ArticleRespiratory research2019
Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study.
Article in Respiratory research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT06538441 (Dynamic Pattern of Etiology, Immunoinflammatory Factors and Their Association With Prognosis of Severe Pneumonia), which is not on this map. Cited by 65 papers, 1 of them a synthesis 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.
Dynamic Pattern of Etiology, Immunoinflammatory Factors and Their Association With Prognosis of Severe Pneumonia: a Longitudinal Observational Study
Who cites it
65 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Research Agenda for Precision Medicine in Sepsis and Acute Respiratory Distress Syndrome: An Official American Thoracic Society Research Statement.American journal of respiratory and critical care medicine · 2021Guideline
- 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
- Clinical impact of metagenomic next-generation sequencing on pathogen detection and outcomes in non-immunocompromised patients with severe pneumonia supported by veno-venous extracorporeal membrane oxygenation.BMC infectious diseases · 2026Article
- Microbial lung-to-blood translocation associates with systemic inflammation in severe pneumonia: evidence from paired plasma and lower respiratory tract metagenomics.Intensive care medicine experimental · 2026Article
- Airway microbiome dysbiosis in severe pneumonia: metagenomic evidence of pathogen expansion and commensal depletion.European journal of medical research · 2026Article
- Amplicon-based sequencing as a diagnostic tool for severe pneumonia in the ICU.Scientific reports · 2026Article
- Review
- Rapid Metagenomic Sequencing of Bronchoalveolar Lavage Fluid for Diagnosis of Infection in Patients With Hematologic Malignancies and Pulmonary Complications.CHEST pulmonary · 2025Article
- Article
- Characteristics of symptoms and establishment of a predictive model for PICS in mechanically ventilated patients with severe pneumonia: a retrospective study.European journal of medical research · 2025Article
- Comparison of Three DNA Isolation Methods and Two Sequencing Techniques for the Study of the Human Microbiota.Life (Basel, Switzerland) · 2025Article
- Host DNA depletion assisted metagenomic sequencing of bronchoalveolar lavage fluids for diagnosis of pulmonary tuberculosis.Annals of clinical microbiology and antimicrobials · 2025Article
- Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study.Scientific reports · 2025Article
- Nanopore targeted sequencing identifies pathogens in patients with postoperative endophthalmitis.International journal of ophthalmology · 2025Article
- Emphysematous pancreatitis: Diagnosis, treatment, and prognosis.World journal of gastroenterology · 2024Article
- Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness.Nature communications · 2024Article
- PathoTracker: an online analytical metagenomic platform for Klebsiella pneumoniae feature identification and outbreak alerting.Communications biology · 2024Article
- Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities.Scientific data · 2024Article
- Clinical application of targeted next-generation sequencing in severe pneumonia: a retrospective review.Critical care (London, England) · 2024Article
5 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
15 authors.
Funding
Abstract
backgroundMetagenomic sequencing of respiratory microbial communities for pathogen identification in pneumonia may help overcome the limitations of culture-based methods. We examined the feasibility and clinical validity of rapid-turnaround metagenomics with Nanopore™ sequencing of clinical respiratory specimens.
methodsWe conducted a case-control study of mechanically-ventilated patients with pneumonia (nine culture-positive and five culture-negative) and without pneumonia (eight controls). We collected endotracheal aspirates and applied a microbial DNA enrichment method prior to metagenomic sequencing with the Oxford Nanopore MinION device. For reference, we compared Nanopore results against clinical microbiologic cultures and bacterial 16S rRNA gene sequencing.
resultsHuman DNA depletion enabled in depth sequencing of microbial communities. In culture-positive cases, Nanopore revealed communities with high abundance of the bacterial or fungal species isolated by cultures. In four cases with resistant clinical isolates, Nanopore detected antibiotic resistance genes corresponding to the phenotypic resistance in antibiograms. In culture-negative pneumonia, Nanopore revealed probable bacterial pathogens in 1/5 cases and Candida colonization in 3/5 cases. In controls, Nanopore showed high abundance of oral bacteria in 5/8 subjects, and identified colonizing respiratory pathogens in other subjects. Nanopore and 16S sequencing showed excellent concordance for the most abundant bacterial taxa.
conclusionsWe demonstrated technical feasibility and proof-of-concept clinical validity of Nanopore metagenomics for severe pneumonia diagnosis, with striking concordance with positive microbiologic cultures, and clinically actionable information obtained from sequencing in culture-negative samples. Prospective studies with real-time metagenomics are warranted to examine the impact on antimicrobial decision-making and clinical outcomes.
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.