Gene flow and Bayesian phylogeography of serogroup C meningococci circulating in Italy
Authors
Alessandra Lo Presti, Giovanni Rezza, Arianna Neri, Cecilia Fazio, Luigina Ambrosio, Annapina Palmieri, Paola Vacca, Paola Stefanelli
Abstract
Introduction
Neisseria meningitidis is a bacterial pathogen that can cause sporadic cases, small outbreaks and large epidemics. Serogroup C and B meningococci are the most common in Italy. In particular, hyperinvasive strains of serogroup C meningococci have caused outbreaks of severe disease in our country. In a previous study we tracked the pattern of dispersal of hyperinvasive strains, focusing the attention on their introduction routes. In the present paper we report the results of the analysis of the migration patterns of C:P1.5-1,10-8:F3-6:ST-11(cc11) meningococcal strains from different Italian regions collected between 2012 and 2017.
Methods
N. meningitidis genomes of isolates collected between January 2012 and December 2017 were sequenced using the Illumina MiSeq platform, through the whole genome sequencing (WGS) method and were analyzed using the BIGSdb Genome Comparator tool implemented within the PubMLST website. The phylogeography was performed using the software package BEAST. The gene out/in flows in Italy were tested by a modified version of the Slatkin and Maddison test using MacClade.
Results
The majority of the Italian C:P1.5-1,10-8:F3-6:ST-11(cc11) strains clustered together and segregated into two main sub-clades. In particular, the hyperinvasive strain, starting from UK reached at first Emilia Romagna region and by 2012 the port of Livorno, causing a small outbreak. Subsequently a wave of migrations involved different Italian regions. The “Tuscany-outbreak strain” was likely introduced in Italy between 2013 and 2014. Most of the observed gene flow events occurred from the Center to Northern part of Italy.
Discussion
The phylogeographic analysis allowed to track the dissemination of this strain belonging to the hypervirulent C:P1.5-1,10-8:F3-6:ST-11(cc11) clone. In particular, Central Italy was identified as a major source of dissemination, with a 54.5% of gene flows to the North and, to a lesser extent, to the South of the country. The information gathered through the application of phylogenetic and evolutionary methods appears consistent with the epidemiological data derived from the national surveillance system.
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