Molecular fingerprinting of Porphyromonas gingivalis by PCR of repetitive extragenic palindromic (REP) sequences and comparison with other fingerprinting methods.

Knowledge of the genetic structure of populations of potentially pathogenic bacteria is important in understanding the epidemiology of diseases. Porphyromonas gingivalis is thought to be an important aetiological agent in periodontal diseases and several methods have been used for typing strains of this species. Here, PCR with primers to repetitive extragenic palindromic sequences (REP-PCR) was compared with three other widely used molecular fingerprinting techniques -- restriction endonuclease analysis (REA), ribotyping and PCR with arbitrary primers (AP-PCR) -- to type P. gingivalis isolates from healthy and diseased periodontal sites. The data obtained with all four methods were in broad agreement and, with one exception, each subject harboured a single unique genotype of P. gingivalis. REP-PCR of P. gingivalis resulted in the production of 5-10 amplicons, which gave unique electrophoretic patterns in each individual (10 REP-PCR types in 10 patients) and similar results were obtained with AP-PCR. Two isolates from one subject appeared identical by REP-PCR and AP-PCR, but could be differentiated by ribotyping, although there was only minor polymorphism. Thus, ribotyping and REA were the most discriminating methods; however, these are time-consuming and expensive relative to the PCR-based techniques. REP-PCR has the advantage that the same pair of primers is used for all species, whereas AP-PCR needs to be optimised by screening a range of primers. These results show that REP-PCR is a useful and rapid technique for typing P. gingivalis.