Genetic diversity of the Mycobacterium tuberculosis Beijing family based on SNP and VNTR typing profiles in Asian countries.
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.
National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan.
Yih-Yuan
YY
Chen
Jia-Ru
JR
Chang
Wei-Feng
WF
Huang
Shu-Chen
SC
Kuo
Ih-Jen
IJ
Su
Jun-Ren
JR
Sun
Tzong-Shi
TS
Chiueh
Tsi-Shu
TS
Huang
Yao-Shen
YS
Chen
Horng-Yunn
HY
Dou
D000483:Alleles; D015373:Bacterial Typing Techniques; D004269:DNA, Bacterial / Q000032:analysis*; D056426:Genetic Loci; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D007564:Japan; D018598:Minisatellite Repeats; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000472:pathogenicity; D010802:Phylogeny; D058974:Phylogeography; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D056910:Republic of Korea; D013624:Taiwan; D013785:Thailand
D004269:DNA, Bacterial