ArticleGenome research2019
Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to 3 registered trials, which are not on this map. Cited by 393 papers, 6 of them syntheses that pooled it.
What it found
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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.
Pathogen Detection in HIV-infected Children and Adolescents With Non-malarial Febrile Illnesses Using Metagenomic Next-generation Sequencing Approach in Uganda
Investigation of the Delve Detect Cerebrospinal Fluid (CSF) Metagenomic Next-generation Sequencing (mNGS) Test When Used for the Initial Diagnostic Workup of Patients With Suspected Central Nervous System (CNS) Infection
h Can Provide the Detection Results of Pathogen Type and Resistant Gene. This Study is a Prospective Multi Centers Study to Explore Using the New Diagnostic Tool of " RPIP " and the Different Detection Methods of Next Generation Sequencing and Multiplex PC R in Patients With Pneumonia in ICU. Further Compare the Difference of Pathogen Identification and Clinical Impact by Different Diagnostic Methods.
Who cites it
393 citing papers in PubMed, 6 syntheses or guidelines pooled it, 566 citations in OpenAlex.
- Diagnostic Performance of Metagenomic Next-Generation Sequencing (mNGS) and Culture in Infected Pancreatic Necrosis: A Systematic Review and Meta-Analysis.Digestive diseases and sciences · 2026Pooled it
- Metagenomic next-generation sequencing (mNGS) versus tissue culture technique (TCT) in diagnosis of spinal infection: a systematic review and meta-analysis.Scientific reports · 2025Pooled it
- Metagenomic Next-Generation Sequencing for the Diagnosis of Infectious Uveitis: A Comprehensive Systematic Review.Viruses · 2025Pooled it
- Exploring the clinical and diagnostic value of metagenomic next-generation sequencing for urinary tract infection: a systematic review and meta-analysis.BMC infectious diseases · 2024Pooled it
- Clinical and diagnostic values of metagenomic next-generation sequencing for infection in hematology patients: a systematic review and meta-analysis.BMC infectious diseases · 2024Pooled 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
- Rapid diagnosis ofExperimental and therapeutic medicine · 2026Article
- First case of neonatal bloodstream infection caused byExperimental and therapeutic medicine · 2026Article
- Metagenomic next-generation sequencing in the diagnosis of viral encephalitis.World journal of virology · 2026Review
- Comparative evaluation of probe-capture and conventional metagenomic sequencing across multiple clinical sample types, with analysis of paired bronchoalveolar lavage fluid and blood samples.Microbiology spectrum · 2026Article
- Clinical impact of metagenomic next-generation sequencing for pathogen identification and guided therapy in pediatric intensive care unit patients with severe pulmonary infections.Microbiology spectrum · 2026Article
- Clinical utility of metagenomic next-generation sequencing in precision diagnosis of infectious diseases: a retrospective study based on bronchoalveolar lavage fluid, blood, and cerebrospinal fluid.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Occupational exposure to freshwater crustaceans as a route of paragonimiasis presenting with eosinophilic pleural effusion misdiagnosed as tuberculous pleurisy: A case report and literature review.Experimental and therapeutic medicine · 2026Article
- Postoperative Nocardia cyriacigeorgica infection after glioblastoma resection: correlating metagenomic next-generation sequencing with conventional microbiology.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Validation of an integrated metagenomic pipeline combining optimized wet-lab processing and tiered reporting for CSF pathogen detection.Microbiology spectrum · 2026Article
- Metagenomic next-generation sequencing for comprehensive pathogen detection in intraocular infection.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy.Microbiology spectrum · 2026Article
- Review
- Pathogen detection in central nervous system infections: moving metagenomic sequencing closer to clinical practice.BMC infectious diseases · 2026Article
- Genome-guided generative adversarial learning enables nanopore adaptive sequencing.Nature communications · 2026Article
333 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
18 authors at 6 institutions in 1 country.
Funding
Abstract
Metagenomic next-generation sequencing (mNGS) for pan-pathogen detection has been successfully tested in proof-of-concept case studies in patients with acute illness of unknown etiology but to date has been largely confined to research settings. Here, we developed and validated a clinical mNGS assay for diagnosis of infectious causes of meningitis and encephalitis from cerebrospinal fluid (CSF) in a licensed microbiology laboratory. A customized bioinformatics pipeline, SURPI+, was developed to rapidly analyze mNGS data, generate an automated summary of detected pathogens, and provide a graphical user interface for evaluating and interpreting results. We established quality metrics, threshold values, and limits of detection of 0.2-313 genomic copies or colony forming units per milliliter for each representative organism type. Gross hemolysis and excess host nucleic acid reduced assay sensitivity; however, spiked phages used as internal controls were reliable indicators of sensitivity loss. Diagnostic test accuracy was evaluated by blinded mNGS testing of 95 patient samples, revealing 73% sensitivity and 99% specificity compared to original clinical test results, and 81% positive percent agreement and 99% negative percent agreement after discrepancy analysis. Subsequent mNGS challenge testing of 20 positive CSF samples prospectively collected from a cohort of pediatric patients hospitalized with meningitis, encephalitis, and/or myelitis showed 92% sensitivity and 96% specificity relative to conventional microbiological testing of CSF in identifying the causative pathogen. These results demonstrate the analytic performance of a laboratory-validated mNGS assay for pan-pathogen detection, to be used clinically for diagnosis of neurological infections from CSF.
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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.