Exploring the Population Structure, Recombination Landscape, and Pan-Genome of the Global Neisseria meningitidis Population

Abstract

Neisseria meningitidis is a gram-negative species of bacteria which causes meningitis, septicaemia, urethritis, and pneumonia worldwide. Infections are typically asymptomatic carriage, but those which cause disease are extremely difficult to treat, leading to a high case-fatality rate. As such, there is considerable interest in studying N. meningitidis to understand its spread, what causes development from carriage to invasive disease, and how its evolution impacts efforts to control the disease. The latter has been of particular concern in regions where there have been outbreaks, particularly the ‘meningitis belt’ that spans from West Africa to East Africa, where there is greater disease burden and periodic epidemics which can span the region. Due to difficulties in treatment, the primary method of controlling invasive meningococcal disease is vaccination. Currently, available vaccines target five of the extant serogroups of N. meningitidis, chosen through study of the serogroups most frequently found in disease. However, either the replacement of disease lineages with those of different serogroups or capsular switching within disease-associated lineages may undermine the success of mass vaccination efforts and create the need for additional campaigns. N. meningitidis specifically possesses characteristics which make vaccine escape likely and unpredictable. The most important are the adaptions which allow frequent homologous recombination with other Neisseria. The evolutionary consequences of this sporadic partial chromosomal recombination are not well understood, but the transfer of alleles between distant lineages – including those associated with virulence – has been observed. Another gap in our understanding of bacterial evolution is in the evolutionary effect of population structure. Obilgately human-parasitic species such as N. meningitids have a global distribution and opportunities for rapid migration, and therefore may have a complex population structure. To study these problems, I have assembled a collection of over 15,000 whole-genome sequenced N. meningitids isolates from 70 distinct countries with isolation dates spanning over a hundred years. These data consist of a mixture of publicly published data, and three collections of newly sequenced isolates. Using these data, I determine the global population structure of N. meningitids. Subsequently, I infer phylogenetic trees for and find patterns of recombination within major lineages in the global population. Separately, I also infer and analyse the species-wide pan-genome. The results of these analyses indicate that N. meningitidis has a deep well of generally unsampled diversity in an extremely complex population structure which is primarily made up of a few globally distributed lineages. Within these lineages, population bottlenecks are a frequent occurrence. The 25 major lineages differ significantly in both their rates of recombination and the distribution of recombination across their genomes, but evidence suggest that most recombination occurs within N. meningitidis. In a local population, recombination generally acts to reduce the effect of deleterious mutations, although an example also exists of recombination acting in concert with positive selection. The pan-genome reveals the extent to which recombination can disrupt tree-like evolution, with most major lineages containing patterns of relatedness in their accessory gene content inconsistent with their whole-genome phylogenies. Trends in the pan-genome indicate that most gene gain is from other N. meningitidis isolates, but is governed primarily by evolutionary forces and not recombination rate. Together, these results demonstrate the profound complexity present in the population structure of N. meningitidis, and distinct evolutionary trends in individual lineages. This work also underscores the importance of carriage sampling and the value of a global perspective when studying a globally-distributed species. Further sampling in regions which are under-sampled and ongoing carriage surveillance will be a crucial part of any long-term efforts to successfully control the disease through vaccination.