Epidemiology and genetic diversity of invasive Neisseria meningitidis strains circulating in Portugal from 2003 to 2020

Abstract

Invasive meningococcal disease (IMD) continues to be a public health problem due to its epidemic potential, affecting mostly children. We aimed to present a detailed description of the epidemiology of IMD in Portugal, including insights into the genetic diversity of Neisseria meningitidis strains. Epidemiological analysis included data from the Portuguese National Reference Laboratory of Neisseria meningitidis during 2003 to 2020. Since 2012, N. meningitidis isolates have also been assessed for their susceptibility to antibiotics and were characterized by whole genome sequencing. During 2003-2020, 1392 confirmed cases of IMD were analyzed. A decrease in the annual incidence rate was observed, ranging from 1.99 (2003) to 0.39 (2020), with an average case fatality rate of 7.1%. Serogroup B was the most frequent (69.7%), followed by serogroups C (9.7%), Y (5.7%), and W (2.6%). Genomic characterization of 329 isolates identified 20 clonal complexes (cc), with the most prevalent belonging to serogroup B cc41/44 (26.3%) and cc213 (16.3%). Isolates belonging to cc11 were predominantly from serogroups W (77.3%) and C (76.5%), whereas cc23 was dominant from serogroup Y (65.7%). Over the past 4 years (2017-2020), we observed an increasing trend of cases assigned to cc213, cc32, and cc11. Regarding antimicrobial susceptibility, all isolates were susceptible to ceftriaxone and 61.8% were penicillin-nonsusceptible, whereas 1.4% and 1.0% were resistant to ciprofloxacin and rifampicin. This is the first detailed study on the epidemiology and genomics of invasive N. meningitidis infections in Portugal, providing relevant data to public health policy makers for a more effective control of this disease.

Keywords: Neisseria meningitidis; Epidemiology; Portugal; Surveillance; Whole genome sequencing.

Fig. 1

Diagram depicting the overall data flow of the IMD surveillance system in Portugal

Fig. 2

Invasive meningococcal disease incidence rates in Portugal from 2003 to 2020. a Incidence rate of IMD per year of onset and per serogroup. The total number of cases has been overlapping the number of confirmed cases over time. “Others” refers to serogroup A, X, E, Z, and capsule null cases. b Average incidence rate of IMD in three successive periods corresponding to three different measures implemented for IMD controlling

Fig. 3

Hierarchical clustering tree showing the genetic relationship of all invasive N. meningitidis strains identified by the Portuguese National Reference Laboratory during the period 2012 to 2020. The genetic diversity among isolates was evaluated by a gene-by-gene analysis using the newly improved cgMLST schema v2, with 1422 N. meningitidis core-loci (Jolley et al. 2018). Phylogenetic tree was constructed using the hierarchical single-linkage method, based on the number of shared cgMLST alleles among 327 validated isolates (two isolates were discarded since displayed < 90% loci-called) and was drawn using microreact (https://microreact.org/). Isolates are depicted by small black circles that are differentially colored, the external ring according to their year of isolation and the internal ring according to their serogroup. The internal shading displayed in several colors shows the partitions of the various clonal complexes

Fig. 4

Genetic clusters identified among invasive Portuguese isolates of N. meningitidis serogroup B during the period 2012 to 2020. The genetic diversity among isolates was evaluated by a gene-by-gene analysis using the cgMLST schema v2, with 1422 N. meningitidis core-loci. The Minimum spanning tree was generated with the MSTreeV2 method of GrapeTree and was based on allelic diversity found among 251 validated MenB isolates (Mixão et al. 2023). For a better visualization of the identified gene clusters, nodes were collapsed. Filled small circles (whose size is proportional to the number of isolates it represents) represent unique allelic profiles and were colored by year of isolation with clonal complexes represented by large, shaded circles. The numbers in grey on the connecting lines represent the allele differences between isolates

Fig. 5

Distribution of antibiotic susceptibility to penicillin, rifampicin, ciprofloxacin, and ceftriaxone of invasive N. meningitidis isolates identified during the period 2012 to 2020 in Portugal. Antimicrobial susceptibility results were interpreted according to the European Committee for Antimicrobial Susceptibility Testing guidelines (EUCAST 2020)