Molecular characterization of serogroup C Neisseria meningitidis isolated in China

Prediction by genetic MATS of 4CMenB vaccine strain coverage of invasive meningococcal serogroup B isolates circulating in Taiwan between 2003 and 2020

Neisseria meningitidis serogroup B (NmB) strains have diverse antigens, necessitating methods for predicting meningococcal serogroup B (MenB) vaccine strain coverage. The genetic Meningococcal Antigen Typing System (gMATS), a correlate of MATS estimates, predicts strain coverage by the 4-component MenB (4CMenB) vaccine in cultivable and non-cultivable NmB isolates. In Taiwan, 134 invasive, disease-causing NmB isolates were collected in 2003-2020 (23.1%, 4.5%, 5.2%, 29.8%, and 37.3% from individuals aged ≤11 months, 12-23 months, 2-4 years, 5-29 years, and ≥30 years, respectively). NmB isolates were characterized by whole-genome sequencing and vaccine antigen genotyping, and 4CMenB strain coverage was predicted using gMATS. Analysis of phylogenetic relationships with 502 global NmB genomes showed that most isolates belonged to three global hyperinvasive clonal complexes: ST-4821 (27.6%), ST-32 (23.9%), and ST-41/44 (14.9%). Predicted strain coverage by gMATS was 62.7%, with 27.6% isolates covered, 2.2% not covered, and 66.4% unpredictable by gMATS. Age group coverage point estimates ranged from 42.9% (2-4 years) to 66.1% (≤11 months). Antigen coverage estimates and percentages predicted as covered/not covered were highly variable, with higher estimates for isolates with one or more gMATS-positive antigens than for isolates positive for one 4CMenB antigen. In conclusion, this first study on NmB strain coverage by 4CMenB in Taiwan shows 62.7% coverage by gMATS, with predictable coverage for 29.8% of isolates. These could be underestimated since the gMATS calculation does not consider synergistic mechanisms associated with simultaneous antibody binding to multiple targets elicited by multicomponent vaccines or the contributions of minor outer membrane vesicle vaccine components.IMPORTANCEMeningococcal diseases, caused by the bacterium Neisseria meningitidis (meningococcus), include meningitis and septicemia. Although rare, invasive meningococcal disease is often severe and can be fatal. Nearly all cases are caused by six meningococcal serogroups (types), including meningococcal serogroup B. Vaccines are available against meningococcal serogroup B, but the antigens targeted by these vaccines have highly variable genetic features and expression levels, so the effectiveness of vaccination may vary depending on the strains circulating in particular countries. It is therefore important to test meningococcal serogroup B strains isolated from specific populations to estimate the percentage of bacterial strains that a vaccine can protect against (vaccine strain coverage). Meningococcal isolates were collected in Taiwan between 2003 and 2020, of which 134 were identified as serogroup B. We did further investigations on these isolates, including using a method (called gMATS) to predict vaccine strain coverage by the 4-component meningococcal serogroup B vaccine (4CMenB).

Demographic Features of Invasive Meningococcal Disease in Taiwan, 1993 to 2020, and Genetic Characteristics of Neisseria meningitidis Isolates, 2003 to 2020

We present the demographic features of invasive meningococcal disease (IMD) in Taiwan between 1993 and 2020 and the genetic characteristics of Neisseria meningitidis isolates recovered from 2003 to 2020. IMD was rare in Taiwan between 1993 and 2020, with an annual incidence ranging from 0.009 to 0.204 per 100,000 people. The case fatality rate (CFR) declined from 18.1% for patients in 1993 to 2002 to 9.8% in 2003 to 2020. Infants less than 12 months were most susceptible to the disease. N. meningitidis serogroup B (NmB) was most predominant, responsible for 81.2% (134/165) of the IMD cases in 2003 to 2020. The majority of the isolates recovered from 2003 to 2020 belonged to 4 worldwide-spread hyperinvasive clonal complexes (cc), cc4821 (30.3%), cc32 (19.4%), cc41/44 (12.7%), cc23 (7.3%), and also a newly assigned clonal complex, cc3439 (10.3%). Core genome multilocus sequence typing (cgMLST) profile comparisons revealed that the cc4821 isolates with a T-to-I substitution at position 91 in gyrA were closely related to those originating from China. Of the 165 isolates, 20.0% and 53.3% were predicted to be covered by the Bexsero and Trumenba vaccines, respectively, whereas, 77.0% and 46.7% remained indeterminate. In conclusion, N. meningitidis isolates recovered in Taiwan between 2003 and 2020 were mostly highly diverse. Most IMD cases appeared sporadically and were caused by localized strains, although some patients were infected by recently introduced strains. cgMLST is a powerful tool for the rapid comparison of genetic relatedness among a large number of isolates. cgMLST profiling, based on 1,241 core genes, and strain tracking can be performed on the website of cgMLST@Taiwan (http://rdvd.cdc.gov.tw/cgMLST/). IMPORTANCE N. meningitidis can cause life-threatening invasive meningococcal disease (IMD), including meningitis and sepsis, resulting in a high CFR and long-term sequelae in survivors. Here, we report the demographic features of IMD in Taiwan over a 28-year period (1993 to 2020) and the genetic characteristics of N. meningitidis isolates recovered from patients with IMD over an 18-year period (2003 to 2020). We conducted a whole-genome sequence analysis to characterize the genetic features of the isolates and developed a cgMLST scheme for epidemiological investigation and strain tracking. The findings can be beneficial in understanding the epidemiology of IMD in Taiwan, the genetic characteristics of the bacterial strains, and the distribution of vaccine antigens for vaccine development and implementation.

