ArticleJournal of molecular neuroscience : MN2020
Reduction of Human DNA Contamination in Clinical Cerebrospinal Fluid Specimens Improves the Sensitivity of Metagenomic Next-Generation Sequencing.
Article in Journal of molecular neuroscience : MN, 2020. 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 40 papers, 3 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.
An External Evaluation of a Metagenomic Next Generation Sequencing Workflow for Infection Diagnosis Using Oxford Nanopore Sequencing.
Who cites it
40 citing papers in PubMed, 3 syntheses or guidelines pooled it, 54 citations in OpenAlex.
- Diagnostic accuracy of metagenomic next-generation sequencing in pulmonary tuberculosis: a systematic review and meta-analysis.Systematic reviews · 2024Pooled it
- An umbrella review of the diagnostic value of next-generation sequencing in infectious diseases.International journal of clinical pharmacy · 2024Pooled it
- Metagenomic next generation sequencing for the diagnosis of tuberculosis meningitis: A systematic review and meta-analysis.PloS one · 2020Pooled it
- Harnessing next-generation microbial diagnostics to optimize infection management in immunocompromised hosts.Current opinion in infectious diseases · 2026Review
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- Molecular insights into antimicrobial resistance in human bacterial pathogens: mechanisms, resistance genes, and translational diagnostic applications.Frontiers in microbiology · 2026Review
- Clinical features ofFrontiers in cellular and infection microbiology · 2026Article
- Application of targeted metagenomic next-generation sequencing in pneumonia patients.Microbiology spectrum · 2025Article
- Article
- Diagnostic Significance of Metagenomic Next-Generation Sequencing in Immunocompromised Patients With Suspected Pulmonary Infection.Immunology · 2025Article
- The application value and challenges of metagenomic next-generation sequencing in the diagnosis of periprosthetic joint infection after arthroplasty.Frontiers in medicine · 2025Review
- Exploring vaginal microbiome: from traditional methods to metagenomic next-generation sequencing-a systematic review.Frontiers in microbiology · 2025Review
- Enhancing bloodstream infection diagnostics: a novel filtration and targeted next-generation sequencing approach for precise pathogen identification.Frontiers in microbiology · 2025Article
- Article
- Metagenomic next-generation sequencing of cell-free DNA for the identification of viruses causing central nervous system infections.Microbiology spectrum · 2024Article
- Application of metagenomic next-generation sequencing and targeted metagenomic next-generation sequencing in diagnosing pulmonary infections in immunocompetent and immunocompromised patients.Frontiers in cellular and infection microbiology · 2024Article
- The value of metagenomic next-generation sequencing with different nucleic acid extracting methods of cell-free DNA or whole-cell DNA in the diagnosis of non-neutropenic pulmonary aspergillosis.Frontiers in cellular and infection microbiology · 2024Article
- Tuberculous meningitis diagnosis and treatment: classic approaches and high-throughput pathways.Frontiers in immunology · 2024Review
- Combination of metagenomic next-generation sequencing and conventional tests unraveled pathogen profiles in infected patients undergoing allogeneic hematopoietic stem cell transplantation in Jilin Province of China.Frontiers in cellular and infection microbiology · 2024Article
- Diagnostic performance of metagenomic next-generation sequencing for Pneumocystis jirovecii pneumonia.BMC infectious diseases · 2023Review
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Metagenomics next-generation sequencing (mNGS) is increasingly available for the detection of obscure infectious diseases of the central nervous system. However, human DNA contamination from elevated white cells, one of the characteristic cerebrospinal fluid (CSF) features in meningitis patients, greatly reduces the sensitivity of mNGS in the pathogen detection. Currently, effective approaches to selectively reduce host DNA contamination from clinical CSF samples are still lacking. In this study, a total of 20 meningitis patients were enrolled, including 10 definitively diagnosed tuberculous meningitis (TBM) and 10 definite cryptococcal meningitis (CM) cases. To evaluate the effect of reduced human DNA in the sensitivity of mNGS detection, three specimen-processing protocols were performed: (i) To remove human DNA, saponin, a nonionic surfactant, was used to selectively lyse white cells in CSF followed by DNase treatment prior to the extraction of DNA; (ii) to reduce host DNA, CSF was centrifuged to remove human cells, and the supernatant was collected for DNA extraction; and (iii) DNA extraction from the unprocessed specimens was set as the control. We found that saponin processing significantly elevated the NGS unique reads for Cryptococcus (P < 0.01) compared with the control but had no effects for Mycobacterium tuberculosis (P > 0.05). However, detection of centrifuged supernatants improved the NGS unique reads for both TBM and CM compared with controls (P < 0.01). Our results demonstrate that the use of mNGS of centrifuged supernatants from clinical CSF samples in patients with TBM and CM is a simple and effective method to improve the sensitivity of pathogen detection.
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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.