ArticleMolecular diagnosis & therapy2025
Optimization of Metagenomic Next-Generation Sequencing Workflow with a Novel Host Depletion Method for Enhanced Pathogen Detection.
Article in Molecular diagnosis & therapy, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Oxford Nanopore Sequencing, a Promising Technology for Precision Diagnostics in Intensive Care Units: A Narrative Review.Biomedicines · 2026Review
- Harnessing next-generation microbial diagnostics to optimize infection management in immunocompromised hosts.Current opinion in infectious diseases · 2026Review
- Nucleosome-targeted host DNA depletion enables automated plasma metagenomic sequencing for sensitive detection of bloodstream pathogens.Journal of translational medicine · 2026Article
- Genome-guided generative adversarial learning enables nanopore adaptive sequencing.Nature communications · 2026Article
- Next-generation sequencing: Driving a paradigm shift from pathogen detection to systems-level analysis.Infectious medicine · 2026Article
- Challenges in early detection and prognostication of sepsis: new approaches from the emergency department and intensive care unit.EClinicalMedicine · 2026Review
- Case report: Laboratory diagnosis methods on brain abscess pathogens caused by anaerobic species andIDCases · 2025Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
introductionSepsis is a critical condition requiring timely and accurate pathogen identification. Traditional blood cultures are slow and often yield low sensitivity. Metagenomic next-generation sequencing (mNGS) offers broad and rapid pathogen detection but is hindered by excessive human DNA background in blood samples. This study evaluated a novel Zwitterionic Interface Ultra-Self-assemble Coating (ZISC)-based filtration device designed to deplete host cells and enhance microbial DNA recovery for improved mNGS diagnostics.
methodsWe assessed the novel filter's performance in depleting white blood cells (WBCs) while preserving microbial integrity using spiked blood samples. Comparisons were made with other host depletion techniques, including differential lysis and CpG-methylated DNA removal. Analytical sensitivity was tested using spiked microbial communities at varying genome equivalents (GEs). Clinical validation involved eight blood culture-positive sepsis patient samples, processed with and without filtration, for both genomic DNA (gDNA) and cell-free DNA (cfDNA)-based mNGS. All libraries were sequenced on a NovaSeq600 with at least 10 million reads per sample.
resultsThe novel filter achieved > 99% WBC removal across various blood volumes and allowed unimpeded passage of bacteria and viruses. Compared to other depletion methods, the novel filtration was more efficient, less labor-intensive, and preserved microbial reads. mNGS with filtered gDNA detected all expected pathogens in 100% (8/8) of clinical samples, with an average microbial read count of 9351 reads per million (RPM), over tenfold higher than unfiltered samples (925 RPM). In contrast, cfDNA-based mNGS showed inconsistent sensitivity and was not significantly enhanced by filtration (1251-1488 RPM). Finally, the novel filtration did not alter the microbial composition, making it suitable for accurate pathogen profiling.
conclusionThe workflow with the novel host depletion method significantly enhanced the analytical sensitivity of gDNA-based mNGS by reducing the host DNA background and enriching microbial content. This approach improved diagnostic yield in sepsis and may be a valuable tool for further clinical infectious disease diagnostics.
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