Genomic Surveillance of a Globally Circulating Distinct Group W Clonal Complex 11 Meningococcal Variant, New Zealand, 2013-2018

Abstract

Genomic surveillance is an essential part of effective disease control, enabling identification of emerging and expanding strains and monitoring of subsequent interventions. Whole-genome sequencing was used to analyze the genomic diversity of all Neisseria meningitidis isolates submitted to the New Zealand Meningococcal Reference Laboratory during 2013-2018. Of the 347 isolates submitted for whole-genome sequencing, we identified 68 sequence types belonging to 18 clonal complexes (CC). The predominant CC was CC41/44; next in predominance was CC11. Comparison of the 45 New Zealand group W CC11 isolates with worldwide representatives of group W CC11 isolates revealed that the original UK strain, the 2013 UK strain, and a distinctive variant (the 2015 strain) were causing invasive group W meningococcal disease in New Zealand. The 2015 strain also demonstrated increased resistance to penicillin and has been circulating in Canada and several countries in Europe, highlighting that close monitoring is needed to prevent future outbreaks around the world.

Keywords: Neisseria meningitidis; New Zealand; Public Health Surveillance; bacteria; evolution; group W; invasive meningococcal disease; meningitis/encephalitis; meningococcal disease; whole-genome sequencing.

Figure 1

Epidemiology of meningococcal disease, New Zealand, 2013–2018. A) Number of confirmed and probable cases. B) Number of cases per 100,000 population of meningococcal disease. C) Proportion of meningococcal disease by group.

Figure 2

Age group distribution of meningococcal disease, by isolate group, New Zealand, 2013–2018

Figure 3

Phylogenetic analysis of New Zealand Neisseria meningitidis isolates, 2013–2018. Maximum-likelihood phylogeny was constructed by using a generalized time reversible substitution model and core single-nucleotide polymorphism alignments with RAxML version 8.2.12 (33). Branches with >90% bootstrap consensus (200 bootstrap replications) are highlighted with a red dot. Isolate names and clades are colored according to their clonal complex designation. The inner ring indicates the group and outer ring designates the year of isolation of the isolates. N1 lineage corresponds to sequence type that does not have clonal complex designation. NA corresponds to individual isolates where clonal complex is not assigned. Scale bar indicates average number of substitutions per site.

Figure 4

Diversity and prevalence of PorA variable region (VR) variants in common Neisseria meningitidis strains in New Zealand, 2013–2018. PorA VR1 and VR2 variant diversity and numbers of common strains are depicted. Strain is defined by group and clonal complex. Only strains with >10 isolates were analyzed.

Figure 5

Phylogenetic position of New Zealand group W clonal complex 11 (W:CC11) Neisseria meningitidis isolates within the global W:CC11 major lineages. Maximum-likelihood phylogeny was generated by RAxML version 8.2.12 (33) on the basis of the core single-nucleotide polymorphism alignment of 198 W:CC11 isolates. Branches with a bootstrap (200 replications) value >90% are indicated with a red dot. Excluding the basal older sublineages, all other isolates form 2 strongly supported clades marked as clade I and clade II, which correspond to the Hajj strain sublineage and the South America strain sublineage. All the major defined lineages of W:CC11 are marked and indicated by consistent background color of isolate’s identification number and branches. The inner ring and outer ring designate the region and year of isolation for each isolate. Scale bar indicates average number of substitutions per site.