Department of Periodontology, University Hospital Münster, Münster, Germany.
Infect Genet Evol. 2012 Jun;12(4):748-54. doi: 10.1016/j.meegid.2012.01.021. Epub 2012 Feb 10.
Molecular diagnostics and genotyping of pathogens have become indispensable tools in clinical microbiology and disease surveillance. For isolates of the Mycobacterium tuberculosis complex (MTBC, causative agents of tuberculosis), multilocus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRU) has been internationally adopted as the new standard, portable, reproducible, and discriminatory typing method. Here, we review new sets of specialized web based bioinformatics tools that have become available for analyzing MLVA data especially in combination with other, complementary genotyping markers (polyphasic analysis). Currently, there are only two databases available that are not restricted to store one kind of genotyping data only, namely SITVIT/SpolDB4 and MIRU-VNTRplus. SITVIT/SpolDB4 (http://www.pasteur-guadeloupe.fr:8081/SITVITDemo) contains spoligotyping data from a large number of strains of diverse origin. However, besides options to query the data, the actual version of SITVIT/SpolDB4 offers no functionality for more complex analysis e.g. tree-based analysis. In comparison, the MIRU-VNTRplus web application (http://www.miru-vntrplus.org), represents a freely accessible service that enables users to analyze genotyping data of their strains alone or in comparison with a currently limited but well characterized reference database of strains representing the major MTBC lineages. Data (MLVA-, spoligotype-, large sequence polymorphism, and single nucleotide polymorphism) can be visualized and analyzed using just one genotyping method or a weighted combination of several markers. A variety of analysis tools are available such as creation of phylogenetic and minimum spanning trees, semi-automated phylogenetic lineage identification based on comparison with the reference database and mapping of geographic information. To facilitate scientific communication, a universal, expanding genotype nomenclature (MLVA MtbC15-9 type) service that can be queried via a web- or a SOAP-interface has been implemented. An extensive documentation guides users through all application functions. Perspectives for future development, including generalization to other bacterial species, are presented.
分子诊断和病原体基因分型已成为临床微生物学和疾病监测中不可或缺的工具。对于结核分枝杆菌复合群（MTBC，结核病的病原体）的分离株，针对分枝杆菌插入重复单位（MIRU）的多位点可变数串联重复分析（MLVA）已被国际采用为新的标准、便携、可重复和有区别的分型方法。在这里，我们回顾了一些新的专门的基于网络的生物信息学工具，这些工具已经可用于分析 MLVA 数据，特别是与其他互补的基因分型标记（多相分析）结合使用。目前，只有两个数据库可用，它们不限于仅存储一种基因分型数据，即 SITVIT/SpolDB4 和 MIRU-VNTRplus。SITVIT/SpolDB4（http://www.pasteur-guadeloupe.fr:8081/SITVITDemo）包含来自多种来源的大量菌株的 spoligotyping 数据。然而，除了查询数据的选项外，SITVIT/SpolDB4 的实际版本没有提供更复杂分析的功能，例如基于树的分析。相比之下，MIRU-VNTRplus 网络应用程序（http://www.miru-vntrplus.org）代表了一个免费访问的服务，使用户能够单独分析其菌株的基因分型数据，或者与目前有限但具有代表性的 MTBC 主要谱系的菌株参考数据库进行比较。数据（MLVA-、 spoligotype-、大片段多态性和单核苷酸多态性）可以使用一种或几种标记的加权组合进行可视化和分析。提供了各种分析工具，例如创建系统发育和最小生成树、基于与参考数据库比较的半自动系统发育谱系识别以及地理信息映射。为了促进科学交流，实现了一个通用的、扩展的基因型命名法（MLVA MtbC15-9 型）服务，可以通过网络或 SOAP 接口进行查询。详细的文档指导用户使用所有应用程序功能。还介绍了未来发展的前景，包括推广到其他细菌物种。
