ArticleFrontiers in cellular and infection microbiology2021
Prospective Evaluation of a Rapid Clinical Metagenomics Test for Bacterial Pneumonia.
Article in Frontiers in cellular and infection microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it, 32 citations in OpenAlex.
- Nanopore sequencing for microbiological diagnosis of bacterial pneumonia: A systematic review and meta-analysis.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Pooled it
- Lung Microbiome Diversity, Infection Dynamics, and Microbe-Mediated Cross-Protection.MicrobiologyOpen · 2026Review
- Spinal Tuberculosis Diagnosed by Metagenomics Capture (MetaCAP) in a Patient Undergoing Maintenance Hemodialysis: A Case Report.The American journal of case reports · 2026Article
- Metagenomic and Targeted Next-Generation Sequencing in Infectious Disease Diagnostics: Current Applications, Challenges, and Future Perspectives.Diagnostics (Basel, Switzerland) · 2026Review
- Diagnostic performance and clinical utility of metagenomic next-generation sequencing in suspected pulmonary infections: a comparative study stratified by immune status.Frontiers in cellular and infection microbiology · 2026Article
- Multiple IntracranialInfection and drug resistance · 2026Article
- Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens.Gut pathogens · 2025Article
- The application value and challenges of metagenomic next-generation sequencing in the diagnosis of periprosthetic joint infection after arthroplasty.Frontiers in medicine · 2025Review
- Application of metagenomic next-generation sequencing in pathogen detection of lung infections.Frontiers in cellular and infection microbiology · 2025Article
- Applying nanopore sequencing in the etiological diagnosis of bloodstream infection.Frontiers in microbiology · 2025Review
- A Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples.Diagnostics (Basel, Switzerland) · 2024Article
- Clinical applications of metagenomics next-generation sequencing in infectious diseases.Journal of Zhejiang University. Science. B · 2024Review
- Review
- Routine Metagenomics Service for ICU Patients with Respiratory Infection.American journal of respiratory and critical care medicine · 2024Article
- Application of metagenomic next-generation sequencing in the diagnosis of infectious diseases.Frontiers in cellular and infection microbiology · 2024Review
- Application of Nanopore Sequencing in the Diagnosis and Treatment of Pulmonary Infections.Molecular diagnosis & therapy · 2023Review
- Clinical evaluation of metagenomic next-generation sequencing in unbiased pathogen diagnosis of urinary tract infection.Journal of translational medicine · 2023Article
- Lung microbiome on admission in critically ill patients with acute bacterial and viral pneumonia.Scientific reports · 2023Article
- Clinical metagenomics-challenges and future prospects.Frontiers in microbiology · 2023Review
- Early appropriate diagnostics and treatment of MDR Gram-negative infections.JAC-antimicrobial resistance · 2022Review
Corrections and comments
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Authors and funding
15 authors at 5 institutions in 2 countries.
Funding
Abstract
Background: The diagnosis of bacterial pathogens in lower respiratory tract infections (LRI) using conventional culture methods remains challenging and time-consuming. Objectives: To evaluate the clinical performance of a rapid nanopore-sequencing based metagenomics test for diagnosis of bacterial pathogens in common LRIs through a large-scale prospective study. Methods: We enrolled 292 hospitalized patients suspected to have LRIs between November 2018 and June 2019 in a single-center, prospective cohort study. Rapid clinical metagenomics test was performed on-site, and the results were compared with those of routine microbiology tests. Results: 171 bronchoalveolar lavage fluid (BAL) and 121 sputum samples were collected from patients with six kinds of LRIs. The turnaround time (from sample registration to result) for the rapid metagenomics test was 6.4 ± 1.4 hours, compared to 94.8 ± 34.9 hours for routine culture. Compared with culture and real-time PCR validation tests, rapid metagenomics achieved 96.6% sensitivity and 88.0% specificity and identified pathogens in 63 out of 161 (39.1%) culture-negative samples. Correlation between enriched anaerobes and lung abscess was observed by Gene Set Enrichment Analysis. Moreover, 38 anaerobic species failed in culture was identified by metagenomics sequencing. The hypothetical impact of metagenomics test proposed antibiotic de-escalation in 34 patients compared to 1 using routine culture. Conclusions: Rapid clinical metagenomics test improved pathogen detection yield in the diagnosis of LRI. Empirical antimicrobial therapy could be de-escalated if rapid metagenomics test results were hypothetically applied to clinical management.
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Registered trials
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