Neisseria meningitidis (the meningococcus) is a naturally competent bacterial species in which intra-and interspecific horizontal gene transfer is a major source of genetic diversity. In strains of the electrophoretic type 37 (ET-37) complex and of the A4 cluster, we identified genomic DNA coding for a novel restrictionmodification system and for the tail of a previously unidentified prophage. Furthermore, a novel 7.2-kb DNA segment restricted to clones of the ET-37 complex and the A4 cluster was isolated and shown to occur both as a plasmid (pJS-B) and as a chromosomal integration. Neither the genomic loci nor pJS-B was present in ET-5 complex, lineage 3, or serogroup A meningococci. The differential distribution of the DNA segments described herein, as well as of opcA, porB, nmeAI, nmeBI, and nmeDI described previously, supports the concept of genetic isolation of hypervirulent lineages responsible for most cases of serogroup C disease worldwide.The species Neisseria meningitidis is composed of a large variety of clones and clonal groupings (reviewed in reference 1). The majority of clones colonizing the nasopharynx of humans should be regarded as avirulent (7), and only a few hypervirulent clonal groupings are responsible for the majority of disease in humans. In Europe, serogroup B disease is caused mainly by the electrophoretic type 5 (ET-5) complex and lineage 3 whereas serogroup C disease is caused by the ET-37 complex and the A4 cluster (reviewed in reference 1). Horizontal gene transfer within the naturally competent species and with commensal neisseriae has resulted in genetic variability (2,(11)(12)(13)27), but it has been demonstrated that hypervirulent lineages of both serogroups B and C can be readily distinguished by the presence or absence of several genomic loci; e.g., the ET-5 complex and lineage 3 are characterized by a class 3 porB gene, whereas a class 2 gene is found in the ET-37 complex and the A4 cluster (9, 43). Isotype I of the tbpB gene is restricted to meningococci of the ET-37 complex, while other hypervirulent lineages harbour isotype II (31). Furthermore, the latter lack the gene encoding the adhesin OpcA (32,44).We recently demonstrated a differential distribution of three novel restriction-modification (R-M) systems, nmeAI, nmeBI, and nmeDI (10), while a lineage 3-specific R-M system was described by Bart et al. (3). The differential distribution of meningococcal genes can be caused by rapid expansion of lineages with increased fitness, bottlenecking, periodic selection, and immune selection, which are mechanisms antagonizing the effects of recombination (2,15,16,26,33). In addition, we recently provided evidence that sexual isolation of clonal groupings is caused by differentially distributed R-M systems which partially disrupt genetic transformation (10). In the present study we have extended the list of currently known differentially distributed genes. We compared the ET-37 complex with the ET-5 complex by plasmid profiling and representational difference analysis (RDA). We id...