Whole-Genome Characterization of Epidemic Neisseria meningitidis Serogroup C and Resurgence of Serogroup W, Niger, 2015

Abstract

In 2015, Niger reported the largest epidemic of Neisseria meningitidis serogroup C (NmC) meningitis in sub-Saharan Africa. The NmC epidemic coincided with serogroup W (NmW) cases during the epidemic season, resulting in a total of 9,367 meningococcal cases through June 2015. To clarify the phylogenetic association, genetic evolution, and antibiotic determinants of the meningococcal strains in Niger, we sequenced the genomes of 102 isolates from this epidemic, comprising 81 NmC and 21 NmW isolates. The genomes of 82 isolates were completed, and all 102 were included in the analysis. All NmC isolates had sequence type 10217, which caused the outbreaks in Nigeria during 2013-2014 and for which a clonal complex has not yet been defined. The NmC isolates from Niger were substantially different from other NmC isolates collected globally. All NmW isolates belonged to clonal complex 11 and were closely related to the isolates causing recent outbreaks in Africa.

Keywords: Meningococcal meningitis; Neisseria meningitidis serogroup C; Niger; bacteria; meningitis belt; whole-genome sequencing.

Figure 1

Distribution of Neisseria meningitidis isolates by district in Niger during the 2015 epidemic. Dogon-doutchi: 23 (NmC 15; NmW 8); Filingue: 2 (NmC 2); Gaya 2 (NmC 1; NmW 1); Guidan-Roumji: 1 (NmW 1); Illela: 1 (NmC 1); Kollo: 10 (NmC 5; NmW 5); Madaoua: 1 (NmW 1); Madarounfa: 1 (NmW 1); Niamey: 39 (NmC 37; NmW 2); Ouallam: 3 (NmC 2; NmW 1); Say: 3 (NmC 2; NmW 1); Téra: 11 (NmC 11).

Figure 2

Phylogenetic tree of the Neisseria meningitidis serogroup C isolates, labeled with country of origin, year of isolation, and multilocus sequence typing (MLST) group (clonal complex or sequence type). Internal nodes are labeled with bootstrap values. The scale bar is based on the 13,746 positions in the core single nucleotide polymorphism (SNP) matrix and indicates nucleotide substitutions per site.

Figure 3

Phylogenetic tree of a subset of the Neisseria meningitidis serogroup W (NmW) isolates, labeled with country of origin, year of isolation, and clonal complex (CC). Clades comprising isolates from a single country and year are collapsed, with the isolate count in parentheses. Internal nodes are labeled with bootstrap values, and the number of single nucleotide polymorphisms (SNPs) distinguishing different groups is provided at right. The scale bar is based on the 11,324 positions in the core SNP matrix and indicates nucleotide substitutions per site.