The effect of recombination on the evolution of a population of Neisseria meningitidis

Neisseria meningitidis (the meningococcus) is a major human pathogen with a history of high invasive disease burden, particularly in sub-Saharan Africa. Our current understanding of the evolution of meningococcal genomes is limited by the rarity of large-scale genomic population studies and lack of in-depth investigation of the genomic events associated with routine pathogen transmission. Here, we fill this knowledge gap by a detailed analysis of 2839 meningococcal genomes obtained through a carriage study of over 50,000 samples collected systematically in Burkina Faso, West Africa, before, during, and after the serogroup A vaccine rollout, 2009–2012. Our findings indicate that the meningococcal genome is highly dynamic, with highly recombinant loci and frequent gene sharing across deeply separated lineages in a structured population. Furthermore, our findings illustrate how population structure can correlate with genome flexibility, as some lineages in Burkina Faso are orders of magnitude more recombinant than others. We also examine the effect of selection on the population, in particular how it is correlated with recombination. We find that recombination principally acts to prevent the accumulation of deleterious mutations, although we do also find an example of recombination acting to speed the adaptation of a gene. In general, we show the importance of recombination in the evolution of a geographically expansive population with deep population structure in a short timescale. This has important consequences for our ability to both foresee the outcomes of vaccination programs and, using surveillance data, predict when lineages of the meningococcus are likely to become a public health concern.

Neisseria meningitidis, the meningococcus, is a species of bacteria found exclusively in humans. It can cause meningitis, an infection of the membranes covering the brain and spinal cord, as well as septicemia (Stephens et al. 2007). These infections are difficult to treat, even with antimicrobials, and have a high case fatality rate. Of the 12 serogroups defined on the basis of the structure of the capsular polysaccharide, six (A, B, C, W, X, and Y) are responsible for nearly all cases of invasive meningococcal disease (IMD) worldwide. In contrast to strains that are capable of causing disease, non-disease-causing carriage isolates are typically unencapsulated. However, most infections of encapsulated and unencapsulated N. meningitidis are asymptomatic, with the bacteria being carried in the oropharynx of human populations without causing disease with a prevalence of ∼5%–10% (Christensen et al. 2010). It is likely that essentially all individuals will be colonized by potentially IMD-causing bacteria once or even several times during their lifetimes, so there are an uncertain number of carriage infections and transmission events in a human population. This presents a challenge for controlling the disease, and in order to reduce the incidence of IMD, effective polysaccharide-conjugate vaccines against serogroups A, C, W, and Y have been developed and introduced in national vaccination programs. These vaccines are, however, expensive and not affordable for low-income countries. Therefore, a monovalent conjugate serogroup A vaccine was produced and successfully introduced in large-scale vaccination campaigns in countries of the so-called “meningitis belt” of sub-Saharan Africa (Diomandé et al. 2015; Trotter et al. 2017) a region stretching from the Gambia and Senegal to Ethiopia (Molesworth et al. 2002).Prior to the vaccination campaigns that started at the end of 2010, the overall incidence of meningococcal meningitis in the region was substantially higher than anywhere else in the world and included epidemics that occurred in the winter months every five to 12 years (Trotter and Greenwood 2007). Though the vaccine has been very effective at controlling meningitis epidemics caused by serogroup A, the main cause of IMD in the meningitis belt (Diomandé et al. 2015; Trotter et al. 2017), other serogroups (C, W, and X) have emerged or expanded in the region, reducing the initial impact of the vaccine (Topaz et al. 2019). There is also concern that virulent strains circulating in the population might switch capsule or that less virulent strains not covered by the current vaccine might acquire virulence genes (Bårnes et al. 2017; Brynildsrud et al. 2019).Both of these potential scenarios are driven by the ability of bacteria from the genus Neisseria to be naturally transformable and to readily recombine their DNA with one another (Obergfell and Seifert 2015), in concert with selection (Arnold et al. 2020). Various mechanisms of recombination have been described in N. meningitidis (Schoen et al. 2009; Marri et al. 2010; Joseph et al. 2011), involving abundant and diverse repetitive DNA sequences in its chromosome. The evolutionary and epidemiological effects of recombination in N. meningitidis have been studied in some detail (Marri et al. 2010; Joseph et al. 2011; Retchless et al. 2018), but less work has been undertaken to describe how the extent of recombination varies both between different lineages of N. meningitidis and between different regions of its complete genome in a single circulating carriage population. In particular, there is little understanding of how this recombination affects the process of natural selection. Studies across diverse populations and species have suggested that there is likely some variation (Castillo-Ramírez et al. 2012; Ezewudo et al. 2015), and this variation in recombination rate is particularly relevant amid the disruption of population structure caused by large-scale vaccine introduction (Potts et al. 2018).Burkina Faso, located in the center of the meningitis belt, historically has had a high burden of disease caused by serogroup A meningococci (Nicolas et al. 2005) and was one of the first countries to introduce the serogroup A conjugate vaccine in a mass vaccination campaign in 2010 (Kristiansen et al. 2013). Since then, the incidence of IMD has decreased overall, but there have been meningitis outbreaks caused by serogroups W and X, belonging, respectively, to the sequence types (STs) 11 and 181 (Kristiansen et al. 2013).Here, we present a detailed population genetic analysis, focusing on recombination, in a collection of 2838 N. meningitidis carriage isolates collected from three areas of Burkina Faso over the course of the implementation of the serogroup A vaccine, from 2009 to 2012. This collection has been previously studied using molecular typing techniques (Kristiansen et al. 2013, 2014) which identified ST-181 as the dominant lineage in this population during the time period when sampling was performed. It further showed that the vaccine was effective at reducing the incidence of its target, serogroup A isolates, with none of the previously prevalent serogroup A ST-2859 clone detected after vaccination. This was, however, associated with an increase in the incidence of the disease-causing serogroup X ST-181 complex and also with the introduction and expansion of the disease-causing serogroup W ST-11complex. In this study, we use whole-genome sequencing with Illumina short-read technology to generate de novo assemblies for each isolate, which are then used to construct phylogenies, infer recombination events, and perform tests for selection. Our study recapitulates the finding of previous molecular studies on this population, but leveraging whole-genome data, this study additionally sought to determine whether lineages that make up this population have significantly different recombination rate phenotypes; if different lineages have specific recombination hotspot regions—loci where much more recombination takes place compared to elsewhere in their genomes; to what extent recombination is occurring between the different lineages which make up this population; and finally, whether it is possible to ascertain the evolutionary causes and effects for recombination in this population. Though recombination in N. meningitidis has been a known phenomenon and studied for some time (Zhu et al. 1999), we believe this study to be the first to detail the extent of variation in recombination rate within a sampled population and to characterize how and why recombination affects the evolution of the population.