Reconstruction of Dispersal Patterns of Hypervirulent Meningococcal Strains of Serogroup C:cc11 by Phylogenomic Time Trees

Abstract

Neisseria meningitidis is one of the few commensal bacteria that can even cause large epidemics of invasive meningococcal disease (IMD). N. meningitis serogroup C belonging to the hypervirulent clonal complex 11 (cc11) represents an important public health threat worldwide. We reconstructed the dispersal patterns of hypervirulent meningococcal strains of serogroup C:cc11 by phylogenomic time trees. In particular, we focused the attention on the epidemic dynamics of C:P1.5.1,10-8:F3-6;ST-11(cc11) meningococci causing outbreaks, as occurred in the Tuscany region, Italy, in 2015 to 2016. A phylogeographic analysis was performed through a Bayesian method on 103 Italian and 208 foreign meningococcal genomes. The C:P1.5.1,10-8:F3-6;ST-11(cc11) genotype dated back to 1995 (1992 to 1998) in the United Kingdom. Two main clades of the hypervirulent genotype were identified in Italy. The Tuscany outbreak isolates were included in different clusters in a specific subclade which originated in the United Kingdom around 2011 and was introduced in Tuscany in 2013 to 2014. In this work, phylogeographic analysis allowed the identification of multiple introductions of these strains in several European countries and connections with extra-European areas. Whole-genome sequencing (WGS) combined with phylogeography enables us to track the dissemination of meningococci and their transmission. The C:P1.5.1,10-8:F3-6;ST-11(cc11) genotype analysis revealed how a hypervirulent strain may be introduced in previously naïve areas, causing a large and long-lasting outbreak.

Keywords: Neisseria meningitidis; invasive meningococcal disease; phylogeography; public health surveillance.

FIG 1

Maximum likelihood phylogenetic tree of N. meningitidis core genome SNP alignment of the whole data set. The tree was midpoint rooted. Branch lengths were estimated with the best-fitting nucleotide substitution model according to a hierarchical likelihood ratio test. The scale bar represents genetic distances based on nucleotide substitutions per SNP site. An asterisk along a branch represents significant statistical support for the clusters subtending that branch (bootstrap support > 90%). The main clades and clusters are highlighted. The colors of the tips represent strains from different locations (United Kingdom, blue; Malta, green; France, fuchsia; Ireland, light blue; Spain, orange; Canada, violet; Italy, red; Slovenia, ochre yellow; South Africa, light green). The subclade of the larger clade is highlighted by an arrow. The small letters indicate the supported clusters located inside this subclade. A full triangle symbol next to the tips indicates “Tuscany-outbreak-strains.” The values around the tree (supported zoomed clusters and area of the subclade) highlight the phylogenetic relationships of the Italian genomes between them and respect to foreign isolates.

FIG 2

Bayesian phylogenetic tree of the first subset of N. meningitidis core genome SNP alignment. The tree was rooted using the midpoint rooting method. Branch lengths were estimated with the best-fitting nucleotide substitution model according to a hierarchical likelihood ratio test. The scale bar represents genetic distances based on nucleotide substitutions per SNP site. An asterisk along a branch represents significant statistical support for the clade subtending that branch (posterior probability > 90%). A full triangle symbol next to the tips indicates “Tuscany-outbreak-strains.” The four isolates from cases occurred on a cruise ship docked in the port of Livorno in Italy are indicated by a # symbol next to the tips. The main clades and clusters are highlighted.

FIG 3

Bayesian phylogeographic tree of N. meningitidis strains of the whole data set. The axis below the tree shows the time (in years) before the present. The main statistically supported clades and clusters are indicated. An asterisk along a branch represents significant statistical support for the clade subtending that branch (posterior probability > 90%). A full triangle symbol next to the tips indicates “Tuscany-outbreak-strains.” The four isolates from cases that occurred on a cruise ship docked in the port of Livorno in Italy are indicated by a # symbol next to the tips. Geographic locations are indicated by different colors in the tree and reported in the location key.

FIG 4

Temporal dynamics of spatial diffusion of N. meningitidis strains (whole data set), obtained from the location annotated MCCT. The snapshots of the main dispersal pattern were reported. The lines connecting different locations represent branches in the MCCT on which state exchanges occur and circle areas reflect the number of branches maintaining a particular state at that time point. The maps were based on satellite pictures made available in Google Earth (Google Earth Pro V.7.3.2.5491).

FIG 5

The frequently invoked rates identified by SpreaD (using Bayes factor test) were indicated and reconstructed as a map based on satellite pictures made available in Google Earth (Google Earth Pro V.7.3.2.5491).