TB-Lineage: An online tool for classification and analysis of strains of Mycobacterium tuberculosis complex

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• 作者：Amina Shabbeer^a ; ^{shabba@cs.rpi.edu} ; Lauren S. Cowan^c ; ^los4@cdc.gov ; Cagri Ozcaglar^a ; ^{ozcagc2@cs.rpi.edu} ; Nalin Rastogi^d ; ^{nrastogi@pasteur-guadeloupe.fr} ; Scott L. Vandenberg^e ; ^{vandenberg@siena.edu} ; Bü ; lent Yener^a ; ^{yener@cs.rpi.edu} ; Kristin P. Bennett^a ; ^b ; ^{bennek@rpi.edu}
• 关键词：Tuberculosis ; Classification ; Spoligotype ; MIRU-VNTR ; Spoligoforest ; Lineage
• 刊名：Infection ; Genetics and Evolution
• 出版年：2012
• 期刊代码：119_15671348
• 类别：med
• 出版时间：June, 2012
• 卷：12
• 期：4
• 页码：789-797
• 文件大小：1278 K

摘要

This paper formulates a set of rules to classify genotypes of the Mycobacterium tuberculosis complex (MTBC) into major lineages using spoligotypes and MIRU-VNTR results. The rules synthesize prior literature that characterizes lineages by spacer deletions and variations in the number of repeats seen at locus MIRU24 (alias VNTR2687). A tool that efficiently and accurately implements this rule base is now freely available at . When MIRU24 data is not available, the system utilizes predictions made by a Na茂ve Bayes classifier based on spoligotype data. This website also provides a tool to generate spoligoforests in order to visualize the genetic diversity and relatedness of genotypes and their associated lineages. A detailed analysis of the application of these tools on a dataset collected by the CDC consisting of 3198 distinct spoligotypes and 5430 distinct MIRU-VNTR types from 37,066 clinical isolates is presented. The tools were also tested on four other independent datasets. The accuracy of automated classification using both spoligotypes and MIRU24 is >99%, and using spoligotypes alone is >95%. This online rule-based classification technique in conjunction with genotype visualization provides a practical tool that supports surveillance of TB transmission trends and molecular epidemiological studies.