Evaluation of four candidate VNTR Loci for genotyping 225 Chinese clinical Mycobacterium tuberculosis complex strains.
- Author:
Yi JIANG
1
;
Hai Can LIU
;
Hua Jun ZHENG
;
Biao TANG
;
Xiang Feng DOU
;
Xiu Qin ZHAO
;
Yong Qiang ZHU
;
Bing LU
;
Sheng Yue WANG
;
Hai Yan DONG
;
Guo Ping ZHAO
;
Yuan Yuan ZHANG
;
Biao KAN
;
Kang Lin WAN
Author Information
- Publication Type:Journal Article
- MeSH: Cluster Analysis; Genotyping Techniques; Humans; Minisatellite Repeats; Mycobacterium bovis; genetics; Mycobacterium tuberculosis; genetics
- From: Biomedical and Environmental Sciences 2012;25(1):82-90
- CountryChina
- Language:English
-
Abstract:
OBJECTIVETo evaluate four candidate variable number tandem repeat (VNTR) loci for genotyping Mycobacterium tuberculosis complex strains.
METHODSGenomic sequences for two M. tuberculosis strains (CCDC5079 and CCDC5180) were generated, and using published sequence data, four candidate VNTR loci were identified. The VNTRs were used to genotype 225 Chinese clinical M. tuberculosis complex strains. The discriminatory power of the VNTRs was evaluated using BioNumerics 5.0 software.
RESULTSThe Hunter-Gaston Index (HGI) for BJ1, BJ2, BJ3, and BJ4 loci was 0.634, 0.917, 0.697, and 0.910, respectively. Combining all four loci gave an HGI value of 0.995, thus confirming that the genotyping had good discriminatory power. The HGI values for BJ1, BJ2, BJ3, and BJ4, obtained from Beijing family strain genotyping, were 0.447, 0.878, 0.315, and 0.850, respectively. Combining all four loci produced an HGI value of 0.988 for genotyping the Beijing family strains. We observed unique patterns for M. bovis and M. africanum strains from the four loci.
CONCLUSIONWe have shown that the four VNTR loci can be successfully used for genotyping M. tuberculosis complex strains. Notably, these new loci may provide additional information about Chinese M. tuberculosis isolates than that currently afforded by established VNTR loci typing.
