title: TB-Lineage: an online tool for classification and analysis of strains of Mycobacterium tuberculosis complex.
abstract: 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 http://tbinsight.cs.rpi.edu/run_tb_lineage.html. When MIRU24 data is not available, the system utilizes predictions made by a Naïve 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.
authors.affiliation: Computer Science Dept., Rensselaer Polytechnic Institute, Troy, NY, USA. shabba@cs.rpi.edu
authors.forename: Amina
authors.initials: A
authors.lastname: Shabbeer
authors.forename: Lauren S
authors.initials: LS
authors.lastname: Cowan
authors.forename: Cagri
authors.initials: C
authors.lastname: Ozcaglar
authors.forename: Nalin
authors.initials: N
authors.lastname: Rastogi
authors.forename: Scott L
authors.initials: SL
authors.lastname: Vandenberg
authors.forename: Bülent
authors.initials: B
authors.lastname: Yener
authors.forename: Kristin P
authors.initials: KP
authors.lastname: Bennett
mesh_terms: D015373:Bacterial Typing Techniques; D019295:Computational Biology / Q000379:methods; D004269:DNA, Bacterial; D005838:Genotype; D006801:Humans; D020407:Internet; D018598:Minisatellite Repeats; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D012984:Software; D014376:Tuberculosis / Q000453:epidemiology / Q000635:transmission
chemical_list: D004269:DNA, Bacterial