ArticleBMC infectious diseases2013
Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data.
Article in BMC infectious diseases, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers, 4 of them syntheses that pooled it.
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Who cites it
122 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- ClinicalFrontiers in microbiology · 2025Pooled it
- Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark.The Lancet. Microbe · 2021Pooled it
- Methods for Detecting Mycobacterial Mixed Strain Infections-A Systematic Review.Frontiers in genetics · 2020Pooled it
- Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review.BMC medicine · 2016Pooled it
- Trial
- Comparing subsampling strategies for efficient pairwise analysis of large pathogen genomic and spatial datasets: An application to Mycobacterium tuberculosis transmission.PLoS computational biology · 2026Article
- A tiled amplicon protocol for culture-free whole-genome sequencing ofJournal of clinical microbiology · 2026Article
- Long-term refined genomic analysis of tuberculosis clusters to distinguish between ongoing transmission, reactivations or diagnostic delays, Almería, Spain, 2003 to 2024.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2026Article
- Nationwide whole-genome sequencing reveals local transmission of Mycobacterium tuberculosis in Poland, 2003-2020.BMC infectious diseases · 2025Article
- Redefinition of transmission clusters by accessing to additional diversity inPathogens and global health · 2025Article
- Integrating whole-genome sequencing and epidemiology to characterise Mycobacterium bovis transmission in Ireland: a proof of concept.Irish veterinary journal · 2025Article
- UShER-TB: Scalable, Comprehensive, Accessible Phylogenomic Analysis ofmedRxiv : the preprint server for health sciences · 2025Article
- Phylodynamic assessment of SNP distances from whole genome sequencing for determining Mycobacterium tuberculosis transmission.Scientific reports · 2025Article
- Drug Resistance and Epidemiological Success of Modern Mycobacterium tuberculosis Lineages in Western India.The Journal of infectious diseases · 2025Article
- TBpore cluster: A novel phylogenetic pipeline for tuberculosis transmission studies using nanopore next-generation sequencing data.PloS one · 2025Article
- Article
- Whole-Genome sequencing in routineMicrobial genomics · 2024Article
- Unraveling tuberculosis patient cluster transmission chains: integrating WGS-based network with clinical and epidemiological insights.Frontiers in public health · 2024Article
- InvestigatingMicrobiology spectrum · 2023Article
- Clinical Whole-Genome Sequencing Assay for RapidMicroorganisms · 2023Article
62 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors.
Funding
Abstract
backgroundMycobacterium tuberculosis is characterised by limited genomic diversity, which makes the application of whole genome sequencing particularly attractive for clinical and epidemiological investigation. However, in order to confidently infer transmission events, an accurate knowledge of the rate of change in the genome over relevant timescales is required.
methodsWe attempted to estimate a molecular clock by sequencing 199 isolates from epidemiologically linked tuberculosis cases, collected in the Netherlands spanning almost 16 years.
resultsMultiple analyses support an average mutation rate of ~0.3 SNPs per genome per year. However, all analyses revealed a very high degree of variation around this mean, making the confirmation of links proposed by epidemiology, and inference of novel links, difficult. Despite this, in some cases, the phylogenetic context of other strains provided evidence supporting the confident exclusion of previously inferred epidemiological links.
conclusionsThis in-depth analysis of the molecular clock revealed that it is slow and variable over short time scales, which limits its usefulness in transmission studies. However, the superior resolution of whole genome sequencing can provide the phylogenetic context to allow the confident exclusion of possible transmission events previously inferred via traditional DNA fingerprinting techniques and epidemiological cluster investigation. Despite the slow generation of variation even at the whole genome level we conclude that the investigation of tuberculosis transmission will benefit greatly from routine whole genome sequencing.
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