Genetic characterization of clonal complex sequence type 2057 (cc2057) serogroup B Neisseria meningitidis strains unique to Japan and identification of a capsular-switched serogroup Y isolate cc2057

Introduction. Only approximately 40 cases of invasive meningococcal diseases are reported annually in Japan, and the dominant strains are serogroup Y meningococci (MenY) followed by serogroup B meningococci (MenB). Within the last 10 years, Neisseria meningitidis strains belonging to clonal complex (cc)2057 have become dominant among Japanese MenB and have not been identified in countries other than Japan.Hypothesis/Gap Statement. The uniqueness of cc2057 N. meningitidis strains was considered to be epidemiologically of importance, and some genetic features could be hidden in the genome of cc2057 meningococci.Method. We investigated 22 cc2057 MenB and one cc2057 MenY using whole genome sequencing (WGS) and also predicted the potential coverage of 4CMenB and bivalent rLP2086 vaccines in silico.Results. cc2057 N. meningitidis strains were phylogenetically assigned to two clades. Three hypothetical genes homologous to those in Neisseria lactamica and sequences related to a new CRISPR Cas9 system were found only in the genome of cc2057 strains. Moreover, one cc2057 MenY strain was presumed to be capsular-switched at the capsule synthesis (cps) locus. The potential coverage of 4CMenB and rLP2086 for cc2057 MenB strains was estimated to be very low.Conclusion. To the best of our knowledge, this is the first study to provide genetic insights from epidemiologically unique N. meningitidis cc2057 strains isolated only in Japan, an island country.

Meningococcal vaccines in China

Meningococcal meningitis caused by Neisseria meningitidis is a reportable infectious disease in China, due to the high incidence of meningitis in the era before the availability of vaccines. The disease incidence was markedly reduced after meningococcal vaccination was introduced in the 1980s. Currently, there are polysaccharide, conjugate, and combined vaccine formulations against meningococcal meningitis in the Chinese market, almost all of which are produced by domestic manufacturers. It is necessary to further enhance national meningococcal surveillance to improve the level of prevention and control of meningococcus. However, the immune efficacy and persistence of immunity of vaccines should be monitored. More importantly, additional investments should be made to develop serogroup B meningococcal vaccines.

Genomic analysis of the meningococcal ST-4821 complex-Western clade, potential sexual transmission and predicted antibiotic susceptibility and vaccine coverage

INTRODUCTION

The ST-4821 complex (cc4821) is a leading cause of serogroup C and serogroup B invasive meningococcal disease in China where diverse strains in two phylogenetic groups (groups 1 and 2) have acquired fluoroquinolone resistance. cc4821 was recently prevalent among carriage isolates in men who have sex with men in New York City (USA). Genome-level population studies have thus far been limited to Chinese isolates. The aim of the present study was to build upon these with an extended panel of international cc4821 isolates.

METHODS

Genomes of isolates from Asia (1972 to 2017), Europe (2011 to 2018), North America (2007), and South America (2014) were sequenced or obtained from the PubMLST Neisseria database. Core genome comparisons were performed in PubMLST.

RESULTS

Four lineages were identified. Western isolates formed a distinct, mainly serogroup B sublineage with alleles associated with fluoroquinolone susceptibility (MIC <0.03 mg/L) and reduced penicillin susceptibility (MIC 0.094 to 1 mg/L). A third of these were from anogenital sites in men who have sex with men and had unique denitrification gene alleles. Generally 4CMenB vaccine strain coverage was reliant on strain-specific NHBA peptides.

