ArticleJournal of clinical microbiology2023
Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination, and Drug Susceptibility Prediction.
Article in Journal of clinical microbiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it, 26 citations in OpenAlex.
- Diagnostic accuracy of nanopore sequencing for detecting Mycobacterium tuberculosis and drug-resistant strains: a systematic review and meta-analysis.Scientific reports · 2025Pooled it
- Diagnostic value of nanopore-based targeted sequencing technology for subclinical tuberculosis.BMC microbiology · 2026Article
- Direct nanopore sequencing ofMicrobial genomics · 2026Article
- Long-term refined genomic analysis of tuberculosis clusters to distinguish between ongoing transmission, reactivations or diagnostic delays, Almería, Spain, 2003 to 2024.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2026Article
- Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples.BMC medical genomics · 2025Article
- Targeted sputum sequencing for rapid and broad drug resistance of Mycobacterium tuberculosis.Infection · 2025Article
- Matrix-based DNA Extraction for Targeted Next-Generation Sequencing on Decontaminated Sputum Samples.Journal of visualized experiments : JoVE · 2025Article
- Sputum culture contamination and associated characteristics in a diagnostic clinical trial, Papua New Guinea.Public health action · 2024Article
- Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data.eLife · 2024Article
- Bridging the gap between molecular and genomic epidemiology in tuberculosis: inferring MIRU-VNTR patterns from genomic data.Journal of clinical microbiology · 2024Article
- Genetic diversity within diagnostic sputum samples is mirrored in the culture of Mycobacterium tuberculosis across different settings.Nature communications · 2024Article
- Predictive phage therapy forProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data.GigaScience · 2024Article
- Targeted genome sequencing for tuberculosis drug susceptibility testing in South Africa: a proposed diagnostic pipeline.Access microbiology · 2024Review
- Evaluation of Nanopore Sequencing for Diagnosing Pulmonary Tuberculosis Using Negative Smear Clinical Specimens.Infection and drug resistance · 2024Article
- Molecular epidemiology of SARS-CoV-2 in Mongolia, first experience with nanopore sequencing in lower- and middle-income countries setting.Immunity, inflammation and disease · 2023Article
Corrections and comments
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Authors and funding
17 authors at 4 institutions in 6 countries.
Funding
Abstract
Universal access to drug susceptibility testing for newly diagnosed tuberculosis patients is recommended. Access to culture-based diagnostics remains limited, and targeted molecular assays are vulnerable to emerging resistance mutations. Improved protocols for direct-from-sputum Mycobacterium tuberculosis sequencing would accelerate access to comprehensive drug susceptibility testing and molecular typing. We assessed a thermo-protection buffer-based direct-from-sample M. tuberculosis whole-genome sequencing protocol. We prospectively analyzed 60 acid-fast bacilli smear-positive clinical sputum samples in India and Madagascar. A diversity of semiquantitative smear positivity-level samples were included. Sequencing was performed using Illumina and MinION (monoplex and multiplex) technologies. We measured the impact of bacterial inoculum and sequencing platforms on genomic read depth, drug susceptibility prediction performance, and typing accuracy. M. tuberculosis was identified by direct sputum sequencing in 45/51 samples using Illumina, 34/38 were identified using MinION-monoplex sequencing, and 20/24 were identified using MinION-multiplex sequencing. The fraction of M. tuberculosis reads from MinION sequencing was lower than from Illumina, but monoplexing grade 3+ samples on MinION produced higher read depth than Illumina (
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What OpenQuestion holds
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.