ArticlePloS one2013
Use of whole genome sequencing to determine the microevolution of Mycobacterium tuberculosis during an outbreak.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 3 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
45 citing papers in PubMed, 3 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
- Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review.BMC medicine · 2016Pooled it
- Trial
- Applications and advances in molecular diagnostics: revolutionizing non-tuberculous mycobacteria species and subspecies identification.Frontiers in public health · 2024Review
- Lineage classification and antitubercular drug resistance surveillance ofMicrobiology spectrum · 2023Article
- Clinical Whole-Genome Sequencing Assay for RapidMicroorganisms · 2023Article
- Genome-Wide Study of Drug ResistantMicroorganisms · 2022Article
- Use of Whole-Genome Sequencing to Unravel the Genetic Diversity of a PrevalentFrontiers in microbiology · 2022Article
- Comprehensive and accurate genetic variant identification from contaminated and low-coverageMicrobial genomics · 2021Article
- Phylogenetic relationships investigation of Mycobacterium caprae strains from sympatric wild boar and goats based on whole genome sequencing.Transboundary and emerging diseases · 2021Article
- Pediatric Tuberculosis: The Impact of "Omics" on Diagnostics Development.International journal of molecular sciences · 2020Review
- Review
- Phylogenomic assessment of drug-resistant Mycobacterium tuberculosis strains from Beira, Mozambique.Tuberculosis (Edinburgh, Scotland) · 2020Article
- Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters.PLoS computational biology · 2019Article
- Genomic sequencing is required for identification of tuberculosis transmission in Hawaii.BMC infectious diseases · 2018Article
- Spatial Patterns of Extensively Drug-Resistant Tuberculosis Transmission in KwaZulu-Natal, South Africa.The Journal of infectious diseases · 2018Article
- Genetic profiling of Mycobacterium bovis strains from slaughtered cattle in Eritrea.PLoS neglected tropical diseases · 2018Article
- Review
- Molecular epidemiology of cattle tuberculosis in Mexico through whole-genome sequencing and spoligotyping.PloS one · 2018Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
rationaleCurrent tools available to study the molecular epidemiology of tuberculosis do not provide information about the directionality and sequence of transmission for tuberculosis cases occurring over a short period of time, such as during an outbreak. Recently, whole genome sequencing has been used to study molecular epidemiology of Mycobacterium tuberculosis over short time periods.
objectiveTo describe the microevolution of M. tuberculosis during an outbreak caused by one drug-susceptible strain. METHOD AND MEASUREMENTS: We included 9 patients with tuberculosis diagnosed during a period of 22 months, from a population-based study of the molecular epidemiology in San Francisco. Whole genome sequencing was performed using Illumina's sequencing by synthesis technology. A custom program written in Python was used to determine single nucleotide polymorphisms which were confirmed by PCR product Sanger sequencing. MAIN
resultsWe obtained an average of 95.7% (94.1-96.9%) coverage for each isolate and an average fold read depth of 73 (1 to 250). We found 7 single nucleotide polymorphisms among the 9 isolates. The single nucleotide polymorphisms data confirmed all except one known epidemiological link. The outbreak strain resulted in 5 bacterial variants originating from the index case A1 with 0-2 mutations per transmission event that resulted in a secondary case.
conclusionsWhole genome sequencing analysis from a recent outbreak of tuberculosis enabled us to identify microevolutionary events observable during transmission, to determine 0-2 single nucleotide polymorphisms per transmission event that resulted in a secondary case, and to identify new epidemiologic links in the chain of transmission.
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