Increase in meningococcal disease associated with the emergence of a novel ST-11 variant of serogroup C Neisseria meningitidis in Victoria, Australia, 1999-2000

Characterisation of Neisseria meningitidis cc11/ET-15 variant by whole genome sequencing

BACKGROUND

Neisseria meningitidis strains belonging to clonal complex 11 is the cause of numerous outbreaks and epidemics in the United States, Canada and Europe, accounting for 49.5% of cases of meningococcal disease caused by serogroup C worldwide. In Brazil, it is the second most frequent clonal complex within this serogroup. The genetic characterisation of cc11/ET-15 variants is important for the epidemiological monitoring of meningococcal disease, through the identification of circulating epidemic clones, to support specific actions of Health Surveillance aiming outbreaks control.

OBJECTIVES

The objective of this study was to identify features in the genome of cc11/ET-15 clones through whole-genome sequencing (WGS), that differ from cc11/non-ET-15 strains that could explain their virulence.

METHODS

The whole genome of three cc11/ET-15 representative strains were sequenced with a minimum coverage of 100X with the MiSeq System and compared to the genome of cc11/non-ET-15 strains.

RESULTS

Genome analysis of cc11/ET-15 variants showed the presence of resistance factors, mobile genetic elements and virulence factors not found in cc11/non-ET-15 strains.

MAIN CONCLUSIONS

Our results show that these strains carry virulence factors not identified in cc11/non-ET-15 strains, which could explain the high lethality rates attributed to this clone worldwide.

Differences in the population structure of Neisseria meningitidis in two Australian states: Victoria and Western Australia

Neisseria meningitidis is the causative agent of invasive meningococcal disease (IMD). A recombinant vaccine called Bexsero® incorporates four subcapsular antigens (fHbp, NHBA, NadA and PorA) which are used to assign a Bexsero® antigen sequence type (BAST) to each meningococcal strain. The vaccine elicits an immune response against combinations of variants of these antigens which have been grouped into specific BAST profiles that have been shown to have different distributions within geographical locations thus potentially affecting the efficacy of the vaccine. In this study, invasive meningococcal disease isolates from the western seaboard of Australia (Western Australia; WA) were compared to those from the south-eastern seaboard (Victoria; VIC) from 2008 to 2012. Whole-genome sequencing (WGS) of 131 meningococci from VIC and 70 meningococci from WA were analysed for MLST, FetA and BAST profiling. Serogroup B predominated in both jurisdictions and a total of 10 MLST clonal complexes (cc) were shared by both states. Isolates belonging to cc22, cc103 and cc1157 were unique to VIC whilst isolates from cc60 and cc212 were unique to WA. Clonal complex 41/44 represented one-third of the meningococcal population in each state but the predominant ST was locally different: ST-6058 in VIC and ST-146 in WA. Of the 108 BAST profiles identified in this collection, only 9 BASTs were simultaneously observed in both states. A significantly larger proportion of isolates in VIC harboured alleles for the NHBA-2 peptide and fHbp-1, antigenic variants predicted to be covered by the Bexsero® vaccine. The estimate for vaccine coverage in WA (47.1% [95% CI: 41.1-53.1%]) was significantly lower than that in VIC (66.4% [95% CI: 62.3-70.5%]). In conclusion, the antigenic structure of meningococci causing invasive disease in two geographically distinct states of Australia differed significantly during the study period which may affect vaccine effectiveness and highlights the need for representative surveillance when predicting potential impact of meningococcal B vaccines.

Changing epidemiology of invasive meningococcal disease in Australia 1994–2016

Invasive meningococcal disease (IMD) has a relatively low incidence in Australia, however remains a serious public health issue, with a case fatality rate of approximately 10% despite antimicrobial treatment. IMD is particularly seen in young children, but can affect all age groups. The disease has non-specific early symptoms, rapid clinical progression mainly manifesting as septicaemia and/or meningitis, and has the potential for long term sequelae in the survivors, including skin scarring, amputation, deafness and seizures. There are 13 serogroups, although most invasive infections worldwide are caused by serogroups A, B, C, W, and Y, with some recent outbreaks in Africa caused by serogroup X. The prevalent circulating serogroups can undergo dynamic shifts, generating dramatic changes in IMD epidemiology. Such serogroup shifts have important ramifications for vaccination programs and constant surveillance is crucial.

Resolution of a meningococcal disease outbreak from whole-genome sequence data with rapid Web-based analysis methods

The increase in the capacity and reduction in cost of whole-genome sequencing methods present the imminent prospect of such data being used routinely in real time for investigations of bacterial disease outbreaks. For this to be realized, however, it is necessary that generic, portable, and robust analysis frameworks be available, which can be readily interpreted and used in real time by microbiologists, clinicians, and public health epidemiologists. We have achieved this with a set of analysis tools integrated into the PubMLST.org website, which can in principle be used for the analysis of any pathogen. The approach is demonstrated with genomic data from isolates obtained during a well-characterized meningococcal disease outbreak at the University of Southampton, United Kingdom, that occurred in 1997. Whole-genome sequence data were collected, de novo assembled, and deposited into the PubMLST Neisseria BIGSdb database, which automatically annotated the sequences. This enabled the immediate and backwards-compatible classification of the isolates with a number of schemes, including the following: conventional, extended, and ribosomal multilocus sequence typing (MLST, eMLST, and rMLST); antigen gene sequence typing (AGST); analysis based on genes conferring antibiotic susceptibility. The isolates were also compared to a reference isolate belonging to the same clonal complex (ST-11) at 1,975 loci. Visualization of the data with the NeighborNet algorithm, implemented in SplitsTree 4 within the PubMLST website, permitted complete resolution of the outbreak and related isolates, demonstrating that multiple closely related but distinct strains were simultaneously present in asymptomatic carriage and disease, with two causing disease and one responsible for the outbreak itself.

