用全基因组测序评价VNTR分型在泛耐药结核分枝杆菌传播中的应用

近年来，随着技术的进步、测序成本的降低，全基因组测序(whole-genome sequencing，WGS)技术开始应用于结核分枝杆菌传播的研究。本研究采用基于单核苷酸多态性(single nucleotide polymorphism，SNP)的分型方法评价多位点数目可变串联重复序列(variable-number tandem-repeat，VNTR)分型判断泛耐药结核分枝杆菌(extensively drug-resistant Mycobacterium tuberculosis，XDR-TB)传播及成簇特征的准确性。对2003-2009年重庆市肺科医院诊断的55例XDR-TB菌株分别进行9＋3个位点的VNTR分型和WGS分析，分别构建系统进化树，并比较两种方法判断成簇的一致性与差异。VNTR分型方法鉴定出45个基因型，其中39株为单一基因型，16株(29.1%)分别归入6个基因簇。规定菌株间差异不超过12个SNP即为成簇，WGS将20株(36.4%)分为5个簇。两种方法判断成簇的一致性为 63.6%。与WGS相比，VNTR分型的灵敏度为 40.0%，特异度为 77.1%。相比于WGS，VNTR分型特异度较高，但仅凭其结果可能会错误估计XDR-TB的传播性。因此，规定菌株间相差不超过12个SNP即有近期传播关系是否适用于XDR-TB，有待进一步研究。

Validation of VNTR’s application for spreading of extensively drug-resistant Mycobacterium tuberculosis by whole-genome sequencing

Whole-genome sequencing (WGS) is a new technology to study the transmission of Mycobacterium tuberculosis (M. tuberculosis), in addition to variable-number tandem-repeat (VNTR) typing and clustering. In this study, a total of 55 XDR-TB strains isolated from a hospital in Chongqing from 2003 to 2009 were genotyped and clustered (≤12 SNPs) by 9＋3 loci VNTR and WGS respectively. The evolutionary trees by the two methods were built, and the consistency and differences in clustering were compared. By VNTR, 55 strains of M. tuberculosis could be divided into 45 genotypes, of which 39 were single genotypes and 16 were in 6 clusters. Twenty of the 55 strains (36.4%) were divided into 5 clusters by WGS. The consistency of the two methods in identifying clusters was 63.6%. Compared with WGS, VNTR typing method had a sensitivity of 40.0% and a specificity of 77.1%. VNTR typing method had a higher specificity than WGS. The results indicate that VNTR typing alone might incorrectly estimate the transmission of XDR-TB, and clustering by no more than 12 SNPs for recent transmission of XDR-TB is a practical standard deserving more studies.