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

Genomic Surveillance of Invasive Meningococcal Disease During a National MenW Outbreak in Australia, 2017-2018

Background

In Australia, invasive meningococcal disease (IMD) incidence rapidly increased between 2014 and 2017 due to rising serogroup W (MenW) and MenY infections. We aimed to better understand the genetic diversity of IMD during 2017 and 2018 using whole genome sequencing data.

Methods

Whole genome sequencing data from 440 Australian IMD isolates collected during 2017 and 2018 and 1737 international MenW:CC11 isolates collected in Europe, Africa, Asia, North America, and South America between 1974 and 2020 were used in phylogenetic analyses; genetic relatedness was determined from single-nucleotide polymorphisms.

Results

Australian isolates were as follows: 181 MenW (41%), 144 MenB (33%), 88 MenY (20%), 16 MenC (4%), 1 MenW/Y (0.2%), and 10 nongenogroupable (2%). Eighteen clonal complexes (CCs) were identified, and 3 (CC11, CC23, CC41/44) accounted for 78% of isolates (343/440). These CCs were associated with specific serogroups: CC11 (n = 199) predominated among MenW (n = 181) and MenC (n = 15), CC23 (n = 80) among MenY (n = 78), and CC41/44 (n = 64) among MenB (n = 64). MenB isolates were highly diverse, MenY were intermediately diverse, and MenW and MenC isolates demonstrated the least genetic diversity. Thirty serogroup and CC-specific genomic clusters were identified. International CC11 comparison revealed diversification of MenW in Australia.

Conclusions

Whole genome sequencing comprehensively characterized Australian IMD isolates, indexed their genetic variability, provided increased within-CC resolution, and elucidated the evolution of CC11 in Australia.

Antimicrobial susceptibility profiles and genotyping of Neisseria meningitidis of serogroup C, Italy, 2000-2020

Background

In Italy the introduction of meningococcal C conjugate vaccine in 2005 has led to a significant reduction of invasive meningococcal disease (IMD) caused by Neisseria meningitidis of serogroup C (MenC). However, this serogroup is still responsible of sporadic cases, clusters and local outbreaks. The study aims to investigate the genotype and antimicrobial susceptibility profile of MenC isolates collected in Italy from 2000 to 2020.

Methods

Bacterial isolates and biological samples (blood or cerebrospinal fluid) from invasive meningococcal cases are collected and characterized at the National Reference Laboratory for IMD of Istituto Superiore di Sanità. Antimicrobial susceptibility was determined by MIC Test Strip Method and interpreted according to the EUCAST breakpoints guideline. Genotypic characteristics, including multi locus sequence typing (MLST), finetype, and antimicrobial resistance target genes were performed and analyzed using the PubMLST database. Genomic comparison of core genome MLST (cgMLST) of MenC genomes was also carried out.

Results

From 2000 to 2020, a total of 665 MenC isolates were investigated for antimicrobial susceptibility and 301 for genotyping. Over two decades, almost all MenC isolates resulted susceptible to antimicrobials with few isolates resulting resistant to ciprofloxacin (N = 2), penicillin G (N = 13), and rifampicin (N = 9), respectively. Molecular typing of MenC obtained from isolates or clinical specimens identified mostly the genotype C:P1.5-1,10-8:F3-6:ST-11(cc11). However, phylogenetic analysis, performed on genomes from MenC isolates, identified two sub lineages, 11.1 and 11.2, among cc11, of which the sub lineage 11.2 was the predominant.

Conclusion

Wider application of the genomic analysis and monitoring of antimicrobial susceptibility represent key aspects of IMD surveillance and to monitor the continued evolution of these hyperinvasive strains.

Evaluating the effect of targeted strategies as control tools for hypervirulent meningococcal C outbreaks: a case study from Tuscany, Italy, 2015 to 2016

BackgroundMeningococcus (Neisseria meningitidis) is the causative bacteria of invasive meningococcal disease (IMD), a major cause of meningitis and sepsis. In 2015-16, an outbreak caused by serogroup C meningococci (MenC), belonging to the hyperinvasive strain ST-11(cc-11), resulted in 62 IMD cases in the region of Tuscany, Italy.AimWe aimed to estimate the key outbreak parameters and assess the impact of interventions used in the outbreak response.MethodsWe developed a susceptible-carrier-susceptible individual-based model of MenC transmission, accounting for transmission in households, schools, discos/clubs and the general community, which was informed by detailed data on the 2015-16 outbreak (derived from epidemiological investigations) and on the implemented control measures.ResultsThe outbreak reproduction number (Re) was 1.35 (95% prediction interval: 1.13-1.47) and the IMD probability was 4.6 for every 1,000 new MenC carriage episodes (95% confidence interval: 1.8-12.2). The interventions, i.e. chemoprophylaxis and vaccination of close contacts of IMD cases as well as age-targeted vaccination, were effective in reducing Re and ending the outbreak. Case-based interventions (including ring vaccination) alone would have been insufficient to achieve outbreak control. The definition of age groups to prioritise vaccination had a critical impact on the effectiveness and efficiency of control measures.ConclusionsOur findings suggest that there are no effective alternatives to widespread reactive vaccination during outbreaks of highly transmissible MenC strains. Age-targeted campaigns can increase the effectiveness of vaccination campaigns. These results can be instrumental to define effective guidelines for the control of future meningococcal outbreaks caused by hypervirulent strains.

