Representational difference analysis of Neisseria meningitidis identifies sequences that are specific for the hyper-virulent lineage III clone

Neisseria meningitidis may cause meningitis and septicemia. Since the early 1980s, an increased incidence of meningococcal disease has been caused by the lineage III clone in many countries in Europe and in New Zealand. We hypothesized that lineage III meningococci have specific DNA sequences, providing an opportunity to facilitate epidemiological studies by detecting lineage III isolates rapidly. Applying representational difference analysis on one lineage III tester strain and two non-lineage III driver strains, we identified three lineage III-specific sequences, probably part of a single locus encoding a restriction modification system. A PCR based on one of these sequences identified lineage III meningococcal isolates with a sensitivity of 100% and a specificity of 93%, which is superior to the serological identification of lineage III isolates