A generic mechanism in Neisseria meningitidis for enhanced resistance against bactericidal antibodies

The presence of serum bactericidal antibodies is a proven correlate of protection against systemic infection with the important human pathogen Neisseria meningitidis. We have identified three serogroup C N. meningitidis (MenC) isolates recovered from patients with invasive meningococcal disease that resist killing by bactericidal antibodies induced by the MenC conjugate vaccine. None of the patients had received the vaccine, which has been successfully introduced in countries in North America and Europe. The increased resistance was not caused by changes either in lipopolysaccharide sialylation or acetylation of the α2-9–linked polysialic acid capsule. Instead, the resistance of the isolates resulted from the presence of an insertion sequence, IS1301, in the intergenic region (IGR) between the sia and ctr operons, which are necessary for capsule biosynthesis and export, respectively. The insertion sequence led to an increase in the transcript levels of surrounding genes and the amount of capsule expressed by the strains. The increased amount of capsule was associated with down-regulation of the alternative pathway of complement activation, providing a generic mechanism by which the bacterium protects itself against bactericidal antibodies. The strains with IS1301 in the IGR avoided complement-mediated lysis in the presence of bactericidal antibodies directed at the outer membrane protein, PorA, or raised against whole cells.

IS1301 fingerprint analysis of Neisseria meningitidis strains belonging to the ET-15 clone

Meningococci of the ET-15 clone frequently cause clusters of invasive meningococcal disease (IMD) and are associated with a high case-fatality ratio. Timely typing of strains from outbreaks of IMD caused by this clone is hampered by the low variability of its surface antigens. We present a new Southern blot-based typing method for ET-15 meningococci based on the insertion element IS1301, which was present in all 70 ET-15 strains tested. Fingerprints were stable in vitro over a period of 100 days of cultivation on agar plates. The discriminatory power of IS1301 fingerprinting exceeded that of typing by serogrouping and antigen sequencing of the outer membrane proteins PorA and FetA, as determined by the analysis of 52 epidemiologically unrelated strains. In addition, the method provided conclusive results with regard to the comparison of strains from clusters of IMD. The investigation of insertion sites of IS1301 revealed several new intragenic insertions, among others, into open reading frames homologous to mafB and tspB. A previously described insertion in nadA was present in more than two-thirds of the strains analyzed, suggesting that NadA is probably an unreliable vaccine candidate for the prevention of ET-15 disease.

Population-based seroprevalence of Neisseria meningitidis serogroup C capsular antibody before the introduction of conjugate vaccine, in Australia

Neisseria meningitidis serogroup C (NMC) conjugate vaccine was introduced, in Australia, in 2003. Our aims were to determine pre-immunisation IgG NMC seroprevalence and evaluate an enzyme-linked immunosorbent assay (ELISA), previously validated against the serum bactericidal assay (SBA). 2409 sera, collected in 2002, from subjects aged 2-34 years, were tested. The geometric mean concentration (GMC) of NMC anticapsular IgG was 0.38 U/mL in subjects under 19 years and it increased to 0.67 U/mL for those aged 30-34 years. Variation in GMC correlated with reported NMC disease incidence and was higher in males than females (0.52 U/mL versus 0.41 U/mL; p=0.005). The ELISA appears suitable for serosurveillance but the IgG level that correlates with protection needs further investigation. Serosurveys will be repeated to monitor the impact of vaccination.

Molecular epidemiology and emergence of worldwide epidemic clones of Neisseria meningitidis in Taiwan

Background

Meningococcal disease is infrequently found in Taiwan, a country with 23 million people. Between 1996 and 2002, 17 to 81 clinical cases of the disease were reported annually. Reported cases dramatically increased in 2001–2002. Our record shows that only serogroup B and W135 meningococci have been isolated from patients with meningococcal disease until 2000. However, serogroup A, C and Y meningococci were detected for the first time in 2001 and continued to cause disease through 2002. Most of serogroup Y meningococcus infections localized in Central Taiwan in 2001, indicating that a small-scale outbreak of meningococcal disease had occurred. The occurrence of a meningococcal disease outbreak and the emergence of new meningococcal strains are of public health concern.

Methods

Neisseria meningitidis isolates from patients with meningococcal disease from 1996 to 2002 were collected and characterized by serogrouping, pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The genetic relatedness and clonal relationship between the isolates were analyzed by using the PFGE patterns and the allelic profiles of the sequence types (STs).

