Evaluation of Four Candidate VNTR Loci for Genotyping 225 Chinese Clinical Mycobacterium Tuberculosis Complex Strains
Abstract: Objective To evaluate four candidate variable number tandem repeat (VNTR) loci for genotyping Mycobacterium tuberculosis complex strains.Methods Genomic 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. Results The 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,B J3,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.Conclusion We 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.
|Citation:||JIANG Yi, LIU Hai Can, ZHENG Hua Jun, TANG Biao, DOU Xiang Feng, ZHAO Xiu Qin, ZHU Yong Qiang, LU Bing, WANG Sheng Yue, DONG Hai Yan, ZHAO Guo Ping, ZHANG Yuan Yuan, KAN Biao, WAN Kang Lin. Evaluation of Four Candidate VNTR Loci for Genotyping 225 Chinese Clinical Mycobacterium Tuberculosis Complex Strains[J]. Biomedical and Environmental Sciences, 2012, 25(1): 82-90. doi: 10.3967/0895-3988.2012.01.012|