Population Genetics of Neisseria meningitidis

Proc. Natl. Acad. Sci. U.S.A.

2015

The three species Neisseria meningitidis, Neisseria gonorrheae, and Neisseria lactamica are often regarded as highly recombining bacteria. N. meningitidis has been considered a paradigmatic case of the "semiclonal model" or of "epidemic clonality," demonstrating occasional bouts of clonal propagation in an otherwise recombining species. In this model, occasional clonality generates linkage disequilibrium in the short term. In the long run, however, the effects of clonality are countered by recombination. We show that many data are at odds with this proposal and that N. meningitidis fits the criteria that we have proposed for predominant clonal evolution (PCE). We point out that (i) the proposed way to distinguish epidemic clonality from PCE may be faulty and (ii) the evidence of deep phylogenies by microarrays and whole-genome sequencing is at odds with the predictions of the semiclonal model. Last, we revisit the species status of N. meningitidis, N. gonorrheae, and N. lactamica in the light of the PCE model.T he clonality/sexuality controversy in microbiology has gone on for more than 35 y in bacteria (1, 2) as well as in parasitic protozoa (3-6). Early on, several instances of bacterial and parasitic species were removed from the clonal paradigm and instead were considered as "highly recombining" (5). The controversy now can be reconsidered in the light of major results obtained with modern technologies, such as whole-genome sequencing (WGS), single nucleotide polymorphism analysis (SNP), microarrays, and megacomputing, which have made possible considerable advances in evolutionary biology, population genetics, and molecular epidemiology. We reconsider the issue of the population structure of Neisseria meningitidis in the light of these advances.N. meningitidis and the "Epidemic Clonality" and "Semiclonal" Models The molecular epidemiology and population genetics of N. meningitidis, a major agent of meningitis, has received much attention. Thousands of strains have been characterized by various markers, including multilocus enzyme electrophoresis (MLEE), multilocus sequence analysis (MLST), random primed polymorphic DNA (RAPD), and WGS and SNP analysis (reviewed in ref. 7). Pioneering MLEE studies showed that, although this pathogen has a drastically restricted ecological niche, infecting only humans, it exhibits considerable genetic diversity, suggesting that N. meningitidis undergoes extensive genetic recombination. However, the natural populations of this species consistently exhibit a strong linkage disequilibrium (LD), i.e., nonrandom association between genotypes at different loci (8). To reconcile these two observations, which at first appear mutually inconsistent, Maynard Smith et al. (5) proposed the epidemic clonality model, which states that the species under study undergoes occasional bouts of clonal propagation in an otherwise recombining population structure. "Epidemic" clones, which are greatly favored by both positive and purging selection, are repeatedly represented in natural populations as ...

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Section: Some Problems With the Semiclonal/epidemic Clonality Modelmentioning

confidence: 99%

Section: The Predominant Clonal Evolution Modelmentioning

confidence: 99%

Section: Some Problems With the Semiclonal/epidemic Clonality Modelmentioning

confidence: 99%

Section: Some Problems With the Semiclonal/epidemic Clonality Modelmentioning

confidence: 99%

Section: Some Problems With the Semiclonal/epidemic Clonality Modelmentioning

confidence: 99%

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How clonal are Neisseria species? The epidemic clonality model revisited

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Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

Advances in Parasitology

2017

Reproductive clonality of pathogens: A perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa

Proc. Natl. Acad. Sci. U.S.A.

2012

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