ArticleJournal of clinical microbiology2016
Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing.
Article in Journal of clinical microbiology, 2016. 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 156 papers, 1 of them a synthesis 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
156 citing papers in PubMed, 1 synthesis or guideline pooled it, 250 citations in OpenAlex.
- Clinical values of metagenomic next-generation sequencing in patients with severe pneumonia: a systematic review and meta-analysis.Frontiers in cellular and infection microbiology · 2023Pooled it
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 2026Review
- Evaluation of amplicon-based nanopore sequencing for foot-and-mouth disease viruses in clinical and environmental samples.Microbiology spectrum · 2026Article
- Nucleosome-targeted host DNA depletion enables automated plasma metagenomic sequencing for sensitive detection of bloodstream pathogens.Journal of translational medicine · 2026Article
- Rapid and modular workflows for same-day sequencing-based detection of bloodstream infections and antimicrobial resistance determinants using culture-enriched samples.Microbiology spectrum · 2026Article
- Optimisation and validation of capture mNGS for predicting antimicrobial resistance.EBioMedicine · 2026Article
- Genome-guided generative adversarial learning enables nanopore adaptive sequencing.Nature communications · 2026Article
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- Effects of aquaculture practices onApplied and environmental microbiology · 2026Article
- Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies.BMC microbiology · 2026Article
- Sequenoscope: a modular tool for nanopore adaptive sequencing analytics and beyond.Access microbiology · 2026Article
- Development and optimization of host DNA depletion in blood cultures using a saponin and salt-activated nuclease-based method.Frontiers in microbiology · 2026Article
- Rapid Metagenomic Sequencing of Bronchoalveolar Lavage Fluid for Diagnosis of Infection in Patients With Hematologic Malignancies and Pulmonary Complications.CHEST pulmonary · 2025Article
- High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion.NPJ biofilms and microbiomes · 2025Article
- Clinical utility of metagenomic next-generation sequencing (mNGS) and a novel PCR-based point-of-care testing (POCT) for pathogen detection in pulmonary infections: a retrospective study.BMC infectious diseases · 2025Article
- Use of the CHM13-T2T genome improves metagenomic analysis by minimizing host DNA contamination.mSystems · 2025Article
- Typing ofMicroorganisms · 2025Article
- China Expert consensus on the application of metagenomic next-generation sequencing for the etiological diagnosis of infections in hematological disorders (2024).Blood science (Baltimore, Md.) · 2025Article
- Integrative study of pulmonary microbiome and clinical diagnosis in pulmonary tuberculosis patients.Microbiology spectrum · 2025Article
- Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.NPJ biofilms and microbiomes · 2025Article
96 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
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS) technology has shown promise for the detection of human pathogens from clinical samples. However, one of the major obstacles to the use of NGS in diagnostic microbiology is the low ratio of pathogen DNA to human DNA in most clinical specimens. In this study, we aimed to develop a specimen-processing protocol to remove human DNA and enrich specimens for bacterial and viral DNA for shotgun metagenomic sequencing. Cerebrospinal fluid (CSF) and nasopharyngeal aspirate (NPA) specimens, spiked with control bacterial and viral pathogens, were processed using either a commercially available kit (MolYsis) or various detergents followed by DNase prior to the extraction of DNA. Relative quantities of human DNA and pathogen DNA were determined by real-time PCR. The MolYsis kit did not improve the pathogen-to-human DNA ratio, but significant reductions (>95%;P< 0.001) in human DNA with minimal effect on pathogen DNA were achieved in samples that were treated with 0.025% saponin, a nonionic surfactant. Specimen preprocessing significantly decreased NGS reads mapped to the human genome (P< 0.05) and improved the sensitivity of pathogen detection (P< 0.01), with a 20- to 650-fold increase in the ratio of microbial reads to human reads. Preprocessing also permitted the detection of pathogens that were undetectable in the unprocessed samples. Our results demonstrate a simple method for the reduction of background human DNA for metagenomic detection for a broad range of pathogens in clinical samples.
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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.