Mokrousov Igor
Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg 197101 Russia.
Tuberculosis (Edinb). 2018 May;110:91-95. doi: 10.1016/j.tube.2018.04.004. Epub 2018 Apr 10.
CRISPR-spoligotyping and MIRU-VNTR typing, SITVIT_WEB and MIRU-VNTRplus are the methods and online resources most widely used for Mycobacterium tuberculosis genotype family assignment and clustering analysis. They have been proven invaluable for molecular epidemiological studies of this important human pathogen in setting up the terminology and classification framework. However, they are inherently limited by insufficient knowledge of evolution of the targeted genome loci (especially, CRISPR). The situation is aggravated by the dogmatic, iconographic perception of these increasingly user-friendly online tools. Here, I present a critical essay on hot practical aspects related to the use of SITVIT_WEB and MIRU-VNTRplus, in particular, partly inadequate (sub)clade assignment due to imperfect decision rules, partly outdated methodological options offered to the users that permit to build scientifically unsound phylogenies from spoligotyping data. A confusing terminology, misclassification and false clustering are not abstract issues but make a scientific discussion meaningless, and I propose some courses for improvement.
CRISPR-间隔寡核苷酸分型和MIRU-VNTR分型，SITVIT_WEB和MIRU-VNTRplus是用于结核分枝杆菌基因型家族归属和聚类分析的最广泛使用的方法和在线资源。在建立术语和分类框架方面，它们已被证明对这种重要人类病原体的分子流行病学研究具有极高价值。然而，它们本质上受到对目标基因组位点（特别是CRISPR）进化了解不足的限制。这些日益用户友好的在线工具的教条式、图像化认知加剧了这种情况。在此，我撰写一篇评论文章，探讨与使用SITVIT_WEB和MIRU-VNTRplus相关的热门实际问题，特别是由于决策规则不完善导致部分（亚）分支归属不充分，以及向用户提供的部分过时方法选项，这些选项允许从间隔寡核苷酸分型数据构建科学上不合理的系统发育树。令人困惑的术语、错误分类和错误聚类并非抽象问题，而是会使科学讨论变得毫无意义，我提出了一些改进措施。
