ArticleEBioMedicine2018
The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology.
Article in EBioMedicine, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers, 2 of them syntheses that pooled it.
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Who cites it
89 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Molecular epidemiology of M. tuberculosis in Ethiopia: A systematic review and meta-analysis.Tuberculosis (Edinburgh, Scotland) · 2019Pooled it
- Spatially targeted screening to reduce tuberculosis transmission in high-incidence settings.The Lancet. Infectious diseases · 2019Pooled it
- Trial
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- Whole-genome sequencing reveals genetic diversity and transmission dynamics ofMicrobial genomics · 2026Article
- Snapshot based on whole-genome sequencing revealing the species and antimicrobial susceptibility profiles of Mycobacterium tuberculosis complex recovered at a major tertiary care center in Lebanon.BMC infectious diseases · 2026Article
- Genetic Diversity and Molecular Epidemiology ofPathogens (Basel, Switzerland) · 2026Article
- Spatio-temporal patterns of tuberculosis revealed by routineThe Lancet regional health. Western Pacific · 2026Article
- Assessing the impact of Enhanced-Case-Finding on tuberculosis case notifications and transmission in The Gambia using epidemiological and phylodynamic approaches.Open research Europe · 2026Article
- Integrating whole-genome sequencing and epidemiology to characterise Mycobacterium bovis transmission in Ireland: a proof of concept.Irish veterinary journal · 2025Article
- M. caprae in northern Italy: a comprehensive analysis through whole-genome sequencing on the genetic variability in bovine herds.Veterinary research · 2025Article
- UShER-TB: Scalable, Comprehensive, Accessible Phylogenomic Analysis ofmedRxiv : the preprint server for health sciences · 2025Article
- Whole-Genome Sequence-Based Diversity ofPathogens (Basel, Switzerland) · 2025Article
- Molecular typing of Mycobacterium tuberculosis: a review of current methods, databases, softwares, and analytical tools.FEMS microbiology reviews · 2025Review
- Empowering tuberculosis genomic surveillance in Limpopo, South Africa through capacity building.Frontiers in public health · 2025Article
- Transmission characteristics of tuberculosis in the high-TB-burden region of Southwest China.Frontiers in public health · 2025Article
- Population structure and history ofMicrobiology spectrum · 2024Article
- Characteristic SNPs defining the major multidrug-resistantEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2024Article
29 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTracking recent transmission is a vital part of controlling widespread pathogens such as Mycobacterium tuberculosis. Multiple methods with specific performance characteristics exist for detecting recent transmission chains, usually by clustering strains based on genotype similarities. With such a large variety of methods available, informed selection of an appropriate approach for determining transmissions within a given setting/time period is difficult.
methodsThis study combines whole genome sequence (WGS) data derived from 324 isolates collected 2005-2010 in Kinshasa, Democratic Republic of Congo (DRC), a high endemic setting, with phylodynamics to unveil the timing of transmission events posited by a variety of standard genotyping methods. Clustering data based on Spoligotyping, 24-loci MIRU-VNTR typing, WGS based SNP (Single Nucleotide Polymorphism) and core genome multi locus sequence typing (cgMLST) typing were evaluated.
findingsOur results suggest that clusters based on Spoligotyping could encompass transmission events that occurred almost 200 years prior to sampling while 24-loci-MIRU-VNTR often represented three decades of transmission. Instead, WGS based genotyping applying low SNP or cgMLST allele thresholds allows for determination of recent transmission events, e.g. in timespans of up to 10 years for a 5 SNP/allele cut-off.
interpretationWith the rapid uptake of WGS methods in surveillance and outbreak tracking, the findings obtained in this study can guide the selection of appropriate clustering methods for uncovering relevant transmission chains within a given time-period. For high resolution cluster analyses, WGS-SNP and cgMLST based analyses have similar clustering/timing characteristics even for data obtained from a high incidence setting.
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