The effect of recombination on the evolution of a population of Neisseria meningitidis
- Neil MacAlasdair1,8,
- Maiju Pesonen2,8,
- Ola Brynildsrud3,4,
- Vegard Eldholm3,
- Paul A. Kristiansen3,9,
- Jukka Corander1,5,6,
- Dominique A. Caugant3,7 and
- Stephen D. Bentley1
- 1Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom;
- 2Oslo Centre for Biostatistics and Epidemiology (OCBE), Oslo University Hospital Research Support Services, Blindern, 0317 Oslo, Norway;
- 3Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, 0213 Oslo, Norway;
- 4Department of Food Safety and Infection Biology, Faculty of Veterinary Science, Norwegian University of Life Science, 0454 Oslo, Norway;
- 5University of Oslo, Department of Biostatistics, Blindern, 0317 Oslo, Norway;
- 6Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland;
- 7Department of Community Medicine, Faculty of Medicine, University of Oslo, Blindern, 0316 Oslo, Norway
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↵8 These authors contributed equally to this work.
Abstract
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.264465.120.
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Freely available online through the Genome Research Open Access option.
- Received April 8, 2020.
- Accepted April 22, 2021.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
