DNA fingerprinting of Neisseria strains by rep-PCR

A directly repeated 26mer DNA sequence, Ngrep, from Neisseria gonorrhoeae and Neisseria meningitidis was used as the primer binding site for rep-PCR based DNA fingerprinting of bacterial strains. Oligonucleotide primers were synthesized complementary to, and in a direction 5'→3' facing outwards from the repetitive element. These primers were used in the PCR and yielded DNA fingerprints when differently sized rep-PCR products were separated by agarose gel electrophoresis. Specificity of rep-PCR based primer complementarity to the Ngrep repetitive DNA sequence was established by direct comparison with results obtained with primers complementary to a randomized Ngrep sequence. The rep-PCR method, based on Ngrep elements, yielded distinct DNA fingerprints in 5 of 8 eubacterial phyla tested suggesting conservation of related sequences in diverse bacterial species. Individual strains of N. gonerrhoeae and N. meningitidis were differentiated most effectively by the 18mer Ngrep oligonucleotide primers, probably due to increased specificity and stability of these primers relative to 14mer Ngrep primers. Furthermore, dendrogram analysis based on repPCR fingerprinting using either Ngrep oligonucleotide primer set readily distinguished gonococcal from meningococcal isolates by placing them in two distinct clusters.