ArticleTuberculosis (Edinburgh, Scotland)2014
PolyTB: a genomic variation map for Mycobacterium tuberculosis.
Article in Tuberculosis (Edinburgh, Scotland), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
What it found
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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.
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Who cites it
57 citing papers in PubMed.
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- Examination of Genetic Mutations of Clofazimine Resistance in Drug-Resistant Mycobacterium TB Isolates.Current microbiology · 2025Article
- Genome wide analyses reveal the role of mutator phenotypes in Mycobacterium tuberculosis drug resistance emergence.npj antimicrobials and resistance · 2025Article
- An unusual activity of mycobacterial MutT1 Nudix hydrolase domain as a protein phosphatase regulates nucleoside diphosphate kinase function.Journal of bacteriology · 2025Article
- Article
- Genetic diversity and antibiotic resistance ofFrontiers in cellular and infection microbiology · 2025Article
- Prevalence and genetic basis of Mycobacterium tuberculosis resistance to pretomanid in China.Annals of clinical microbiology and antimicrobials · 2024Article
- SNPs in genes related to the repair of damage to DNA in clinical isolates of M. tuberculosis: A transversal and longitudinal approach.PloS one · 2024Article
- Exploring the role of wastewater-based epidemiology in understanding tuberculosis burdens in Africa.Environmental research · 2023Article
- Insight into Population Structure and Drug Resistance of Pediatric Tuberculosis Strains from China and Russia Gained through Whole-Genome Sequencing.International journal of molecular sciences · 2023Article
- Article
- How a PCR Sequencing Strategy Can Bring New Data to Improve the Diagnosis of Ethionamide Resistance.Microorganisms · 2022Article
- A Rapid Drug Resistance Genotyping Workflow for Mycobacterium tuberculosis, Using Targeted Isothermal Amplification and Nanopore Sequencing.Microbiology spectrum · 2021Article
- CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing.GigaScience · 2021Article
- A genome epidemiological study of mycobacterium tuberculosis in subpopulations with high and low incidence rate in Guangxi, South China.BMC infectious diseases · 2021Article
- CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.PLoS computational biology · 2021Article
- Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis.BMC genomics · 2020Article
- Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak.PLoS pathogens · 2020Article
- Pulmonary non-tuberculous mycobacterial infections: current state and future management.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2020Review
- Extensive Homoplasy but No Evidence of Convergent Evolution of Repeat Numbers at MIRU Loci in ModernFrontiers in public health · 2020Article
Corrections and comments
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Authors and funding
16 authors.
Funding
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is the second major cause of death from an infectious disease worldwide. Recent advances in DNA sequencing are leading to the ability to generate whole genome information in clinical isolates of M. tuberculosis complex (MTBC). The identification of informative genetic variants such as phylogenetic markers and those associated with drug resistance or virulence will help barcode Mtb in the context of epidemiological, diagnostic and clinical studies. Mtb genomic datasets are increasingly available as raw sequences, which are potentially difficult and computer intensive to process, and compare across studies. Here we have processed the raw sequence data (>1500 isolates, eight studies) to compile a catalogue of SNPs (n = 74,039, 63% non-synonymous, 51.1% in more than one isolate, i.e. non-private), small indels (n = 4810) and larger structural variants (n = 800). We have developed the PolyTB web-based tool (http://pathogenseq.lshtm.ac.uk/polytb) to visualise the resulting variation and important meta-data (e.g. in silico inferred strain-types, location) within geographical map and phylogenetic views. This resource will allow researchers to identify polymorphisms within candidate genes of interest, as well as examine the genomic diversity and distribution of strains. PolyTB source code is freely available to researchers wishing to develop similar tools for their pathogen of interest.
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Registered trials
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