Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06

BMC Genomics Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06 Julia S Bennett 0 Stephen D Bentley 1 Georgios S Vernikos 1 Michael A Quail 1 Inna Cherevach 1 Brian White 1 Julian Parkhill 1 Martin CJ Maiden 0 0 Department of Zoology, University of Oxford , South Parks Road, Oxford, OX1 3PS , UK 1 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus , Hinxton, CB10 1SA , UK Background: The genus Neisseria contains two important yet very different pathogens, N. meningitidis and N. gonorrhoeae, in addition to non-pathogenic species, of which N. lactamica is the best characterized. Genomic comparisons of these three bacteria will provide insights into the mechanisms and evolution of pathogenesis in this group of organisms, which are applicable to understanding these processes more generally. Results: Non-pathogenic N. lactamica exhibits very similar population structure and levels of diversity to the meningococcus, whilst gonococci are essentially recent descendents of a single clone. All three species share a common core gene set estimated to comprise around 1190 CDSs, corresponding to about 60% of the genome. However, some of the nucleotide sequence diversity within this core genome is particular to each group, indicating that cross-species recombination is rare in this shared core gene set. Other than the meningococcal cps region, which encodes the polysaccharide capsule, relatively few members of the large accessory gene pool are exclusive to one species group, and cross-species recombination within this accessory genome is frequent. Conclusion: The three Neisseria species groups represent coherent biological and genetic groupings which appear to be maintained by low rates of inter-species horizontal genetic exchange within the core genome. There is extensive evidence for exchange among positively selected genes and the accessory genome and some evidence of hitch-hiking of housekeeping genes with other loci. It is not possible to define a 'pathogenome' for this group of organisms and the disease causing phenotypes are therefore likely to be complex, polygenic, and different among the various disease-associated phenotypes observed. - Background Comparison of the genomes of related bacteria that exhibit distinct pathogenic phenotypes can identify the genetic traits required for invasion and elucidate key steps in the evolution of virulence. The genus Neisseria, which comprises Gram negative oxidase positive diplococci that colonise the mucosa of humans and animals, provides an excellent model for this type of study as it includes species that are never or rarely pathogenic and two human pathogens of global significance, Neisseria meningitidis (the meningococcus) and Neisseria gonorrhoeae (the gonococcus) [1]. Neisseria lactamica is closely related to the pathogenic Neisseria [2,3] and, like them, is only ever isolated from humans; consequently, a number of studies have been undertaken to compare the non-pathogen N. lactamica with meningococci and gonococci in the hope of identifying key genetic determinants of meningococcal or gonococcal disease [4-13]. Phenotypically, the gonococcus is the most divergent of the three organisms as it colonises the urogenital tract and can be considered to be an obligate pathogen of the mucosal surface that occasionally causes disseminated infection [14]. The meningococcus and N. lactamica are more similar in their life histories: both are obligate commensal inhabitants of the human nasopharynx that establish long-term normally asymptomatic colonisation. Carriage of N. lactamica is high in infants and young children and declines as the age of the human host population rises. The converse is true for the meningococcus, the carriage prevalence of which is low in infants and young children but rises with host age, generally reaching its highest in adolescents and young adults [15,16]. Unlike N. lactamica, which is only anecdotally associated with invasive disease [17-19], the meningococcus can be a dangerous pathogen occasionally invading the nasal mucosa to cause septicaemia and meningitis [20]. Although devastating for the patient, neither of these syndromes is of any benefit to the meningococcus itself as they do not normally lead to onward transmission of the bacterium, which is therefore best categorised as an accidental pathogen [21]. Nonetheless, meningococcal disease is a global phenomenon which, in some settings, occurs in large outbreaks [22]. The idea that the colonisation of children with N. lactamica plays a role in the development of immunity to the meningococcus [23-25] has further stimulated comparative investigations of these two organisms and anti-meningococcal vaccines based N. lactamica have been proposed at various times [26,27]. The meningococcus, gonococcus, and N. lactamica are closely related at the genetic level [2] and appear to have recently descended from the same ancestral population. Multilocus studies have indicated that these are maintained as separate populations by the absence or low frequency of genetic exchange among them, although rates of recombination within each of the microbiological species groups are high [3] and some genetic sequences are shared among species groups. The low genetic diversity observed at seven housekeeping genes of the gonococcus is consistent with this organism having evolved from a single clone that changed niche from the nasopharyngeal to the urogenital tract [28]. N. lactamica and meningococcal populations, on the other hand, are more diverse and both populations consists of a number of clonal complexes, each comprising related genotypes [29,30]. In the case of the meningococcus, some of these, the so-called hyperinvasive lineages, are particularly associated with invasive disease [31]. Knowledge of the population structures of these organisms has been used to design studies of the genetic elements that are involved in virulence [4,8,13,32], but to date a pathogenic genotype has yet to be determined and it seems probable that the invasive phenotype of the hyperinvasive genotypes is complex and polygenic. Here we examine the genealogical relationships among the three species, describe the determination and annotation of the first complete genome sequence of N. lactamica (isolate 020-06) and discuss the insights that this provides into the evolution of the pathogenic Neisseria. Methods Genealogical relationships among species Relationships among N. meningitidis, N. lactamica and N. gonorrhoeae were investigated by an analysis of nucleotide sequences from 19 housekeeping gene loci. The loci included were those used for Neisseria MLST (abcZ, adk, aroE, fumC, gdh, pdhC, and pgm) [29,33] supplemented with 12 additional loci (aspA, carB, dhpS, glnA, gpm, pilA, pip, ppk, pykA, rpiA, serC, talA) with alleles generated as described previously [34]. The analysis (...truncated)