Results

Serogroups A, B, C, W135, Y, and non-serogroupable Neisseria meningitidis were, respectively, responsible for 2%, 50%, 2%, 35%, 9%, and 2% of 158 culture-confirmed cases of meningococcal disease in 1996–2002. Among 100 N. meningitidis isolates available for PFGE and MLST analyses, 51 different PFGE patterns and 30 STs were identified with discriminatory indices of 0.95 and 0.87, respectively. Of the 30 STs, 21 were newly identified and of which 19 were found in serogroup B isolates. A total of 40 PFGE patterns were identified in 52 serogroup B isolates with the patterns distributed over several distinct clusters. In contrast, the isolates within each of the serogroups A, C, W135, and Y shared high levels of PFGE pattern similarity. Analysis of the allelic profile of the 30 STs suggested the serogroup B isolates be assigned into 5 clonally related groups/ clonal complexes and 7 unique clones. The ST-41/44 complex/Lineage 3, and the ST-3439 and ST-3200 groups represented 79% of the serogroup B meningococci. In contrast, isolates within serogroups A, serogroup W135 (and C), and serogroup Y, respectively, simply belonged to ST-7, ST-11, and ST-23 clones.

Conclusion

Our data suggested that serogroup B isolates were derived from several distinct lineages, most of which could either be indigenous or were introduced into Taiwan a long time ago. The serogroup A, W135 (and C), and Y isolates, respectively, belonged to the ST-7, ST-11, and ST-23, and the represented clones that are currently the major circulating clones in the world and are introduced into Taiwan more recently. The emergence of serogroup A, C and Y strains contributed partly to the increase in cases of meningococcal disease in 2001–2002.

Molecular tests can allow confirmation of invasive meningococcal disease when isolates yield atypical maltose, glucose or gamma-glutamyl peptidase test results

Analysis of atypical meningococci from invasive disease that either (i) did not produce acid from maltose and glucose or (ii) were gamma-glutamyl peptidase test negative for porA and porB DNA variable region (VR) type, multilocus sequence type, and for presence of capsule transport gene ctrA, conclusively demonstrated that these are Neisseria meningitidis.

Australian public health policy in 2003 - 2004

In Australia, compared with other developed countries the many and varied programs which comprise public health have continued to be funded poorly and unsystematically, particularly given the amount of publicly voiced political support.In 2003, the major public health policy developments in communicable disease control were in the fields of SARS, and vaccine funding, whilst the TGA was focused on the Pan Pharmaceutical crisis. Programs directed to health maintenance and healthy ageing were approved. The tertiary education sector was involved in the development of programs for training the public health workforce and new professional qualifications and competencies. The Abelson Report received support from overseas experts, providing a potential platform for calls to improve national funding for future Australian preventive programs; however, inconsistencies continued across all jurisdictions in their approaches to tackling national health priorities. Despite 2004 being an election year, public health policy was not visible, with the bulk of the public health funding available in the 2004/05 federal budget allocated to managing such emerging risks as avian flu. We conclude by suggesting several implications for the future.

Epidemiology of meningococcal disease in Switzerland, 1999-2002

In Switzerland, immunisation against serogroup C meningococcal disease is recommended for persons at increased risk but is not included in the national vaccination programme. The aim of this study was to present the nationwide surveillance data on invasive meningococcal disease collected from 1999 to 2002, emphasising the evolution in the absence of extended vaccination. The number of reported cases of meningococcal disease peaked at 178 cases in 2000 (incidence rate of 2.5/100,000 person-years), with 61% of all cases attributed to serogroup C meningococci (incidence rate, 1.5/100,000 person-years). Since 2001, a spontaneous decrease in the reported cases was observed, resulting in an overall incidence rate of 1.4/100,000 person-years in 2002 (serogroup C cases, 0.8/100,000 person-years). On the other hand, the case-fatality rate of serogroup C cases increased to 18% in 2002, leading to an increase in the overall case-fatality rate from 8% to 14% (P>0.05). The small sample size reduces the interpretability of this observation. However, when the introduction of a generalised vaccination against serogroup C meningococcal disease is discussed, the fluctuations in the number of vaccine-preventable deaths should receive greater attention.

Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases

A unified, bioinformatics-driven, single nucleotide polymorphism (SNP)-based approach to microbial genotyping has been developed. Multilocus sequence typing (MLST) databases consist of known variants of standardized housekeeping genes. Normally, seven fragments are defined; a sequence type (ST) consists of the variants of these fragments that are found in a particular isolate. A computer program that can identify highly informative sets of SNPs in entire MLST databases has been constructed. The SNPs either define a particular user-specified ST or provide a high value for Simpson's index of diversity (D), and may thus be generally applicable to that species. SNP sets that are diagnostic for Neisseria meningitidis ST-11 and ST-42, and high-D SNP sets for N. meningitidis and Staphylococcus aureus, were identified and real-time PCR methods to interrogate these SNPs were demonstrated. High-D SNP sets were also identified in other MLST databases. This widely applicable approach allows rapid genetic fingerprinting of infectious agents.