ArticleScientific reports2023
Evaluation of Mycobacterium tuberculosis enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 34 citations in OpenAlex.
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- Enrichment techniques for clinical metagenomics.Frontiers in cellular and infection microbiology · 2026Review
- Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples.BMC medical genomics · 2025Article
- A comprehensive benchmarking of adaptive sampling tools for nanopore sequencing.Genome biology · 2025Article
- Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm.Genome research · 2025Article
- Nanopore adaptive sampling to identify the NLR gene family in melon (Cucumis melo L.).BMC genomics · 2025Article
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- Capturing clinically relevantMicrobial genomics · 2024Article
- Droplet based whole genome amplification for sequencing minute amounts of purified Mycobacterium tuberculosis DNA.Scientific reports · 2024Article
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- Computational biology and artificial intelligence in mRNA vaccine design for cancer immunotherapy.Frontiers in cellular and infection microbiology · 2024Review
- Validation of Oxford nanopore sequencing for improved New World Leishmania species identification via analysis of 70-kDA heat shock protein.Parasites & vectors · 2023Article
- Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing.Frontiers in microbiology · 2023Article
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Authors and funding
15 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sensitive detection of Mycobacterium tuberculosis (TB) in small percentages in metagenomic samples is essential for microbial classification and drug resistance prediction. However, traditional methods, such as bacterial culture and microscopy, are time-consuming and sometimes have limited TB detection sensitivity. Oxford nanopore technologies (ONT) MinION sequencing allows rapid and simple sample preparation for sequencing. Its recently developed adaptive sequencing selects reads from targets while allowing real-time base-calling to achieve sequence enrichment or depletion during sequencing. Another common enrichment method is PCR amplification of the target TB genes. In this study, we compared both methods using ONT MinION sequencing for TB detection and variant calling in metagenomic samples using both simulation runs and those with synthetic and patient samples. We found that both methods effectively enrich TB reads from a high percentage of human (95%) and other microbial DNA. Adaptive sequencing with readfish and UNCALLDE achieved a 3.9-fold and 2.2-fold enrichment compared to the control run. We provide a simple automatic analysis framework to support the detection of TB for clinical use, openly available at https://github.com/HKU-BAL/ONT-TB-NF . Depending on the patient's medical condition and sample type, we recommend users evaluate and optimize their workflow for different clinical specimens to improve the detection limit.
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