ArticleNature biotechnology2019
Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection.
Article in Nature biotechnology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT04864873 (An External Evaluation of a Metagenomic Next Generation Sequencing Workflow for Infection Diagnosis Using Oxford Nanopore Sequencing.), which is not on this map. Cited by 385 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
An External Evaluation of a Metagenomic Next Generation Sequencing Workflow for Infection Diagnosis Using Oxford Nanopore Sequencing.
Who cites it
385 citing papers in PubMed, 2 syntheses or guidelines pooled it, 706 citations in OpenAlex.
- The added value of metagenomic next-generation sequencing in central nervous system infections: a systematic review of case reports.Infection · 2025Pooled it
- Diagnostic performance of metagenomic next-generation sequencing for the detection of pathogens in cerebrospinal fluid in pediatric patients with central nervous system infection: a systematic review and meta-analysis.BMC infectious diseases · 2024Pooled it
- Cystic Fibrosis Microbiome-directed Antibiotic Therapy Trial in Exacerbations Results Stratified (CFMATTERS): results of a multicentre randomised controlled trial.The European respiratory journal · 2025Trial
- INHALE WP3, a multicentre, open-label, pragmatic randomised controlled trial assessing the impact of rapid, ICU-based, syndromic PCR, versus standard-of-care on antibiotic stewardship and clinical outcomes in hospital-acquired and ventilator-associated pneumonia.Intensive care medicine · 2025Trial
- An NGS-assisted diagnostic workflow for culture-independent detection of bloodstream pathogens and prediction of antimicrobial resistances in sepsis.Frontiers in cellular and infection microbiology · 2025Trial
- Trial
- Metagenomic-driven predictive biosafety and contamination traceability in stem cell manufacturing: Translating outbreak genomics into regenerative medicine.Regenerative therapy · 2026Review
- The role of the respiratory microbiome in acute and chronic respiratory diseases.Nature reviews. Microbiology · 2026Review
- Amplification-Free Nanopore Sequencing for Herpesvirus DNA Detection in Intraocular Fluids.Ophthalmology science · 2026Article
- Bronchoalveolar Lavage Metagenomic Sequencing in the Early Post-Lung Transplantation Period: A Pilot Comparison with Microbiologic Culture.medRxiv : the preprint server for health sciences · 2026Article
- Microbiome Profiling Reveals Prognostic Heterogeneity inmedRxiv : the preprint server for health sciences · 2026Article
- The lung microbiome in childhood-onset severe neuromuscular disease with respiratory insufficiency: rationale, current evidence, and opportunities for oxford nanopore long-read sequencing.Molecular and cellular pediatrics · 2026Review
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 2026Review
- Bacterial metagenomic analysis of patients with chronic kidney disease undergoing hemodialysis based on 16S rDNA amplicon sequencing.Biomedical reports · 2026Article
- Metagenomics for antimicrobial resistance: from resistome surveillance to mechanistic inference.Journal of bacteriology · 2026Review
- Optimizing culture-free approaches to recover high-qualityMicrobial genomics · 2026Article
- Rapid microbiological diagnostics for sepsis in critical care: integrating technological advances with antimicrobial stewardship.Acute and critical care · 2026Article
- A lab-on-a-silicon-chip platform for all-electrical antibiotic susceptibility tests with a sample-to-results time within 20 minutes.Science advances · 2026Article
- [Application of metagenomic next-generation sequencing in the pathogen spectrum analysis of suspected infections in neonatal blood and cerebrospinal fluid].Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics · 2026Article
- Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy.Microbiology spectrum · 2026Article
325 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
13 authors at 4 institutions in 1 country.
Funding
Abstract
The gold standard for clinical diagnosis of bacterial lower respiratory infections (LRIs) is culture, which has poor sensitivity and is too slow to guide early, targeted antimicrobial therapy. Metagenomic sequencing could identify LRI pathogens much faster than culture, but methods are needed to remove the large amount of human DNA present in these samples for this approach to be feasible. We developed a metagenomics method for bacterial LRI diagnosis that features efficient saponin-based host DNA depletion and nanopore sequencing. Our pilot method was tested on 40 samples, then optimized and tested on a further 41 samples. Our optimized method (6 h from sample to result) was 96.6% sensitive and 41.7% specific for pathogen detection compared with culture and we could accurately detect antibiotic resistance genes. After confirmatory quantitative PCR and pathobiont-specific gene analyses, specificity and sensitivity increased to 100%. Nanopore metagenomics can rapidly and accurately characterize bacterial LRIs and might contribute to a reduction in broad-spectrum antibiotic use.
Indexed as
Identifiers
What OpenQuestion holds
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.