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Spoligotyping is based on the polymorphism in the direct repeat (DR) locus of the mycobacterial chromosome (Kamerbeek, 1997). The DR locus is one of the most well studied loci of the MTC genome showing considerable strain-to-strain polymorphism (Fang, 1998). The function of the DR locus in MTC bacteria is presently unknown (van Embden, 2000).
The well-conserved 36-bp direct repeats are interspersed with unique spacer sequences varying from 35 to 41 bp in size. The order of the spacers was found to be well conserved (van Embden, 2000). The region comprised the DR plus the adjacent spacer has been termed the direct variable repeat (DVR) (Groenen, 1993). Currently, 94 different spacer sequences have been identified of which 43 are used for MTC strain differentiation (van Embden, 2000). Clinical isolates of MTC bacteria can be differentiated by the presence or absence of one or more spacers.
Each spoligotype can then be conveniently represented as a 43-dimensional binary vector; for example, the most common
spoligotype pattern of M. tuberculosis Beijing strain is:
. Octal code
designations (
for M. tuberculosis Beijing) are also widely used (Dale,
2001).
Spoligotypes are believed to evolve by deletion of a single or multiple contiguous DVRs (Warren, 2002). Various genetic mechanisms, such as homologous recombination, transposition, DNA replication slippage, or point mutation can cause the deletion (Mostrom, 2002; Warren, 2002). The DR region is one of the hotspots for the IS6110 integration (Groenen, 1993; Legrand, 2001).
Please note that we do not attempt to derive MTC phylogeny based on spoligotyping. Most of the algorithms for phylogenetic trees are based on the assumption of markers independence. The fact that spoligotypes may evolve by a loss of several adjacent DVRs (which means that they are dependent on each other) complicates the use of these patterns for deriving MTC phylogeny (Warren, 2002).