ArticleNature communications2025
Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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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
19 citing papers in PubMed.
- Exploring the Oral Resistome: From Metagenomics to Precision Oral Health.Microorganisms · 2026Review
- Computational Genomics for Resistome Characterization: Current Advancements and Future Challenges Under a One Health Perspective.Antibiotics (Basel, Switzerland) · 2026Review
- Urban green roofs host intrinsic resistomes shaped by management but not dominated by pathogenic resistance.BMC microbiology · 2026Article
- A genomic framework for tracking antibiotic resistance genes: global dissemination ofAntimicrobial agents and chemotherapy · 2026Article
- Application of antibiotics for the selective isolation of previously uncultured species from activated sludge.Microbiology spectrum · 2026Article
- Profiling the gut resistome to unlock antimicrobial resistance biology and inform clinical risk.Nature communications · 2026Review
- Gut Microbiomes of Rainbow Trout and Atlantic Salmon: Nutritional Modulation, Mucosal Immunity, and Resistome Risk.Biology · 2026Review
- Comparison of Environmental Microbiomes, Resistomes and Plasmidomes from a Human Tertiary Hospital and Companion Animal Veterinary Hospital in London, UK.Antibiotics (Basel, Switzerland) · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Microbiomics: Novel Biomarkers of Colorectal Cancer Diagnosis and Prognosis.Diagnostics (Basel, Switzerland) · 2026Review
- Article
- HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.Nucleic acids research · 2026Article
- The transformative impact of ultra-rapid nanopore sequencing in precision medicine.Frontiers in immunology · 2026Review
- Targeted probe capture metagenomics-enabled surveillance of multidrug-resistant organisms and antimicrobial resistance genes in post-handwashing areas of public washrooms.Environmental microbiome · 2025Article
- Mapping the underlying drivers of resistome risk across diverse environments.Research square · 2025Article
- The Gut Microbiome and Colistin Resistance: A Hidden Driver of Antimicrobial Failure.International journal of molecular sciences · 2025Review
- Versatile wastewater monitoring of pathogens and antimicrobial resistance enabled by metatranscriptomics and long-read metagenomics.Research square · 2025Article
- Overcoming challenges in metagenomic AMR surveillance with nanopore sequencing: a case study on fluoroquinolone resistance.Frontiers in microbiology · 2025Article
- Detecting antibiotic resistance: classical, molecular, advanced bioengineering, and AI-enhanced approaches.Frontiers in microbiology · 2025Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Environmental surveillance of antibiotic resistance genes (ARGs) is critical for understanding and mitigating the spread of antimicrobial resistance. Current short-read-based ARG profiling methods are limited in their ability to provide detailed host information, which is indispensable for tracking the transmission and assessing the risk of ARGs. Here, we present Argo, a novel approach that leverages long-read overlapping to rapidly identify and quantify ARGs in complex environmental metagenomes at the species level. Argo significantly enhances the resolution of ARG detection by assigning taxonomic labels collectively to clusters of reads, rather than to individual reads. By benchmarking the performance in host identification using simulation, we confirm the advantage of long-read overlapping over existing metagenomic profiling strategies in terms of accuracy. Using sequenced mock communities with varying quality scores and read lengths, along with a global fecal dataset comprising 329 human and non-human primate samples, we demonstrate Argo's capability to deliver comprehensive and species-resolved ARG profiles in real settings.
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