Department of Microbiology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, Thailand.
Tuberculosis (Edinb). 2010 Jan;90(1):9-15. doi: 10.1016/j.tube.2009.10.006. Epub 2009 Nov 12.
Spoligotyping and variable-number tandem repeats (VNTR) typing have been increasingly used for differentiating Mycobacterium tuberculosis strains with low copy numbers of IS6110. However, there are few studies comparing their potential to type the strains originating from South and Southeast Asia where many of the isolates have only a few copies, or even single copy, of IS6110. Here, we evaluated the genotyping of 187M. tuberculosis isolates harboring 1-6 copies of IS6110, available from a population-based study in Chiangrai, northern Thailand during 1998-2000, using spoligotyping and VNTR typing. The low-copy-number isolates constituted about 34% of all M. tuberculosis isolated in the province. Discriminating capacities and cluster identification by the two methods were compared with each other and to those obtained by the standard IS6110-restriction fragment length polymorphism (RFLP) method. We found that VNTR typing based on the studied 10-loci set generated more distinct patterns (151 patterns) than spoligotyping (54 patterns) and IS6110-RFLP (65 patterns). Most of the RFLP- or spoligotyping-defined clusters were subdivided by VNTR typing. Combining IS6110-RFLP with VNTR typing produced 164 distinct patterns and 21.9% of clustered isolates whereas the combination of IS6110-RFLP and spoligotyping gave 103 different patterns and 59.4% of clustered isolates. Our results confirm the utility of VNTR typing as the secondary method of choice for investigating the epidemiology of M. tuberculosis with low copy numbers of IS6110.
spoligotyping 和可变数目串联重复（VNTR）分型越来越多地用于区分低拷贝数 IS6110 的结核分枝杆菌菌株。然而，关于其对来自南亚和东南亚地区菌株进行分型的潜力的研究较少，这些地区的许多分离株只有少数拷贝，甚至只有单个拷贝的 IS6110。在这里，我们使用 spoligotyping 和 VNTR 分型评估了来自 1998-2000 年泰国北部清莱基于人群的研究中携带 1-6 个拷贝 IS6110 的 187 株结核分枝杆菌分离株的基因分型。低拷贝数分离株约占该省所有结核分枝杆菌分离株的 34%。比较了两种方法的区分能力和聚类识别，并与标准 IS6110 限制性片段长度多态性（RFLP）方法的结果进行了比较。我们发现，基于所研究的 10 个位点集的 VNTR 分型产生了比 spoligotyping（54 种模式）和 IS6110-RFLP（65 种模式）更多不同的模式（151 种模式）。大多数 RFLP 或 spoligotyping 定义的聚类通过 VNTR 分型进一步细分。将 IS6110-RFLP 与 VNTR 分型相结合可产生 164 种不同的模式和 21.9%的聚类分离株，而将 IS6110-RFLP 和 spoligotyping 相结合可产生 103 种不同的模式和 59.4%的聚类分离株。我们的结果证实了 VNTR 分型作为调查低拷贝数 IS6110 的结核分枝杆菌流行病学的首选二级方法的实用性。
