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首页> 外文期刊>Journal of Clinical Microbiology >Combination of Single Nucleotide Polymorphism and Variable-Number Tandem Repeats for Genotyping a Homogenous Population of Mycobacterium tuberculosis Beijing Strains in China
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Combination of Single Nucleotide Polymorphism and Variable-Number Tandem Repeats for Genotyping a Homogenous Population of Mycobacterium tuberculosis Beijing Strains in China

机译：单核苷酸多态性和可变数目串联重复序列的结合用于北京结核分枝杆菌北京菌株的同质群体基因分型

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The standard 15- and 24-locus variable-number tandem repeat (VNTR) genotyping methods have demonstrated adequate discriminatory power and a small homoplasy effect for tracing tuberculosis (TB) transmission and predicting Mycobacterium tuberculosis lineages in European and North American countries. However, its validity for the definition of transmission in homogenous M. tuberculosis populations in settings with high TB burdens has been questioned. Here, we genotyped a population-based collection of 191 Beijing strains based on standard 15-locus VNTR (VNTR-15) and 8 single nucleotide polymorphisms (SNPs) in Shanghai, China. Limited discriminatory power and high rates of VNTR homoplasy were observed in the homogenous population of evolutionarily “modern” Beijing strains. Additional typing of three hypervariable loci (VNTR3820, VNTR4120, and VNTR3232) was performed for VNTR-15-based clusters. High variations of hypervariable alleles were observed in clusters with inconsistent SNP sublineages. We concluded that SNPs and hypervariable VNTR loci are helpful to enhance the discriminatory power and decrease the VNTR homoplasy effect for defining clusters. We recommend the combination of standard VNTR-15 and SNPs as first-line typing methods and the hypervariable loci for second-line typing of clustered strains for molecular epidemiology studies of homogenous M. tuberculosis populations.
机译：在欧洲和北美国家，标准的15位和24位可变数目串联重复（VNTR）基因分型方法已证明具有足够的区分力和小的同质异能，可用于追踪结核病（TB）的传播和预测结核分枝杆菌的血统。然而，对于在结核病高负担地区均质结核分枝杆菌人群中定义传播的有效性提出了质疑。在这里，我们基于标准的15个位点的VNTR（VNTR-15）和8个单核苷酸多态性（SNPs）在中国上海对191个北京菌株进行了基于人群的基因分型。在进化的“现代”北京菌株的同质群体中观察到有限的辨别力和较高的VNTR同质性。对于基于VNTR-15的群集，还对三个高变基因座（VNTR3820，VNTR4120和VNTR3232）进行了附加输入。在具有不一致的SNP亚谱系的簇中观察到高变等位基因的高度变化。我们得出的结论是，SNP和高变VNTR基因座有助于增强判别力并降低VNTR同质异型效应以定义簇。我们建议将标准VNTR-15和SNPs作为一线分型方法，将高变位点用于聚类菌株的二线分型，以用于同质结核分枝杆菌种群的分子流行病学研究。

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