ArticleJournal of clinical microbiology2012
Combination of single nucleotide polymorphism and variable-number tandem repeats for genotyping a homogenous population of Mycobacterium tuberculosis Beijing strains in China.
Article in Journal of clinical microbiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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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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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
20 citing papers in PubMed.
- The Mycobacterium tuberculosis genome at 25 years: lessons and lingering questions.The Journal of clinical investigation · 2023Review
- The geno-spatio analysis of Mycobacterium tuberculosis complex in hot and cold spots of Guangxi, China.BMC infectious diseases · 2020Article
- Extensive Homoplasy but No Evidence of Convergent Evolution of Repeat Numbers at MIRU Loci in ModernFrontiers in public health · 2020Article
- A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages.Scientific reports · 2019Article
- Observational
- A quantitative and efficient approach to select MIRU-VNTR loci based on accumulation of the percentage differences of strains for discriminating divergent Mycobacterium tuberculosis sublineages.Emerging microbes & infections · 2017Article
- Use of GeneXpert Remnants for Drug Resistance Profiling and Molecular Epidemiology of Tuberculosis in Libreville, Gabon.Journal of clinical microbiology · 2017Article
- Genotypic Diversity ofBioMed research international · 2017Article
- Genetic diversity of the Mycobacterium tuberculosis Beijing family based on multiple genotyping profiles.Epidemiology and infection · 2016Article
- [Establishment and preliminary application of detection of Mycobacterium tuberculosis in sputum based on variable number tandem repeat].Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences · 2016Article
- Whole-genome sequencing to detect recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis.Tuberculosis (Edinburgh, Scotland) · 2014Article
- Novel DNA chip based on a modified DigiTag2 assay for high-throughput species identification and genotyping of Mycobacterium tuberculosis complex isolates.Journal of clinical microbiology · 2014Article
- Genotypic diversity analysis of Mycobacterium tuberculosis strains collected from Beijing in 2009, using spoligotyping and VNTR typing.PloS one · 2014Article
- Development of a hierarchical variable-number tandem repeat typing scheme for Mycobacterium tuberculosis in China.PloS one · 2014Article
- Proposal of a consensus set of hypervariable mycobacterial interspersed repetitive-unit-variable-number tandem-repeat loci for subtyping of Mycobacterium tuberculosis Beijing isolates.Journal of clinical microbiology · 2014Article
- Analysis of mutations in streptomycin-resistant strains reveals a simple and reliable genetic marker for identification of the Mycobacterium tuberculosis Beijing genotype.Journal of clinical microbiology · 2013Article
- Primary drug-resistant tuberculosis in Hanoi, Viet Nam: present status and risk factors.PloS one · 2013Article
- Factors associated with genotype clustering of Mycobacterium tuberculosis isolates in an ethnically diverse region of southern California, United States.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2012Article
- Article
- Genetic diversity and transmission characteristics of Beijing family strains of Mycobacterium tuberculosis in Peru.PloS one · 2012Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The standard 15- and 24-locus variable-number tandem repeat (VNTR) genotyping methods have demonstrated adequate discriminatory power and a small homoplasy effect for tracing tuberculosis (TB) transmission and predicting Mycobacterium tuberculosis lineages in European and North American countries. However, its validity for the definition of transmission in homogenous M. tuberculosis populations in settings with high TB burdens has been questioned. Here, we genotyped a population-based collection of 191 Beijing strains based on standard 15-locus VNTR (VNTR-15) and 8 single nucleotide polymorphisms (SNPs) in Shanghai, China. Limited discriminatory power and high rates of VNTR homoplasy were observed in the homogenous population of evolutionarily "modern" Beijing strains. Additional typing of three hypervariable loci (VNTR3820, VNTR4120, and VNTR3232) was performed for VNTR-15-based clusters. High variations of hypervariable alleles were observed in clusters with inconsistent SNP sublineages. We concluded that SNPs and hypervariable VNTR loci are helpful to enhance the discriminatory power and decrease the VNTR homoplasy effect for defining clusters. We recommend the combination of standard VNTR-15 and SNPs as first-line typing methods and the hypervariable loci for second-line typing of clustered strains for molecular epidemiology studies of homogenous M. tuberculosis populations.
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