ArticleGenome medicine2020
Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies.
Article in Genome medicine, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers.
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98 citing papers in PubMed.
- Phenotypic and genotypic features of the Mycobacterium tuberculosis lineage 1 subgroup in central Vietnam.Scientific reports · 2021Trial
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- Mycobacteria Amplicon Sequencing Tool: automated resistance prediction and lineage classification forMicrobiology resource announcements · 2026Article
- Reference-free clustering as an epidemiological tool forMicrobial genomics · 2026Article
- Long-term spatiotemporal evolution of drug-resistant Mycobacterium tuberculosis in China.Nature communications · 2026Article
- Dissecting the effect of single- and co-infection of TB and COVID-19 pathogens on the sputum microbiome.Microbiology spectrum · 2026Article
- Genome-wide analyses of Mycobacterium tuberculosis complex isolates reveal insights into circulating lineages and drug resistance mutations in The Gambia.Scientific reports · 2026Article
- Spatial clustering and genetic diversity of Mycobacterium tuberculosis and associated diagnostic delays in Nairobi County, Kenya.BMC infectious diseases · 2026Article
- Real-time PCR assay for robust detection and global surveillance of the Mycobacterium tuberculosis Haarlem genotype.Scientific reports · 2025Article
- Ongoing evolution of PE/PPE genes inmSystems · 2025Article
- Mycobacterium tuberculosis complex Lineage 1: A neglected cause of tuberculosis.PLoS neglected tropical diseases · 2025Review
- TheeLife · 2025Article
- Enhancing image retrieval through optimal barcode representation.Scientific reports · 2025Article
- UShER-TB: Scalable, Comprehensive, Accessible Phylogenomic Analysis ofmedRxiv : the preprint server for health sciences · 2025Article
- PPE50 variants as novel phylogeographic signatures of host-pathogen co-evolution in tuberculosis.Communications biology · 2025Article
- Dissecting rifampicin heteroresistance inJournal of medical microbiology · 2025Article
- South Asian origin and global transmission history ofmSystems · 2025Article
- Genome-to-genome analysis reveals associations between human and mycobacterial genetic variation in tuberculosis patients from Tanzania.BMC medical genomics · 2025Article
- Immunoinformatics Predictions on VariableMicroorganisms · 2025Article
38 more citing papers are in PubMed but not listed here.
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9 authors.
Funding
Abstract
backgroundTuberculosis, caused by bacteria in the Mycobacterium tuberculosis complex (MTBC), is a major global public health burden. Strain-specific genomic diversity in the known lineages of MTBC is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Fast and accurate tracking of MTBC strains is therefore crucial for infection control, and our previous work developed a 62-single nucleotide polymorphism (SNP) barcode to inform on the phylogenetic identity of 7 human lineages and 64 sub-lineages.
methodsTo update this barcode, we analysed whole genome sequencing data from 35,298 MTBC isolates (~ 1 million SNPs) covering 9 main lineages and 3 similar animal-related species (M. tuberculosis var. bovis, M. tuberculosis var. caprae and M. tuberculosis var. orygis). The data was partitioned into training (N = 17,903, 50.7%) and test (N = 17,395, 49.3%) sets and were analysed using an integrated phylogenetic tree and population differentiation (F
resultsBy constructing a phylogenetic tree on the training MTBC isolates, we characterised 90 lineages or sub-lineages or species, of which 30 are new, and identified 421 robust barcoding mutations, of which a minimal set of 90 was selected that included 20 markers from the 62-SNP barcode. The barcoding SNPs (90 and 421) discriminated perfectly the 86 MTBC isolate (sub-)lineages in the test set and could accurately reconstruct the clades across the combined 35k samples.
conclusionsThe validated 90 SNPs can be used for the rapid diagnosis and tracking of MTBC strains to assist public health surveillance and control. To facilitate this, the SNP markers have now been incorporated into the TB-Profiler informatics platform ( https://github.com/jodyphelan/TBProfiler ).
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