ArticleThe Lancet. Infectious diseases2013
Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study.
Article in The Lancet. Infectious diseases, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 576 papers, 3 of them syntheses that pooled it.
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Who cites it
576 citing papers in PubMed, 3 syntheses or guidelines pooled it, 968 citations in OpenAlex.
- In Host Mutational Adaptation of Mycobacterium Tuberculosis Complex Strains During Tuberculosis Infection.The Journal of infectious diseases · 2026Pooled it
- ClinicalFrontiers in microbiology · 2025Pooled it
- Using molecular methods to delineate norovirus outbreaks: a systematic review.Archives of virology · 2024Pooled it
- Desiccation promotes DNA damage and rifampin resistance in Mycobacterium tuberculosis.Nature microbiology · 2026Article
- Within-host pathogen population diversity predicts treatment response in Tuberculosis.medRxiv : the preprint server for health sciences · 2026Article
- Whole-genome sequencing reveals a novelApplied and environmental microbiology · 2026Article
- Mycobacteria Amplicon Sequencing Tool: automated resistance prediction and lineage classification forMicrobiology resource announcements · 2026Article
- Network analysis of pairwise relative tuberculosis transmission probabilities in Lima, Peru.American journal of epidemiology · 2026Article
- Reference-free clustering as an epidemiological tool forMicrobial genomics · 2026Article
- Characteristics of Plausible Source Cases Responsible for Recent Mycobacterium tuberculosis Transmission, United States, 2018-2022.Emerging infectious diseases · 2026Article
- Whole-genome sequencing suggests recent transmission of rifampicin-resistant tuberculosis in Botswana.BMC infectious diseases · 2026Article
- Genomic comparison of clinical strains ofMicrobial genomics · 2026Article
- Measuring recent in-country TB transmission using a classification model with whole genome sequencing data.IJTLD open · 2026Article
- Using genomic epidemiology and geographic activity spaces to investigate tuberculosis outbreaks in Botswana.International journal of health geographics · 2026Article
- The global phylogeography of rapidly expanding multidrug resistant Ural lineage 4.2 Mycobacterium tuberculosis.Nature communications · 2026Article
- Identification of tuberculosis transmission hotspots in urban China using surveillance data: a machine learning approach based on genomic and spatial analysis.BMC infectious diseases · 2026Article
- Understanding recurrence inJournal of clinical microbiology · 2026Review
- 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
- Molecular epidemiology of drug resistance and transmission ofMicrobiology spectrum · 2026Article
516 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors at 5 institutions in 1 country.
Funding
Abstract
backgroundTuberculosis incidence in the UK has risen in the past decade. Disease control depends on epidemiological data, which can be difficult to obtain. Whole-genome sequencing can detect microevolution within Mycobacterium tuberculosis strains. We aimed to estimate the genetic diversity of related M tuberculosis strains in the UK Midlands and to investigate how this measurement might be used to investigate community outbreaks.
methodsIn a retrospective observational study, we used Illumina technology to sequence M tuberculosis genomes from an archive of frozen cultures. We characterised isolates into four groups: cross-sectional, longitudinal, household, and community. We measured pairwise nucleotide differences within hosts and between hosts in household outbreaks and estimated the rate of change in DNA sequences. We used the findings to interpret network diagrams constructed from 11 community clusters derived from mycobacterial interspersed repetitive-unit-variable-number tandem-repeat data.
findingsWe sequenced 390 separate isolates from 254 patients, including representatives from all five major lineages of M tuberculosis. The estimated rate of change in DNA sequences was 0.5 single nucleotide polymorphisms (SNPs) per genome per year (95% CI 0.3-0.7) in longitudinal isolates from 30 individuals and 25 families. Divergence is rarely higher than five SNPs in 3 years. 109 (96%) of 114 paired isolates from individuals and households differed by five or fewer SNPs. More than five SNPs separated isolates from none of 69 epidemiologically linked patients, two (15%) of 13 possibly linked patients, and 13 (17%) of 75 epidemiologically unlinked patients (three-way comparison exact p<0.0001). Genetic trees and clinical and epidemiological data suggest that super-spreaders were present in two community clusters.
interpretationWhole-genome sequencing can delineate outbreaks of tuberculosis and allows inference about direction of transmission between cases. The technique could identify super-spreaders and predict the existence of undiagnosed cases, potentially leading to early treatment of infectious patients and their contacts.
fundingMedical Research Council, Wellcome Trust, National Institute for Health Research, and the Health Protection Agency.
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