Development of a Hierarchical Variable-Number Tandem Repeat Typing Scheme for Mycobacterium tuberculosis in China
Development of a Hierarchical Variable-Number Tandem Repeat Typing Scheme for Mycobacterium tuberculosis in China
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中国结核分枝杆菌分级可变数量串联重复分型方案的开发
DOI：
10.1371/journal.pone.0089726
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发表时间：
2014-02-25
期刊：
影响因子：
3.7
通讯作者：
Gao, Qian
中科院分区：
文献类型：
--
作者：
Luo, Tao;Yang, Chongguang;Gao, Qian
基于可变数目串联重复序列 (VNTR) 分析的分子分型是识别结核分枝杆菌传播的有前途的工具。然而，目前提出的15位点和24位点VNTR集（VNTR-15/24）的分辨率有限，并且包含太多位点，无法在高负担国家进行大规模分型。为了在中国制定最佳分型方案，我们利用来自全国六个省份的 1362 个临床分离株的人群收集数据，评估了 25 个 VNTR 位点的分辨率和稳健性。大多数位点的分辨率在区域之间表现出相当大的差异。通过计算 20 个稳健基因座的所有可能组合的平均分辨率，我们确定了至少包含 9 个基因座 (VNTR-9) 的最佳基因座集，可以实现与标准 VNTR-15 相当的分辨率。 VNTR-9 在所有六个区域都具有一致的高分辨率，并且在定义聚类和独特基因型方面与 VNTR-15 高度一致。此外，VNTR-9 为结核分枝杆菌谱系/亚谱系的分类提供了系统发育信息。三个高变基因座（HV-3），VNTR 3232、VNTR 3820 和 VNTR 4120，被证明对于进一步区分基于 VNTR-9 的无关聚类菌株非常重要。我们提出优化的VNTR-9作为一线方法和HV-3作为中国及周边国家结核分枝杆菌分子分型的二线方法。开发能够以少量位点实现高分辨率的分层VNTR分型方法可适用于其他高负担国家的分子流行病学研究。
Molecular typing based on variable-number tandem repeats (VNTR) analysis is a promising tool for identifying transmission of Mycobacterium tuberculosis. However, the currently proposed 15- and 24-locus VNTR sets (VNTR-15/24) only have limited resolution and contain too many loci for large-scale typing in high burden countries. To develop an optimal typing scheme in China, we evaluated the resolution and robustness of 25 VNTR loci, using population-based collections of 1362 clinical isolates from six provinces across the country. The resolution of most loci showed considerable variations among regions. By calculating the average resolution of all possible combinations of 20 robust loci, we identified an optimal locus set with a minimum of 9 loci (VNTR-9) that could achieve comparable resolution of the standard VNTR-15. The VNTR-9 had consistently high resolutions in all six regions, and it was highly concordant with VNTR-15 for defining both clustered and unique genotypes. Furthermore, VNTR-9 was phylogenetically informative for classifying lineages/sublineages of M. tuberculosis. Three hypervariable loci (HV-3), VNTR 3232, VNTR 3820 and VNTR 4120, were proved important for further differentiating unrelated clustered strains based on VNTR-9. We propose the optimized VNTR-9 as first-line method and the HV-3 as second-line method for molecular typing of M. tuberculosis in China and surrounding countries. The development of hierarchical VNTR typing methods that can achieve high resolution with a small number of loci could be suitable for molecular epidemiology study in other high burden countries.