Whole genome analysis of Neisseria meningitidis isolates from invasive meningococcal disease collected in the Czech Republic over 28 years (1993-2020)

Invasive meningococcal disease belongs among the most dangerous infectious diseases in the world. Several polysaccharide conjugate vaccines against serogroups A, C, W and Y are available and two recombinant peptide vaccines against serogroup B (MenB vaccines) have been developed: MenB-4C (Bexsero) and MenB-fHbp (Trumenba). The aim of this study was to define the clonal composition of the Neisseria meningitidis population in the Czech Republic, to determine changes in this population over time and to estimate the theoretical coverage of isolates by MenB vaccines. This study presents the analysis of whole genome sequencing data of 369 Czech N. meningitidis isolates from invasive meningococcal disease covering 28 years. Serogroup B isolates (MenB) showed high heterogeneity and the most common clonal complexes were cc18, cc32, cc35, cc41/44, and cc269. Isolates of clonal complex cc11 were predominately serogroup C (MenC). The highest number of serogroup W isolates (MenW) belonged to clonal complex cc865, which we described as exclusive to the Czech Republic. Our study supports the theory that this cc865 subpopulation originated in the Czech Republic from MenB isolates by a capsule switching mechanism. A dominant clonal complex of serogroup Y isolates (MenY) was cc23, which formed two genetically quite distant subpopulations and which showed constant representation throughout the observed period. The theoretical coverage of isolates by two MenB vaccines was determined using the Meningococcal Deduced Vaccine Antigen Reactivity Index (MenDeVAR). Estimated Bexsero vaccine coverage was 70.6% (for MenB) and 62.2% (for MenC, W, Y). For Trumenba vaccine, estimated coverage was 74.6% (for MenB) and 65.7% (for MenC, W, Y). Our results demonstrated sufficient coverage of Czech heterogeneous population of N. meningitidis with MenB vaccines and, together with surveillance data on invasive meningococcal disease in the Czech Republic, were the basis for updating recommendations for vaccination against invasive meningococcal disease.

[Association of sepM gene mutation with mutacin Ⅳ production by Streptococcus mutans]

OBJECTIVE

To investigate the types of sepM gene mutations and their distribution in clinical isolates of Streptococcus mutans (S. mutans) and explore the association of sepM gene mutation with the capacity of mutacin Ⅳ production by S. mutans.

OBJECTIVE

We assessed the capacity of mutacin Ⅳ production in 80 clinical isolates of S. mutans using an inhibition zone assay. The minimum spanning tree and phylogenetic tree of these isolates were constructed using core genome multilocus sequence typing and maximum likelihood method, respectively. GeneMarkS software was used to predict the coding genes of these isolates, and the predicted genes were blasted against the sepM gene sequence of the reference genome UA159 to determine sepM gene mutations and their distribution characteristics in the clinical isolates. The mutation types affecting mutacin Ⅳ production were identified by analyzing the differentially distributed mutations between mutacin Ⅳ-producing isolates and mutacin Ⅳ-free isolates and by comparing the inhibition zones between isolates with sepM gene mutations and those without mutations.

OBJECTIVE

Among the 80 clinical isolates of S. mutans, 25 isolates were capable of mutacin Ⅳ production and 55 did not produce mutacin Ⅳ. The minimum spanning tree showed that the allelic differences were less among the mutacin Ⅳproducing isolates than among the mutacin Ⅳ-free isolates, and the origins of the mutacin Ⅳ-producing isolates were similar. We identified a total of 34 single base mutations in the 80 clinical isolates, and among them, C31T (P=0.001), G533A (P < 0.001), C756T (P=0.025), and C1036T (P=0.003) showed significant differential distributions between the mutacin Ⅳ-producing and mutacin Ⅳ-free isolates. These differentially distributed mutations were positively correlated with the capacity of mutacin Ⅳ production of the bacteria.

OBJECTIVE

sepM gene mutations that affect the capacity of mutacin Ⅳ production are present in the clinical strains of S. mutans.

Using Neisseria meningitidis genomic diversity to inform outbreak strain identification

Meningococcal disease is a life-threatening illness caused by the human-restricted bacterium Neisseria meningitidis. Outbreaks in the USA involve at least two cases in an organization or community caused by the same serogroup within three months. Genome comparisons, including phylogenetic analysis and quantification of genome distances can provide confirmatory evidence of pathogen transmission during an outbreak. Interpreting genome distances depends on understanding their distribution both among isolates from outbreaks and among those not from outbreaks. Here, we identify outbreak strains based on phylogenetic relationships among 141 N. meningitidis isolates collected from 28 outbreaks in the USA during 2010-2017 and 1516 non-outbreak isolates collected through contemporaneous meningococcal surveillance. We show that genome distance thresholds based on the maximum SNPs and allele distances among isolates in the phylogenetically defined outbreak strains are sufficient to separate most pairs of non-outbreak isolates into separate strains. Non-outbreak isolate pairs that could not be distinguished from each other based on genetic distances were concentrated in the clonal complexes CC11, CC103, and CC32. Within each of these clonal complexes, phylodynamic analysis identified a group of isolates with extremely low diversity, collected over several years and multiple states. Clusters of isolates with low genetic diversity could indicate increased pathogen transmission, potentially resulting in local outbreaks or nationwide clonal expansions.