DISCUSSION

The previously identified cc4821 group 2 was resolved into three separate lineages. Clustering of western isolates was surprising given the overall diversity of cc4821. Possible association of this cluster with the anogenital niche is worthy of monitoring given concerns surrounding antibiotic resistance and potential subcapsular vaccine escape.

Comparative genomic analyses of Chinese serogroup W ST-11 complex Neisseria meningitidis isolates

Although serogroup W ST-11 complex (cc11) (W:cc11) Neisseria meningitidis has been widespread in China over the past ten years, its origin and genetic relatedness has not yet been described. In this study, we described the genetic relatedness and discuss the possible origin of Chinese W:cc11 isolates by comparing their genome sequences with those of other cc11 strains globally. Comparative genomic analysis with geo-temporally diverse cc11 isolates showed that the Chinese W:cc11 isolates exclusively formed two closely related subclusters within a distinct sublineage (proposed as the Chinese-strain sublineage) of lineage 11.1 close to the interface between the Hajj-strain sublineage and the South American-strain sublineage. Several isolates from Africa and Europe were closely related to the Chinese subclusters which were largely segregated from one another among distinct provinces of China. No alleles were identified that were unique to the Chinese isolates as a whole, though each subcluster possessed unique alleles differentiating itself from the other subcluster as well as closely related isolates within the extended sublineage. Three genes differentiated the two subclusters with allele combinations that were each present among the non-Chinese isolates within the wider sublineage. These results indicate that the Chinese W:cc11 isolates formed part of a previously undescribed W:cc11 sublineage that is closely related to, but distinct from, the Hajj-strain sublineage and South American-strain sublineage. The geographical source of the Chinese subclusters was indeterminate based on available data.

Evolution of Sequence Type 4821 Clonal Complex Meningococcal Strains in China from Prequinolone to Quinolone Era, 1972-2013

The expansion of hypervirulent sequence type 4821 clonal complex (CC4821) lineage Neisseria meningitidis bacteria has led to a shift in meningococcal disease epidemiology in China, from serogroup A (MenA) to MenC. Knowledge of the evolution and genetic origin of the emergent MenC strains is limited. In this study, we subjected 76 CC4821 isolates collected across China during 1972–1977 and 2005–2013 to phylogenetic analysis, traditional genotyping, or both. We show that successive recombination events within genes encoding surface antigens and acquisition of quinolone resistance mutations possibly played a role in the emergence of CC4821 as an epidemic clone in China. MenC and MenB CC4821 strains have spread across China and have been detected in several countries in different continents. Capsular switches involving serogroups B and C occurred among epidemic strains, raising concerns regarding possible increases in MenB disease, given that vaccines in use in China do not protect against MenB.

Prevalence and genetic characteristics of 4CMenB and rLP2086 vaccine candidates among Neisseria meningitidis serogroup B strains, China

OBJECTIVE

To systematically investigate the prevalence and genetic characteristics of 4CMenB and rLP2086 vaccine candidates among Neisseria meningitidis serogroup B (NmB) in China.

METHODS

A total of 485 NmB strains isolated in 29 provinces of China between 1968 and 2016 were selected from the culture collection of the national reference laboratory according to the isolation year, location, and source. Multi-locus sequence typing (MLST) and porA gene sequencing were performed on all 485 study strains; PCR was used to detect the fHbp, nadA, and nhba gene of 432 strains; positive amplification products from the fHbp and nadA genes from all strains, as well as those of the nhba gene from 172 representative strains, were sequenced.

RESULTS

MLST results showed that the predominant (putative) clonal complexes (CCs) of NmB isolates have changed over time in China. While strains that could not be assigned to existing (p)CCs were the biggest proportion, CC4821 was the most prevalent lineage (36.0%) since 2005. PCR and sequence analysis revealed that the 4CMenB and rLP2086 vaccine candidates were highly diverse. Respectively, 152 PorA genotypes and 83 VR2 sequences were identified with significant diversity within a single CC; the complete nadA gene was found in ten of 432 study strains; fHbp was present in most strains (422/432) with variant 2 predominating (82.9%) in both patient- and carrier- derived isolates; almost all strains harbored the nhba gene while sequences were diverse.

CONCLUSIONS

With regards to clonal lineages and vaccine candidate proteins, NmB isolates from China were generally diverse. Further studies should be performed to evaluate the cross-protection of present vaccines against Chinese NmB strains.

