ArticlePloS one2022
TBProfiler for automated calling of the association with drug resistance of variants in Mycobacterium tuberculosis.
Article in PloS one, 2022. 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 29 papers.
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29 citing papers in PubMed, 38 citations in OpenAlex.
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- Targeted and whole-genome sequencing for drug resistance and genetic relatedness inference of rifampicin-resistantERJ open research · 2026Article
- Temporal and regional dynamics of Mycobacterium tuberculosis in Oman.Scientific reports · 2025Article
- Comparative assessment of annotation tools reveals critical antimicrobial resistance knowledge gaps in Klebsiella pneumoniae.Scientific reports · 2025Article
- Reimagining Tuberculosis Control in the Era of Genomics: The Case for Global Investment inPathogens (Basel, Switzerland) · 2025Review
- Genomic characterization of multidrug-resistant tuberculosis in Shanghai, China: antibiotic resistance, virulence and transmission.JAC-antimicrobial resistance · 2025Article
- Genome wide analyses reveal the role of mutator phenotypes in Mycobacterium tuberculosis drug resistance emergence.npj antimicrobials and resistance · 2025Article
- Interred mechanisms of resistance and host immune evasion revealed through network-connectivity analysis ofmSystems · 2025Article
- Integrating genomic, transcriptomic, and phenotypic information to explore drug resistance in Mycobacterium tuberculosis sub-lineage 4.2.2.2.Journal of applied microbiology · 2025Article
- A large geno-spatial cluster of multi-drug resistant tuberculosis outbreak in a western district of Thailand.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2025Article
- A comparative study of antibiotic resistance patterns in Mycobacterium tuberculosis.Scientific reports · 2025Article
- Machine learning-based prediction of antibiotic resistance in Mycobacterium tuberculosis clinical isolates from Uganda.BMC infectious diseases · 2024Article
- Culture-Free Whole Genome Sequencing ofOpen forum infectious diseases · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Following a huge global effort, the first World Health Organization (WHO)-endorsed catalogue of 17,356 variants in the Mycobacterium tuberculosis complex along with their classification as associated with resistance (interim), not associated with resistance (interim) or uncertain significance was made public In June 2021. This marks a critical step towards the application of next generation sequencing (NGS) data for clinical care. Unfortunately, the variant format used makes it difficult to look up variants when NGS data is generated by other bioinformatics pipelines. Furthermore, the large number of variants of uncertain significance in the catalogue hamper its useability in clinical practice. We successfully converted 98.3% of variants from the WHO catalogue format to the standardized HGVS format. We also created TBProfiler version 4.4.0 to automate the calling of all variants located in the tier 1 and 2 candidate resistance genes along with their classification when listed in the WHO catalogue. Using a representative sample of 339 clinical isolates from South Africa containing 691 variants in a tier 1 or 2 gene, TBProfiler classified 105 (15%) variants as conferring resistance, 72 (10%) as not conferring resistance and 514 (74%) as unclassified, with an average of 29 unclassified variants per isolate. Using a second cohort of 56 clinical isolates from a TB outbreak in Spain containing 21 variants in the tier 1 and 2 genes, TBProfiler classified 13 (61.9%) as unclassified, 7 (33.3%) as not conferring resistance, and a single variant (4.8%) classified as conferring resistance. Continued global efforts using standardized methods for genotyping, phenotyping and bioinformatic analyses will be essential to ensure that knowledge on genomic variants translates into improved patient care.
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