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Genetic Diversity of the Mycobacterium tuberculosis Beijing Family Based on SNP and VNTR Typing Profiles in Asian Countries
- Source :
- PLoS ONE, PLoS ONE, Vol 7, Iss 7, p e39792 (2012)
- Publication Year :
- 2012
- Publisher :
- Public Library of Science (PLoS), 2012.
-
Abstract
- The Mycobacterium tuberculosis (MTB) Beijing strain is highly virulent, drug resistant, and endemic over Asia. To explore the genetic diversity of this family in several different regions of eastern Asia, 338 Beijing strains collected in Taiwan (Republic of China) were analyzed by mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and compared with published MIRU-VNTR profiles and by the Hunter-Gaston diversity index (HGDI) of Beijing strains from Japan and South Korea. The results revealed that VNTR2163b (HGDI>0.6) and five other loci (VNTR424, VNTR4052, VNTR1955, VNTR4156 and VNTR 2996; HGDI>0.3) could be used to discriminate the Beijing strains in a given geographic region. Analysis based on the number of VNTR repeats showed three VNTRs (VNTR424, 3192, and 1955) to be phylogenetically informative loci. In addition, to determine the geographic variation of sequence types in MTB populations, we also compared sequence type (ST) data of our strains with published ST profiles of Beijing strains from Japan and Thailand. ST10, ST22, and ST19 were found to be prevalent in Taiwan (82%) and Thailand (92%). Furthermore, classification of Beijing sublineages as ancient or modern in Taiwan was found to depend on the repeat number of VNTR424. Finally, phylogenetic relationships of MTB isolates in Taiwan, South Korea, and Japan were revealed by a minimum spanning tree based on MIRU-VNTR genotyping. In this topology, the MIRU-VNTR genotypes of the respective clusters were tightly correlated to other genotypic characters. These results are consistent with the hypothesis that clonal evolution of these MTB lineages has occurred.
- Subjects :
- Bacterial Diseases
DNA, Bacterial
Genotype
Taiwan
lcsh:Medicine
Minisatellite Repeats
Biology
Microbiology
Polymerase Chain Reaction
Polymorphism, Single Nucleotide
Mycobacterium
Japan
Beijing
Tandem repeat
Republic of Korea
Genetic variation
Genetics
Tuberculosis
Humans
Evolutionary Systematics
Typing
lcsh:Science
Genotyping
Alleles
Phylogeny
Evolutionary Biology
Genetic diversity
Multidisciplinary
Phylogenetic tree
Multi-Drug-Resistant Tuberculosis
lcsh:R
Genetic Variation
Mycobacterium tuberculosis
Thailand
bacterial infections and mycoses
Bacterial Pathogens
Bacterial Typing Techniques
Phylogenetics
Phylogeography
Variable number tandem repeat
Infectious Diseases
Genetic Loci
Genetics of Disease
Microbial Evolution
Medicine
lcsh:Q
Research Article
Subjects
Details
- ISSN :
- 19326203
- Volume :
- 7
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....368fb763edc24cfd18b30c92e736aaa2