Rapid Methods in Bacterial-DNA Fingerprinting

The characterization and comparison of isolates of bacterial species by comparing restriction enzyme digests of their chromosomal DNA (fingerprints) is highly discriminatory for different strains and allows similarities between them to be readily determined. However, the utility of the technique is dependent on the selection of appropriate restriction enzyme(s) and on the method of determining the similarities between the fingerprints generated. We report here a system which circumvents these two problems. The restriction enzyme is selected from amongst those which have a suitable frequency of restriction for given enzyme-genome combinations. The frequencies of restriction enzyme recognition sites are calculated from the frequencies of di- and trinucleotides in sequenced genes from the species of interest using Markov chain analysis. Fingerprints are compared by dividing them up into sections with DNA size standards, scoring the number of bands in a few of these sections, and comparing these scores (numerical profiles) to establish similarities. In this way a single electrophoretic gel yields easily analysable data which can be compared with data from other gels. The time from the acquisition of bacterial isolates to their final characterization is much reduced in comparison to existing methods.