The classification of MTBC strains into genetic groups is important to track transmission patterns and to develop a better understanding of pathologic specificities in TB. MTBC a genetic groups have been defined at different levels of granularity. TB-Lineage can be used to predict major lineages as defined by the United States Centers for Disease Control and Prevention (CDC). TB-Lineage can be used to predict SIVIT clades or sub-lineages as defined by the WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe (IP).
Major lineages are predicted by two different methods. In the RULES method a set of rules was developed to classify isolates into these strain groups, based on the presence / absence of spacer sequences in the spoligotype pattern and the values of the MIRU loci. TB-Lineage rules requires spoligotypes and can also use MIRU. In the CBN method, major lineages are predicted using a conformal Bayesian network. CBN can predict major lineages using spoligotype alone, MIRU alone, or both. Details on the RULES method can be found in this paper:"A Shabbeer, LS Cowan, C Ozcaglar, N Rastogi, SL Vandenberg, B Yener, KP Bennett, TB-Lineage: An online tool for classification and analysis of strains of Mycobacterium tuberculosis complex Infection, Genetics and Evolution 12 (4), 789-797, 2012.
Details on CBN can be found in "A Shabbeer, LS Cowan, C Ozcaglar, N Rastogi, SL Vandenberg, B Yener, KP Bennett, TB-Lineage: An online tool for classification and analysis of strains of Mycobacterium tuberculosis complex Infection, Genetics and Evolution 12 (4), 789-797, 2012.
Further insights into genetic groups of MTBC can be provided by looking into its SITVIT sublineage/clade as defined by IP. We designed a knowledge-based Bayesian network (KBBN) which treats sets of expert rules as prior distribution on classes. KBBN uses data to refine rule-based classifiers when the rule set is incomplete or ambiguous. KBBN is a predictive model for 69 MTBC clades found in the SITVIT international collection. A table of the 69 SITVIT clades predicted by KBBN can be found here.For more information consult the following paper: M. Aminian, D. Couvin, A. Shabbeer, K. Hadley, S. Vandenberg, N. Rastogi, K. P. Bennett, Predicting Mycobacterium tuberculosis Complex Clades Using Knowledge-Based Bayesian Networks, Biomedical Research International, to appear, 2013.