Surikova O V, Voitech D S, Kuzmicheva G, Tatkov S I, Mokrousov I V, Narvskaya O V, Rot M A, van Soolingen D, Filipenko M L
Pharmacogenomics Group, Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia.
Eur J Epidemiol. 2005;20(11):963-74. doi: 10.1007/s10654-005-3636-5.
The W-Beijing family is a widespread Mycobacterium tuberculosis clonal lineage that frequently causes epidemic outbreaks. This family is genetically homogeneous and conserved, so ETR-VNTR (exact tandem repeat-variable number of tandem repeats) typing is insufficient for strain differentiation, due to a common ETR-A to E profile (42435). This leads to the false clustering in molecular epidemiological studies, especially in the regions of predominance of the W-Beijing family. In this study, we searched for VNTR loci with a high evolutionary rate of polymorphism in the W-Beijing genome. Here we further evaluated VNTR typing on a set of 99 Mycobacterium tuberculosis clinical isolates and reference strains. These isolates were characterized and classified into several genotype families based on three ETR loci (A, C, E) and eight additional loci [previously described as QUB (Queen's University Belfast) or MIRU (Mycobacterial Interspersed Repetitive Units) or Mtubs]. Ninety-nine strains were divided into 74 VNTR-types, 51 isolates of the W-Beijing family identified by IS6110 RFLP-typing (the restriction fragment length polymorphism-typing) and/or spoligotyping were subdivided into 30 VNTR-types. HGDI (the Hunter-Gaston discriminatory index) for all studied loci was close to that of IS6110 RFLP typing, a "gold standard" method for subtyping M. tuberculosis complex strains. The QUB 26 and QUB 18 loci located in the PPE genes were highly polymorphic and more discriminative than other loci (HGDI is 0.8). Statistically significant increase of tandem repeats number in loci ETR-A, -E, QUB 26, QUB 18, QUB 11B, Mtub21 was revealed in the W-Beijing group compared to genetically divergent non-W-Beijing strains. Thirty-six isolates were subjected to IS6110 RFLP typing. The congruence between results of the IS6110 RFLP typing and 11-loci VNTR typing was estimated on 23 isolates of the W-Beijing family. These isolates were subdivided into 9 IS6110-RFLP types and 13 VNTR types. The poor profiles correlation (0.767) reflects the differences in the rate and type of evolution between genome regions targeted by IS6110-RFLP and VNTR typing. VNTR typing in proposed format is powerful tool for discrimination of M. tuberculosis strains with different level of genetic relationship.
W-北京家族是一种广泛传播的结核分枝杆菌克隆谱系，经常引发流行疫情。该家族在基因上具有同质性和保守性，因此由于存在共同的ETR-A到E型谱（42435），ETR-VNTR（精确串联重复-串联重复可变数目）分型不足以区分菌株。这导致在分子流行病学研究中出现错误聚类，尤其是在W-北京家族占主导的地区。在本研究中，我们在W-北京基因组中寻找具有高多态性进化速率的VNTR位点。在此，我们进一步对一组99株结核分枝杆菌临床分离株和参考菌株进行了VNTR分型评估。这些分离株基于三个ETR位点（A、C、E）和另外八个位点[先前描述为QUB（贝尔法斯特女王大学）或MIRU（分枝杆菌散布重复单元）或Mtubs]进行特征分析并分类为几个基因型家族。99株菌株分为74种VNTR型，通过IS6110 RFLP分型（限制性片段长度多态性分型）和/或间隔寡核苷酸分型鉴定出的51株W-北京家族分离株又细分为30种VNTR型。所有研究位点的HGDI（Hunter-Gaston鉴别指数）接近IS6110 RFLP分型，IS6110 RFLP分型是结核分枝杆菌复合菌株分型的“金标准”方法。位于PPE基因中的QUB 26和QUB 18位点具有高度多态性，且比其他位点更具鉴别力（HGDI为0.8）。与基因差异较大的非W-北京菌株相比，W-北京组中ETR-A、-E、QUB 26、QUB 18、QUB 11B、Mtub21位点的串联重复数有统计学意义的增加。对36株分离株进行了IS6110 RFLP分型。在23株W-北京家族分离株上评估了IS6110 RFLP分型结果与11位点VNTR分型结果的一致性。这些分离株细分为9种IS6110-RFLP型和
