Loss of Genomic Diversity in a Neisseria meningitidis Clone Through a Colonization Bottleneck

Abstract

Neisseria meningitidis is the leading cause of epidemic meningitis in the "meningitis belt" of Africa, where clonal waves of colonization and disease are observed. Point mutations and horizontal gene exchange lead to constant diversification of meningococcal populations during clonal spread. Maintaining a high genomic diversity may be an evolutionary strategy of meningococci that increases chances of fixing occasionally new highly successful "fit genotypes". We have performed a longitudinal study of meningococcal carriage and disease in northern Ghana by analyzing cerebrospinal fluid samples from all suspected meningitis cases and monitoring carriage of meningococci by twice yearly colonization surveys. In the framework of this study, we observed complete replacement of an A: sequence types (ST)-2859 clone by a W: ST-2881 clone. However, after a gap of 1 year, A: ST-2859 meningococci re-emerged both as colonizer and meningitis causing agent. Our whole genome sequencing analyses compared the A population isolated prior to the W colonization and disease wave with the re-emerging A meningococci. This analysis revealed expansion of one clone differing in only one nonsynonymous SNP from several isolates already present in the original A: ST-2859 population. The colonization bottleneck caused by the competing W meningococci thus resulted in a profound reduction in genomic diversity of the A meningococcal population.

Fig. 1.

—Dynamics of colonization and invasive disease by A: ST-2859 and W: ST-2881 meningococci in a longitudinal study in the KND of Ghana. Carriage rates recorded during twice yearly colonization surveys (April and November each year) and monthly numbers of meningitis cases caused by (A) serogroup A (ST-5, ST-7 and ST-2859) meningococci and (B) serogroup W (ST-11 and ST-2881) meningococci.

Fig. 2.

—(A) Maximum-likelihood tree of N. meningitidis A: ST-2859 isolates from the KND. Phylogenetic analysis was performed using the whole-genome sequence of 43 A: ST-2859 isolates after removal of SNPs associated with the predicted recombination events. Asterisks indicate cerebrospinal fluid isolates. The IDs of the isolates is provided together with the year of isolation. The tree was rooted in the “outlier” A: ST2859 isolate 2524. Branches are colored according to the isolation dates (pink: A: ST-2859 meningococci isolated between spring 2007 and spring 2009: light blue: A: ST-2859 meningococci isolated in 2010 and in 2011). The bootstrap values higher than 50% are labeled by numbers along the branch. (B) SNPs pairwise distance between isolates from the first (2007–2009) and second (2010–2011) A: ST-2859 colonization and disease wave. The variation in pairwise distance for each group of isolates is shown in a box plot, with circles representing outlier sequence pairs. Although the distribution of 120 pairwise genomic comparisons of the A: ST-2859 meningococci isolated in 2007–2009 is represented in pink, the corresponding distribution for 351 pairwise genomic comparisons of the A: ST-2859 meningococci isolated in 2010–2011 is represented in blue. The results were plotted using the software package R (http://www.r-project.org/). Two-tailed Mann–Whitney test, *flags disease isolates, **P-value <0.01.