ArticleNature communications2024
Genetic diversity within diagnostic sputum samples is mirrored in the culture of Mycobacterium tuberculosis across different settings.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The respiratory microbiome in pulmonary tuberculosis: a meta-analysis reveals niche-specific microbial and functional signatures.mSystems · 2026Pooled it
- Towards culture-free sequencing of Mycobacterium tuberculosis: evaluating new targeted and whole-genome approaches for genotyping and drug resistance profiling.Genome medicine · 2026Trial
- Clinical performance of the Abbott RealTime Mycobacterium tuberculosis (MTB) PCR on bronchoscopic specimens for diagnosing pulmonary tuberculosis.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Optimizing culture-free approaches to recover high-qualityMicrobial genomics · 2026Article
- A novel nanosensor for in situ detection of EV-miR-107 enables noninvasive tuberculosis diagnosis and treatment monitoring.Journal of nanobiotechnology · 2026Article
- Within-host pathogen population diversity predicts treatment response in Tuberculosis.medRxiv : the preprint server for health sciences · 2026Article
- Evaluating the Performance of Sputum-Based Targeted Sequencing Against Mycobacterial Whole-Genome Sequencing in Predicting Tuberculosis Drug Resistance.International journal of molecular sciences · 2026Article
- Complete genomes reveal a refined map of Mycobacterium tuberculosis genetic diversity across evolutionary scales.Nature communications · 2026Article
- Detection of heteroresistance in Mycobacterium tuberculosis using nanopore-based amplicon sequencing and adaptive sampling.Scientific reports · 2026Article
- Direct nanopore sequencing ofMicrobial genomics · 2026Article
- A tiled amplicon protocol for culture-free whole-genome sequencing ofJournal of clinical microbiology · 2026Article
- Multicentre field evaluation of Xpert MTB/XDR in sub-Saharan Africa.ERJ open research · 2026Article
- Whole-genome sequencing reveals genetic diversity and transmission dynamics ofMicrobial genomics · 2026Article
- Targeted and whole-genome sequencing for drug resistance and genetic relatedness inference of rifampicin-resistantERJ open research · 2026Article
- Ongoing evolution of PE/PPE genes inmSystems · 2025Article
- Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex.Nature reviews. Microbiology · 2025Review
- A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission.Genome medicine · 2025Article
- Defying barriers to fight tuberculosis in West Africa: a model of equitable partnerships within a research capacity-strengthening network in the subregion.Frontiers in public health · 2025Article
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16 authors.
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Abstract
Culturing and genomic sequencing of Mycobacterium tuberculosis (MTB) from tuberculosis (TB) cases is the basis for many research and clinical applications. The alternative, culture-free sequencing from diagnostic samples, is promising but poses challenges to obtain and analyse the MTB genome. Paradoxically, culture is assumed to impose a diversity bottleneck, which, if true, would entail unexplored consequences. To unravel this paradox we generate high-quality genomes of sputum-culture pairs from two different settings after developing a workflow for sequencing from sputum and a tailored bioinformatics analysis. Careful downstream comparisons reveal sources of sputum-culture incongruences due to false positive/negative variation associated with factors like low input MTB DNA or variable genomic depths. After accounting for these factors, contrary to the bottleneck dogma, we identify a 97% variant agreement within sputum-culture pairs, with a high correlation also in the variants' frequency (0.98). The combined analysis from five different settings and more than 100 available samples shows that our results can be extrapolated to different TB epidemic scenarios, demonstrating that for the cases tested culture accurately mirrors clinical samples.
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