ArticleNature communications2014
A robust SNP barcode for typing Mycobacterium tuberculosis complex strains.
Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 412 papers, 2 of them syntheses that pooled it.
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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.
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Who cites it
412 citing papers in PubMed, 2 syntheses or guidelines pooled it, 784 citations in OpenAlex.
- Quantifying within-household tuberculosis transmission: a systematic review and prospective cohort study.International journal of epidemiology · 2026Pooled it
- Pooled it
- Phenotypic and genotypic features of the Mycobacterium tuberculosis lineage 1 subgroup in central Vietnam.Scientific reports · 2021Trial
- Quantifying the community transmission ofEmerging microbes & infections · 2026Article
- Drug-resistance profiles, population structure, genomic clustering, and temporal trends in drug resistance amongThe Lancet regional health. Europe · 2026Article
- Draft genome sequences of non-endemicMicrobiology resource announcements · 2026Article
- Migration and tuberculosis transmission in Hamburg, Germany: insights from 25 years of molecular epidemiology.Genome medicine · 2026Article
- Pan-genomic analysis of the multi-drug resistant strains of Mycobacterium tuberculosis.World journal of microbiology & biotechnology · 2026Article
- Within-host pathogen population diversity predicts treatment response in Tuberculosis.medRxiv : the preprint server for health sciences · 2026Article
- Reference-free clustering as an epidemiological tool forMicrobial genomics · 2026Article
- Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens.PLoS biology · 2026Article
- Whole-genome sequencing suggests recent transmission of rifampicin-resistant tuberculosis in Botswana.BMC infectious diseases · 2026Article
- Convolutional neural networks quantify antibiotic resistance in Mycobacterium tuberculosis with diagnostic grade accuracy and predict treatment response.Nature communications · 2026Article
- Reducing mapping reference and lineage bias inMicrobial genomics · 2026Article
- High treatment success among individuals with rifampicin-resistant tuberculosis in Botswana: A retrospective cohort study.Journal of infection and public health · 2026Article
- Human genetic ancestry,eLife · 2026Article
- Tuberculosis transmission and resistance among Ukrainian migrants and its impact on multidrug-resistant tuberculosis dynamics in high-influx host countries.BMC microbiology · 2026Article
- The Role of Youths in Within-Household Tuberculosis Transmission: A Household Contact Cohort Study.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2026Article
- Mutations in sugar metabolism-related genes driving global drug-resistant Mycobacterium tuberculosis transmission revealed by whole-genome sequencing.BMC infectious diseases · 2026Article
- Population structure and spatial distribution ofFrontiers in microbiology · 2026Article
352 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 6 institutions in 3 countries.
Funding
Abstract
Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ~92 k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ~7 k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type.
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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.