ArticleMicrobiome2019
Identification and reconstruction of novel antibiotic resistance genes from metagenomes.
Article in Microbiome, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers, 1 of them a synthesis that pooled it.
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Who cites it
71 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic review of human gut resistome studies revealed variable definitions and approaches.Gut microbes · 2020Pooled it
- AResKGLM: a graph-grounded language-model framework for interpretable multi-hop antimicrobial resistance reasoning.Briefings in bioinformatics · 2026Article
- Evolution, Mechanisms, and Therapeutic Implications of Mobile Tetracycline Destructases.BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Molecular bioindicators for assessing environmental impacts of emerging contaminants.Fundamental research · 2026Review
- Conserved protein sequence-structure signatures identify antibiotic resistance genes from the human microbiome.Microbiome · 2026Article
- Long-read metagenomics and methylation-based binning support the discovery of antibiotic resistance gene-host associations in complex communities.Genome biology · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Effects of different cultivation methods on microbial community structure of lettuce based on metagenomic analysis.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- resLens: genomic language models to enhance antibiotic resistance gene detection.npj antimicrobials and resistance · 2026Article
- Artificial intelligence for antimicrobial resistance: advancing reproducibility, interpretability, and clinical deployment.Briefings in bioinformatics · 2026Review
- A Genomic Catalog of Migratory Microbiomes from Wild Birds across China's Habitats.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Antimicrobial resistance varies with warming in active layer soil and permafrost.Scientific reports · 2026Article
- Integrating AMR surveillance into wastewater monitoring systems in 2025: a position on the implementation of Article 17 of the Urban Wastewater Treatment Directive (UWWTD).Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2026Article
- Comparative Evaluation of Sequencing Technologies for Detecting Antimicrobial Resistance in Bloodstream Infections.Antibiotics (Basel, Switzerland) · 2025Review
- Comparative assessment of annotation tools reveals critical antimicrobial resistance knowledge gaps in Klebsiella pneumoniae.Scientific reports · 2025Article
- Enrichment of Antibiotic Resistance Genes on Plastic Waste in Aquatic Ecosystems, Aquatic Animals, and Fishery Products.Antibiotics (Basel, Switzerland) · 2025Review
- Assessing the Antibiotic Resistance in Food Lactic Acid Bacteria: Risks in the Era of Widespread Probiotic Use.Food science & nutrition · 2025Review
- A Novel Metallo-β-Lactamase AMM-1 From Alteromonas mangrovi Reveals a Cryptic Environmental Reservoir of Carbapenem Resistance.Microbial biotechnology · 2025Article
- Global health risks lurking in livestock resistome.Science advances · 2025Article
- Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEnvironmental and commensal bacteria maintain a diverse and largely unknown collection of antibiotic resistance genes (ARGs) that, over time, may be mobilized and transferred to pathogens. Metagenomics enables cultivation-independent characterization of bacterial communities but the resulting data is noisy and highly fragmented, severely hampering the identification of previously undescribed ARGs. We have therefore developed fARGene, a method for identification and reconstruction of ARGs directly from shotgun metagenomic data.
resultsfARGene uses optimized gene models and can therefore with high accuracy identify previously uncharacterized resistance genes, even if their sequence similarity to known ARGs is low. By performing the analysis directly on the metagenomic fragments, fARGene also circumvents the need for a high-quality assembly. To demonstrate the applicability of fARGene, we reconstructed β-lactamases from five billion metagenomic reads, resulting in 221 ARGs, of which 58 were previously not reported. Based on 38 ARGs reconstructed by fARGene, experimental verification showed that 81% provided a resistance phenotype in Escherichia coli. Compared to other methods for detecting ARGs in metagenomic data, fARGene has superior sensitivity and the ability to reconstruct previously unknown genes directly from the sequence reads.
conclusionsWe conclude that fARGene provides an efficient and reliable way to explore the unknown resistome in bacterial communities. The method is applicable to any type of ARGs and is freely available via GitHub under the MIT license.
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