Global Distribution of Mycobacterium tuberculosis Spoligotypes

Abstract

We present a short summary of recent observations on the global distribution of the major clades of the Mycobacterium tuberculosis complex, the causative agent of tuberculosis. This global distribution was defined by data-mining of an international spoligotyping database, SpolDB3. This database contains 11,708 patterns from as many clinical isolates originating from more than 90 countries. The 11,708 spoligotypes were clustered into 813 shared types. A total of 1,300 orphan patterns (clinical isolates showing a unique spoligotype) were also detected.

Identifying Mycobacterium tuberculosis complex strain families using spoligotypes

“…We used the stability, or average best match (Hopcroft et al, 2004), and the log-likelihood to choose a final mixture model. The results were compared to the families that have been identified using the prototypes extracted from the SpolDB3 database (Filliol et al, 2002). A more detailed description of the methods used can be found in the Appendix.…”

“…The SpolDB3-based model had 36 components: 32 corresponding to previously empirically defined families (Filliol et al, 2002) and four added in this study. Figure 1 summarizes the sorted by stability results of our method obtained using this model.…”

“…SpolDB3 is a prominent achievement in the molecular epidemiological studies of TB since the current version of the database and its subsequent updates (SpolDB4 already exists) represent an extensive compilation of worldwide diversity of spoligotypes. Groups of related spoligotypes were interchangeably called (sub)families, (sub)clades, and classes (Filliol et al, 2002;Filliol et al, 2003). Throughout this paper, we will use the term family for a collection of strains with related spoligotypes.…”

“…Spoligotyping differentiates isolates of MTC strains by determining the absence or presence of the 43 defined spacer sequences. Spoligotyping is a fast, highly reproducible method, and the genotyping result has a simple binary format, which permits the exchange of data and facilitates the construction of large collaborative databases (Filliol et al, 2002;Filliol et al, 2003).…”

“…These nine families were further broken down into 36 subfamilies in the global database SpolDB3, using visual rules (Filliol et al, 2002). SpolDB3 is a prominent achievement in the molecular epidemiological studies of TB since the current version of the database and its subsequent updates (SpolDB4 already exists) represent an extensive compilation of worldwide diversity of spoligotypes.…”