Emergence of a New Epidemic Neisseria meningitidis Serogroup A Clone in the African Meningitis Belt: High-Resolution Picture of Genomic Changes That Mediate Immune Evasion

Abstract

In the African “meningitis belt,” outbreaks of meningococcal meningitis occur in cycles, representing a model for the role of host-pathogen interactions in epidemic processes. The periodicity of the epidemics is not well understood, nor is it currently possible to predict them. In our longitudinal colonization and disease surveys, we have observed waves of clonal replacement with the same serogroup, suggesting that immunity to noncapsular antigens plays a significant role in natural herd immunity. Here, through comparative genomic analysis of 100 meningococcal isolates, we provide a high-resolution view of the evolutionary changes that occurred during clonal replacement of a hypervirulent meningococcal clone (ST-7) by a descendant clone (ST-2859). We show that the majority of genetic changes are due to homologous recombination of laterally acquired DNA, with more than 20% of these events involving acquisition of DNA from other species. Signals of adaptation to evade herd immunity were indicated by genomic hot spots of recombination. Most striking is the high frequency of changes involving the pgl locus, which determines the glycosylation patterns of major protein antigens. High-frequency changes were also observed for genes involved in the regulation of pilus expression and the synthesis of Maf3 adhesins, highlighting the importance of these surface features in host-pathogen interaction and immune evasion.

Spontaneous point mutations in the capsule synthesis locus leading to structural and functional changes of the capsule in serogroup A meningococcal populations

“…Our whole genome sequencing analysis of 100 clonally related Neisseria meningitidis serogroup A ST-7 (n = 50) and ST-2859 (n = 50) case and carriage isolates revealed that the csaABCD-ctrABCD-ctrEF capsule polysaccharide synthesis locus represents a spontaneous point mutation hotspot [12]. Thirteen of the 100 analyzed isolates carried spontaneous non-synonymous point mutations or stop codons in the csaABCD-ctrABCD-ctrEF capsule polysaccharide synthesis locus.…”

“…For the longitudinal meningococcal colonization studies with a sample size of about 300 participants, residential compounds in the KND and the NHD were selected and throat swabs were taken twice annually from all consenting members of the selected compounds present at the time of the visit [15,20,21]. Isolation and characterization of bacterial isolates [15,20,21], and the comparative whole genome analysis of these isolates [12] have been described previously. Ethical clearance was obtained from the relevant institutional review boards and the Ministries of Health.…”

“…The ST-7 and the ST-2859 clone were found in Africa for the first time in 1995 and 2003, respectively [9–11]. Comparative whole genome sequencing analyzes showed that the ST-2859 lineage evaded herd immunity elicited by their ST-7 ancestors primarily through rapid homologous replacement of a set of genomic loci affecting non-capsular cell surface components [12]. …”

“…Due to horizontal gene transfer and point mutations, clonal meningococcal populations are, even in the course of an epidemic, not absolutely identical. Analysis of ST-7 and ST-2859 serogroup A isolates isolated between 2001 and 2009 in the framework of longitudinal meningococcal colonization and disease surveys in Ghana and Burkina Faso identified the pilT-pilU locus, which is implicated in the regulation of type IV pilus expression, and the csaABCD-ctrABCD-ctrEF capsule synthesis locus (cps) as point mutation hot spot regions [12]. …”

“…These include phase variation by slipped-strand miss-pairing, transcriptional regulation, post-transcriptional regulation via RNA thermosensors, insertion element (IS) associated on-off switching and ‘capsule switching’ by horizontal gene transfer. Among the 100 clonally related serogroup A isolates analyzed by comparative whole genome sequencing, Lamelas et al [12] identified 13 isolates with non-synonymous single nucleotide polymorphisms (SNPs) or stop codons in the capsule synthesis locus. In contrast, none of the 100 sequenced isolates carried a synonymous point mutation in this locus, speaking for selection of variants.…”