Hierarchical genomic analysis of carried and invasive serogroup A Neisseria meningitidis during the 2011 epidemic in Chad

Abstract

Background: Serogroup A Neisseria meningitidis (NmA) was the cause of the 2011 meningitis epidemics in Chad. This bacterium, often carried asymptomatically, is considered to be an "accidental pathogen"; however, the transition from carriage to disease phenotype remains poorly understood. This study examined the role genetic diversity might play in this transition by comparing genomes from geographically and temporally matched invasive and carried NmA isolates.

Results: All 23 NmA isolates belonged to the ST-5 clonal complex (cc5). Ribosomal MLST comparison with other publically available NmA:cc5 showed that isolates were closely related, although those from Chad formed two distinct branches and did not cluster with other NmA, based on their MLST profile, geographical and temporal location. Whole genome MLST (wgMLST) comparison identified 242 variable genes among all Chadian isolates and clustered them into three distinct phylogenetic groups (Clusters 1, 2, and 3): no systematic clustering by disease or carriage source was observed. There was a significant difference (p = 0.0070) between the mean age of the individuals from which isolates from Cluster 1 and Cluster 2 were obtained, irrespective of whether the person was a case or a carrier.

Conclusions: Whole genome sequencing provided high-resolution characterization of the genetic diversity of these closely related NmA isolates. The invasive meningococcal isolates obtained during the epidemic were not homogeneous; rather, a variety of closely related but distinct clones were circulating in the human population with some clones preferentially colonizing specific age groups, reflecting a potential age-related niche adaptation. Systematic genetic differences were not identified between carriage and disease isolates consistent with invasive meningococcal disease being a multi-factorial event resulting from changes in host-pathogen interactions along with the bacterium.

Trial registration: ClinicalTrials.gov NCT01119482.

Keywords: African meningitis belt; Meningitis epidemic; Pharyngeal carriage; Serogroup A Neisseria meningitidis; Whole genome sequencing.

Figures

Fig. 1

rMLST Neighbor-Joining Tree of cc5 NmA. The relationship from the concatenated nucleotide sequences of the ribosomal genes between the NmA isolates from Chad (n = 23) and other publically available cc5 NmA genomes from the PubMLST database is represented in this tree. The label on each node indicates: the PubMLST ID number, the country, the date and the rST for each isolate represented. A total of 141 other cc5 NmA isolates were found in PubMLST but only one representative of each unique strain (defined as isolates sharing the same alleles at all 53 ribosomal locus) was included in the tree alongside all the Chadian NmA from the 2011 meningitis epidemic; the full list of publically available cc5 NmA isolates is shown in Additional file 1: Table S2. The seven-locus MLST profiles of the isolates are indicated by different colored boxes. The position of the reference genome used in this study (WUE 2594) is represented by a black star

Fig. 2

wgMLST and wgSNP Neighbor Net Tree. The genomic relationship based on wgMLST (2a) and wgSNP (2b) between the Chad NmA isolates is depicted in relation to the reference genome WUE2594. Three clusters are observed and labeled on both trees. The invasive isolates are depicted in red and the carried ones in yellow. The rSTs contained in each cluster are also indicated as well as age and region of the patient/healthy volunteer are indicated when available, ND corresponds to the absence of any epidemiological information for the specific isolate (2a). The tree were produced based on a comparison in terms of n = 2070 loci defined in the reference genome (2a) and the 1942 SNPs identified (2b)