ArticleBMC genomics2019
Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 61 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
61 citing papers in PubMed, 1 synthesis or guideline pooled it, 100 citations in OpenAlex.
- Pooled it
- Algorithmic Determinants of Performance Heterogeneity in Whole-Genome Sequencing-Based Prediction of Drug Resistance inMicroorganisms · 2026Review
- What is new in tuberculosis?Clinical medicine (London, England) · 2026Review
- Optimizing culture-free approaches to recover high-qualityMicrobial genomics · 2026Article
- Detection of heteroresistance in Mycobacterium tuberculosis using nanopore-based amplicon sequencing and adaptive sampling.Scientific reports · 2026Article
- Evaluation of DNA extraction methods from clinical Mycobacterium tuberculosis primary liquid culture for whole-genome sequencing.BMC genomics · 2026Article
- A tiled amplicon protocol for culture-free whole-genome sequencing ofJournal of clinical microbiology · 2026Article
- Benchmarking within-sample minority variant detection with short-read sequencing inbioRxiv : the preprint server for biology · 2026Article
- Diagnostic performance of the FluoroType MTBDR assay for rifampicin and isoniazid resistance in routine laboratory setting.African journal of primary health care & family medicine · 2026Article
- Mixed-strain infection and heteroresistance in drug-resistant tuberculosis: insights from a whole-genome sequencing pilot.Frontiers in epidemiology · 2026Article
- Optimizing culture-free approaches to recover high qualitymedRxiv : the preprint server for health sciences · 2025Article
- Characterization of Drug Resistance Mutations inMicroorganisms · 2025Article
- TEAL-Seq: targeted expression analysis sequencing.mSphere · 2025Article
- Speeding up drug susceptibility testing in Mycobacterium tuberculosis using RNA biomarkers.EBioMedicine · 2025Article
- TBtypeR: Sensitive detection and sublineage classification of Mycobacterium tuberculosis complex mixed-strain infections.Communications biology · 2025Article
- Evaluating methods for genome sequencing ofMicrobial genomics · 2025Article
- A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission.Genome medicine · 2025Article
- Deep Amplicon Sequencing Reveals Culture-dependent Clonal Selection of Mycobacterium tuberculosis in Clinical Samples.Genomics, proteomics & bioinformatics · 2025Article
- Machine learning-based approach for identification of new resistance associated mutations from whole genome sequences ofBioinformatics advances · 2025Article
- Enhancing diagnostic efficiency of pyrazinamide resistance inCurrent research in microbial sciences · 2025Article
1 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
9 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundRepeated culture reduces within-sample Mycobacterium tuberculosis genetic diversity due to selection of clones suited to growth in culture and/or random loss of lineages, but it is not known to what extent omitting the culture step altogether alters genetic diversity. We compared M. tuberculosis whole genome sequences generated from 33 paired clinical samples using two methods. In one method DNA was extracted directly from sputum then enriched with custom-designed SureSelect (Agilent) oligonucleotide baits and in the other it was extracted from mycobacterial growth indicator tube (MGIT) culture.
resultsDNA directly sequenced from sputum showed significantly more within-sample diversity than that from MGIT culture (median 5.0 vs 4.5 heterozygous alleles per sample, p = 0.04). Resistance associated variants present as HAs occurred in four patients, and in two cases may provide a genotypic explanation for phenotypic resistance.
conclusionsCulture-free M. tuberculosis whole genome sequencing detects more within-sample diversity than a leading culture-based method and may allow detection of mycobacteria that are not actively replicating.
Indexed as
Identifiers
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.