IS1245-based restriction fragment length polymorphism (RFLP) analysis has been proposed recently for molecular typing of isolates. As there is no standardised method with respect to the optimal restriction enzyme, three restriction endonucleases were tested for analysis of 17 human isolates. The restriction endonucleases, selected on the basis of the physical maps of IS1245 and of the highly homologous IS1311, were AI, that cleaves IS1245, II, that cleaves IS1311, and I, that cleaves both IS and IS. All the restriction endonucleases yielded polymorphic and complex RFLP patterns. However, AI- and I-generated bands were more evenly distributed and easier to detect than II-generated bands, most of which clustered in a narrow zone of the fingerprint. In some cases, DNA digestion with AI or I yielded probe-specific restriction fragments of molecular size lower than expected. Moreover, digestion with I, which was expected to generate the highest numbers of bands in all the isolates, yielded fewer bands than were obtained with AI or II in 14 and 5 isolates, respectively. These findings might suggest the existence of unidentified IS1245-related insertion element(s) in isolates. Computer analysis of the IS1245-based RFLP patterns of isolates showed that the restriction endonucleases were capable, although with minor differences, of defining distinct banding patterns and clusters of identical or highly related isolates, thus confirming IS1245-based RFLP analysis as a useful technique for epidemiological studies.


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