ArticleBMC genomics2021
Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 53 citations in OpenAlex.
- The lung microbiome in childhood-onset severe neuromuscular disease with respiratory insufficiency: rationale, current evidence, and opportunities for oxford nanopore long-read sequencing.Molecular and cellular pediatrics · 2026Review
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 2026Review
- Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy.Microbiology spectrum · 2026Article
- Rapid identification of microbial pathogens and antimicrobial resistance from bloodstream infections using long-read sequencing.Microbial genomics · 2026Article
- Review
- Enrichment techniques for clinical metagenomics.Frontiers in cellular and infection microbiology · 2026Review
- The transformative impact of ultra-rapid nanopore sequencing in precision medicine.Frontiers in immunology · 2026Review
- Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue.Microbial genomics · 2025Article
- Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.NPJ biofilms and microbiomes · 2025Article
- Article
- A Barcoded ITS Primer-Based Nanopore Sequencing Protocol for Detection ofJournal of fungi (Basel, Switzerland) · 2025Article
- The role of bronchoalveolar lavage fluid metagenomic next-generation sequencing in detecting pathogens and optimising antibiotic therapy in paediatric severe community-acquired pneumonia.Frontiers in cellular and infection microbiology · 2025Article
- Comprehensive pathogen identification and antimicrobial resistance prediction from positive blood cultures using nanopore sequencing technology.Genome medicine · 2024Article
- Antimicrobial resistance prediction by clinical metagenomics in pediatric severe pneumonia patients.Annals of clinical microbiology and antimicrobials · 2024Article
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Selective whole-genome sequencing ofmBio · 2024Article
- Direct RNA sequencing coupled with adaptive sampling enriches RNAs of interest in the transcriptome.Nature communications · 2024Article
- NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples.Pathogens (Basel, Switzerland) · 2024Article
- The 28S rRNA RT-qPCR assay for host depletion evaluation to enhance avian virus detection in Illumina and Nanopore sequencing.Frontiers in microbiology · 2024Article
- Evolution of the urinary microbiota in spinal cord injury patients with decubitus ulcer: A snapshot study.International wound journal · 2024Article
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7 authors at 1 institution in 1 country.
Funding
Abstract
backgroundEnzyme-based host depletion significantly improves the sensitivity of clinical metagenomics. Recent studies found that real-time adaptive sequencing of DNA molecules was achieved using a nanopore sequencing machine, which enabled effective enrichment of microbial sequences. However, few studies have compared the enzyme-based host depletion and nanopore adaptive sequencing for microbial enrichment efficiency.
resultsTo compare the host depletion and microbial enrichment efficiency of enzyme-based and adaptive sequencing methods, the present study collected clinical samples from eight children with respiratory tract infections. The same respiratory samples were subjected to standard methods, adaptive sequencing methods, enzyme-based host depletion methods, and the combination of adaptive sequencing and enzyme-based host depletion methods. We compared the host depletion efficiency, microbial enrichment efficiency, and pathogenic microorganisms detected between the four methods. We found that adaptive sequencing, enzyme-based host depletion and the combined methods significantly enriched the microbial sequences and significantly increased the diversity of microorganisms (p value < 0.001 for each method compared to standard). The highest microbial enrichment efficiency was achieved using the combined method. Compared to the standard method, the combined method increased the microbial reads by a median of 113.41-fold (interquartile range 23.32-327.72, maximum 1812), and the number of genera by a median of 70-fold (interquartile range 56.75-86.75, maximum 164). The combined method detected 6 pathogens in 4 samples with a median read of 547, compared to 5 pathogens in 4 samples with a median read of 4 using the standard method.
conclusionThe combined method is an effective, easy-to-run method for enriching microbial sequences in clinical metagenomics from sputum and bronchoalveolar lavage fluid samples and may improve the sensitivity of clinical metagenomics for other host-derived clinical samples.
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