Evaluation of Four Candidate VNTR Loci for Genotyping 225 Chinese Clinical Mycobacterium Tuberculosis Complex Strains
Evaluation of Four Candidate VNTR Loci for Genotyping 225 Chinese Clinical Mycobacterium Tuberculosis Complex Strains
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DOI：
10.3967/0895-3988.2012.01.012
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发表时间：
2012-02-01
影响因子：
3.5
通讯作者：
Wan Kang Lin
中科院分区：
文献类型：
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作者：
Jiang Yi;Liu Hai Can;Wan Kang Lin
Objective.目的评价4个候选的可变数目串联重复序列（VNTR）位点对结核分枝杆菌复合群菌株进行基因分型的价值。产生了结核菌株（CCDC 5079和CCDC 5180），并使用公开的序列数据，鉴定了四个候选VNTR基因座。用VNTR对225例中国人临床型M.结核复合菌株。结果BJ 1、BJ 2、BJ 3和BJ 4基因座的Hunter-Gaston指数（HGI）分别为0.634、0.917、0.697和0.910。结合所有四个基因座得到0.995的HGI值，从而证实基因分型具有良好的区分能力。从北京家族菌株基因分型获得的BJ 1、BJ 2、BJ 3和BJ 4的HGI值分别为0.447、0.878、0.315和0.850。结合所有四个位点产生的HGI值为0.988的基因分型的北京家庭菌株。我们观察到M的独特模式。bovis和M.结论这4个VNTR基因座可成功用于M.结核复合菌株。值得注意的是，这些新的基因座可能提供更多的信息，中国M。结核病分离株比目前建立的VNTR基因座分型。
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, 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.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.