It has recently become apparent that many bacterial populations undergo extremely high levels of horizontal genetic exchange, such that traditional clonal models of bacterial diversity are now inadequate (1–3). Such recombination is especially apparent in naturally transformable bacteria such as members of the genus Neisseria (4). This has implications for epidemiology, because it is not possible to assign accurate phylogenies to isolates by looking at variation at a single genetic locus if that locus, or part of it, is randomly exchanged within the population (5). Further, apparent phylogenies based on data from different loci are likely to be in disagreement with each other (6). The study of antigen genes, although undoubtedly useful for short-term epidemiology, provides limited information for longer-term analysis of the related-ness of strains as they are under immune selection and hence levels of recombination and mutation proximal to such genes are likely to be significantly higher than around other sites (7,8).