathogens. By screening for ARGs in soil and gut microbiomes and clinical genomes against 13 antibiotics, we demonstrate that this approach substantially expands the list of identified ARGs. Many ARGs have species-specific effects on resistance; they provide a high level of resistance in one bacterial species but yield very limited resistance in a related species. Finally, we identified mobile ARGs against antibiotics that are currently under clinical development or have recently been approved. Overall, DEEPMINE expands the functional metagenomics toolbox for studying microbial communities.
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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.