Neisseria meningitis is a human commensal bacterium that occasionally causes life-threatening disease. As with a number of other bacterial pathogens, meningococcal populations comprise distinct lineages, which persist over many decades and during global spread in the face of high rates of recombination. In addition, the propensity to cause invasive disease is associated with particular ''hyperinvasive'' lineages that coexist with less invasive lineages despite the fact that disease does not contribute to host-to-host transmission. Here, by combining a modeling approach with molecular epidemiological data from 1,108 meningococci isolated in the Czech Republic over 27 years, we show that interstrain competition, mediated by immune selection, can explain both the persistence of multiple discrete meningococcal lineages and the association of a subset of these with invasive disease. The model indicates that the combinations of allelic variants of housekeeping genes that define these lineages are associated with very small differences in transmission efficiency among hosts. These findings have general implications for the emergence of lineage structure and virulence in recombining bacterial populations.bacteria ͉ meningococcus ͉ population structure ͉ strain ͉ mathematical model A spectrum of population structures has been identified among bacterial pathogens by multilocus studies of genetic variation in housekeeping genes (1, 2). It ranges from the extremely low diversity observed in Yersinia pestis (3) and Salmonella enterica var Typhi (4) to the very high levels of unstructured diversity found in Helicobacter pylori (5). The majority of pathogenic bacteria investigated to date, however, occupy an intermediate position within this spectrum, being composed of distinct cocirculating lineages that constitute a small subset of the possible allele combinations (6). These intermediate population structures exhibit apparently conflicting signals of both clonal descent and genetic exchange, and the mechanisms whereby they arise and are maintained remain incompletely understood (7).Neisseria meningitidis, the meningococcus, was one of the first bacteria where such an intermediate population structure was described (8-10). Populations of this highly recombining bacterium (11), which has an essentially commensal relationship with the human host, also present the intriguing feature that only certain lineages, the so-called hyperinvasive lineages, are associated with disease (12). These observations present two conceptual challenges: first, how does lineage structure arise in the face of the observed high rates of recombination; and, second, why are some lineages especially virulent, when invasive disease confers no benefit in terms of host-to-host spread (13)?Here, we address these questions by means of a survey of 1,108 meningococci isolated from asymptomatic carriage and disease in the Czech Republic over a 27-year period. The isolates were characterized at seven housekeeping loci by multilocus sequence typing (MLST) (14) and...