Multilocus variable-number tandem-repeat analysis of Neisseria meningitidis serogroup C in China

This study characterized Neisseria meningitidis serogroup C strains in China in order to establish their genetic relatedness and describe the use of multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) to provide useful epidemiological information. A total of 215 N. meningitidis serogroup C strains, obtained from 2003 to 2012 in China, were characterized by MLVA with different published schemes as well as multilocus sequence typing. (i) Based on the MLVA scheme with a combination of five highly variable loci, 203 genotypes were identified; this level of discrimination supports its use for resolving closely related isolates. (ii) Based on a combination of ten low variable loci, clear phylogenetic relationships were established within sequence type complexes. In addition, there was evidence of microevolution of VNTR loci over the decade as strain lineages spread from Anhui to other provinces, the more distant the provinces from Anhui, the higher the genetic variation.

Application of multiple-locus variable number tandem repeat analysis to identify outbreak-associated Neisseria meningitides serogroup C sequence type 4821 in China

Neisseria meningitidis (N. meningitidis) serogroup C sequence type (ST)-4821 caused an outbreak in 2010 in Shandong province of China. Twenty-one non-outbreak-associated strains were isolated, along with twenty-eight N. meningitides serogroup C ST-4821 isolates. Therefore, it’s essential to identify and clarify characterization of the real outbreak-associated strains with a rapid method during an outbreak investigation. In this study, multiple-locus variable number tandem repeat analysis (MLVA) was applied to analyze 84 N. meningitidis strains, among which 58 were recovered from two outbreaks and 26 were sporadic isolates. Three MLVA schemes with different combination of VNTR loci were tested, and two of them were suitable for isolates from China: scheme 2 with six loci was found to separate ST into finer resolution, and scheme 3 with five loci can be used to identify outbreak-associated isolates from the same outbreak that caused by N. meningitidis serogroup C ST-4821.

Clonal characteristics of invasive Neisseria meningitidis following initiation of an A + C vaccination program in China, 2005-2012

OBJECTIVES

To reveal the population structure of invasive Neisseria meningitidis isolates after the initiation of an A + C vaccination program in China.

METHODS

Multilocus sequence typing (MLST) and PorA typing were used to characterize 238 invasive N. meningitidis isolates collected in China between 2005 and 2012.

RESULTS

During this period, sequence type (ST)-5, ST-4821 and ST-11 complexes were dominant among serogroups A, C and W, accounting for 100%, 98.5% and 100% of each serogroup, respectively. P1.20,9, P1.7-2,14 and P1.5,2 were the dominant PorA types of serogroups A, C and W, respectively. Serogroup B showed high genetic diversity with two dominant lineages: ST-4821 complex and ST-5662 subgroup.

CONCLUSIONS

The population of 238 invasive N. meningitidis isolates was primarily composed of a select group of recognized hypervirulent lineages. Among these clonal complexes, ST-7 serogroup A and ST-11 serogroup W are distributed globally, and other three clones exist only in China.

Prevalence and genetic diversity of two adhesion-related genes, pilE and nadA, in Neisseria meningitidis in China

The main Neisseria meningitidis adhesion molecules, type IV pili (Tfp) and Neisseria adhesion A (NadA), play important roles in the pathogenesis of invasive meningococcal disease. PilE is the major Tfp subunit. In this study, the prevalence and genetic diversity of pilE and nadA were investigated in the prevalent serogroups and clonal complexes (CC) of N. meningitidis isolated in China. All serogroup A strains belonging to CC1 and CC5 and all CC11 serogroup W135 strains were clustered into class II PilE clades. All serogroup C and most of serogroup B isolates except CC8 and ST5642 were class I PilE clades. Class II pilE sequences were highly conserved. All isolates belonging to class I PilE isolates were nadA negative. However, nadA-positive strains were exclusively found in CC5 and CC11 isolates (class II PilE). This study showed that PilE and NadA may be related to epidemic or endemic meningococcal disease.

An expanded age range for meningococcal meningitis: molecular diagnostic evidence from population-based surveillance in Asia

Background

To understand epidemiologic patterns of meningococcal disease in Asia, we performed a retrospective molecular analysis of cerebrospinal fluid (CSF) specimens collected in prospective surveillance among children aged < 5 years of age in China, South Korea, and Vietnam.

