NATURE OF DNA POLYMORPHISM IN THE DIRECT REPEAT CLUSTER OF MYCOBACTERIUM-TUBERCULOSIS - APPLICATION FOR STRAIN DIFFERENTIATION BY A NOVEL TYPING METHOD

Mycobacterium tuberculosis complex strains contain a unique chromosoma l region, which consists of multiple 36 bp direct repeats (DRs), which are interspersed by unique spacers 35 to 41 bp in length. In this stu dy we investigated the nature of the DNA polymorphism of this DR clust er by sequencing part of this region in a large number of M. tuberculo sis complex strains. Two types of genetic rearrangements were observed . One type consists of the variation in one or a few discrete, contigu ous DRs plus spacer sequences. This variation is probably driven by ho mologous recombination between adjacent or distant DRs. The other type of polymorphism is probably driven by transpositional events of the i nsertion sequence, IS6110, which is almost invariably present in the D R cluster of M. tuberculosis complex strains. Based on the nature of t he DNA polymorphism in the DR cluster, we developed a novel method of strain differentiation, direct variable repeat polymer chain reaction (DVR-PCR), which enables typing of individual M. tuberculosis strains in a single PCR. The method allows an excellent differentiation of epi demiologically unrelated isolates and, in principle, the DVR-PCR allow s the detection of M. tuberculosis and strain differentiation at the s ame time.