Methods and kits for typing prokaryotes and eukaryotes are disclosed. A specific DNA fragment in the rRNA intergene region is amplified by PCR using two universal oligonucleotide primers. The labeled PCR product is cleaved with a variety of restriction endonucleases and electrophoresed on an automated DNA sequencer. The methods and kits are beneficial in, for example, a clinical laboratory because they allow for rapid strain identification of pathogenic bacteria. The DNA fingerprinting methods and kits of the present invention are more definitive, since genomic bacterial DNA is used. One advantage of the methods of the present invention is the speed with which results are obtained. For example, a preliminary screen by agarose gel electrophoresis of a PCR product can be completed five to six hours after receiving hospital isolates. The preliminary screen can then be confirmed in approximately 24 hours by RFLP analysis on an automated sequencer. The speed of the methods of the present invention provide infection control personnel with adequate information to contain and prevent the spread of nosocomial infections, rather than having analyses done retrospectively.