Methods

A total of 295 isolates and 2,302 CSFs were tested by a meningococcal species- and serogroup-specific polymerase chain reaction (PCR) assay targeting the Neisseria meningitidis (Nm) ctrA gene. Multi-locus sequence typing (MLST) was performed in Nm gene amplification analysis and incidence rates for meningococcal meningitis were estimated.

Results

Among 295 isolates tested, 10 specimens from Vietnam were confirmed as serogroup B and all were Sequence Type (ST) 1576 by MLST. Among the 2,032 CSF specimen tested, 284 (14%) were confirmed by PCR (ctrA gene), including 67 (23.6%) from China, 92 (32.4%) from Korea, and 125 (44.0%) from Vietnam. Neonates and infants aged < 6 months of age accounted for more than 50% of Nm-PCR positive CSF. Two CSF specimens from Vietnam were identified as serogroup B using MLST. In addition, 44 specimens underwent sequencing to confirm meningococcal serogroup; of these, 21 (48%) were serogroup C, 12 (27%) were serogroup X, 9 (20%) were serogroup Y and 2 (5%) were serogroup B. The incidence rates of meningococcal meningitis among children < 5 years of age was highest in Vietnam (7.4/100,000 [95% CI, 3.6—15.3] followed by Korea (6.8/100,000 [95% CI, 3.5-13.5] and China (2.1/100,000) [95% CI, 0.7-6.2]).

Conclusions

These results suggest that there is a previously undetected, yet substantial burden of meningococcal meningitis among infants and young children. Standardized, sensitive and specific molecular diagnostic assays with Nm serogrouping capacity are needed throughout Asia to understand the true burden of N. meningitidis disease.

Characterization of Neisseria meningitidis isolates from Egypt using multilocus sequence typing

To characterize Neisseria meningitidis isolates collected from cerebrospinal fluid of meningitis cases in Egypt (1998-2003) as part of surveillance studies, 67 isolates were serogrouped, tested for antibiotic sensitivity and analyzed using multilocus sequence typing (MLST). Results show that isolates expressing serogroup B (50.7%) and serogroup A (34.3%) antigens were predominant in Egypt during the surveillance period, possibly due to suppression of other serogroups by meningococcal vaccines in current use. Intermediate resistance to penicillin was observed in 71% of the isolates, suggesting a need for physicians to shift to third-generation cephalosporins during the empirical treatment of infection. Recurrent lineages of N. meningitidis in Egypt appear to originate from Europe and other Middle Eastern countries. Of 19 sequence types detected, five were unique to Africa and 10 were not observed previously in the MLST database. The information obtained illustrates the changing dynamics of meningitis after vaccine introduction in Egypt.

Meningococcal disease in Asia: an under-recognized public health burden

A literature search traced existing information on meningococcal disease in Asia. Reviewed data describing the epidemiology of meningococcal disease in Asia are incomplete, due in part to absence of surveillance in many countries, poor bacterial detection methods and social and healthcare barriers to disease reporting. This suggests that meningococcal disease in some Asian countries may be under-recognized, with a need to introduce/improve existing surveillance and case identification systems. Nevertheless, in some developing Asian countries, the disease burden may be significant. Serogroup A meningococcal epidemics are responsible for high morbidity and mortality in some countries and continue to be an ongoing threat, particularly in developing countries. There is an increasing role played by serogroups C, Y, and W-135 in invasive disease, indicating evolving meningococcal disease epidemiology in some countries. Multivalent meningococcal conjugate vaccines offer new opportunities in the region for reducing the meningococcal disease burden.

Proteome analysis of Neisseria meningitidis serogroup strains C associated with outbreaks in China

OBJECTIVE

During 2003-2005, an outbreak of meningitis due to Neisseria meningitidis serogroup C occurred in China. With the aim to find strain clues result in the final epidemics, the ancestral strain 053442, a clinical isolate, and a carrier strain 053426 with different gene type were analyzed.

METHODS

Clinical strain 053442 and carrier strain 053426 were cultured on GC agar plates under the same condition. Two-dimensional electrophoresis was performed using the pH 3-10 nonlinear IPG strips of 24 cm length, and all the protein spots were identified by matrix-assisted laser desorption/ionization time of flight spectrometry.

RESULTS

502 and 380 protein spots were identified in 053426 and 053442 respectively, relating to 266 and 202 different genes covering a wide range of cellular functions. The express volume and number of proteins involved in energy metabolism, protein synthesis and amino acid biosynthesis in 053426 were higher than in 053442. Virulence factor Opa, Opc and a series of proteins involved in pilus assembly and retraction were identified in 053442, which appear to be of primary importance in colonization and invasion of human cells. