Computer Analysis of IS6110 RFLP Patterns of Mycobacterium tuberculosis

The discovery of polymorphic, repetitive DNA in the Mycobacterzum tuberculosis complex has led to many methods for differentiating clinical isolates belonging to this spectes of pathogenic bacteria. The most widely used method 1s restriction fragment-length polymorphism (RFLP) analysis of msernon sequence IS6110, based on Southern blotting of PvuII-digested genomrc DNA and hybridization. IS6110 is a mobile genettc element of 1.3 kb that is present in virtually all Ad. tuberculosn strains (1). Because the number of IS6110 copies varies between 1 and 25, and the sites of insertion (IS) in the chromosome differ from strain to strain, an enormous diversity in IS6110 banding patterns is found among clmical isolates of hf. tuberculosis. This diversity is the basis for using IS6110 fingerprinting for epidemiological purposes. Generally, strains from outbreaks, or from patients with a common transmission route, display an identical banding pattern, although in large outbreaks, small variattons in banding patterns may be observed, such as the loss or gam of a single band (1,2,3). Strains with identical IS6120 banding patterns will be referred to as matching or “clustered” strains. Such clustered strains are very likely to be derived from a common ancestor in the recent past (perhaps two to ten years ago). Although the exact pace of the “molecular clock” of IS6210 is not known, strains do not usually change in then fingerprmt pattern during transmission chains lasting l-3 yr (2J-6).