ArticleThe ISME journal2017
Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses.
Article in The ISME journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 226 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
226 citing papers in PubMed, 449 citations in OpenAlex.
- Trial
- Beyond Co-Occurrence: A Framework for Interpreting Antibiotic-ARG Decoupling in Aquatic Systems and Its Implications for Aquatic Animal Health in a Changing World.Animals : an open access journal from MDPI · 2026Review
- Article
- High-quality phage assembly from metagenomes with PALACE.Nature biotechnology · 2026Article
- Prophage genomics of carbapenemase-producing Klebsiella pneumoniae from animal-derived food sources.Scientific reports · 2026Article
- CRISPR-based gene editing for antimicrobial resistance control in human medicine.Archives of microbiology · 2026Review
- Bacteriophages in the Rhizosphere: Roles in Nutrient Cycling, Bacterial Community Structure, and Animal-Mediated Dispersal.MicrobiologyOpen · 2026Review
- Nested mobile genetic elements mediating antimicrobial resistance genes mobility within and betweeniScience · 2026Article
- The Unified Human Virome Database: A toolkit for expanded human virome analysis.bioRxiv : the preprint server for biology · 2026Article
- On the Low Abundance of Antibiotic Resistance Genes in Bacteriophage Genomes and Their Random Acquisition via Specialized Transduction.Genome biology and evolution · 2026Article
- Klebsiella pneumoniae in the global AMR: resistance mechanisms and genomic adaptation.World journal of microbiology & biotechnology · 2026Review
- Highly Resolved Community Sewage Metagenomics Unveiling Landscape and Transmission Patterns of Antibiotic Resistome in Hong Kong Populations.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genome-wide comparative and taxonomic characterization of prophages in Stenotrophomonas maltophilia.Archives of microbiology · 2026Article
- Article
- Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages.NPJ biofilms and microbiomes · 2026Article
- Article
- Diversity, transfer potential, and transcriptional activity of virus-carried antibiotic resistance genes in global estuaries.iMetaOmics · 2026Article
- Pharmacokinetic/pharmacodynamic relationships and development of resistance of enrofloxacin and cefquinome in combination therapy against Klebsiella pneumoniae in chicks.BMC veterinary research · 2026Article
- Large-scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome.Nature communications · 2026Article
- VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.Nucleic acids research · 2026Article
166 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Antibiotic resistance genes (ARGs) are pervasive in gut microbiota, but it remains unclear how often ARGs are transferred, particularly to pathogens. Traditionally, ARG spread is attributed to horizontal transfer mediated either by DNA transformation, bacterial conjugation or generalized transduction. However, recent viral metagenome (virome) analyses suggest that ARGs are frequently carried by phages, which is inconsistent with the traditional view that phage genomes rarely encode ARGs. Here we used exploratory and conservative bioinformatic strategies found in the literature to detect ARGs in phage genomes, and experimentally assessed a subset of ARG predicted using exploratory thresholds. ARG abundances in 1181 phage genomes were vastly overestimated using exploratory thresholds (421 predicted vs 2 known), due to low similarities and matches to protein unrelated to antibiotic resistance. Consistent with this, four ARGs predicted using exploratory thresholds were experimentally evaluated and failed to confer antibiotic resistance in Escherichia coli. Reanalysis of available human- or mouse-associated viromes for ARGs and their genomic context suggested that bona fide ARG attributed to phages in viromes were previously overestimated. These findings provide guidance for documentation of ARG in viromes, and reassert that ARGs are rarely encoded in phages.
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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.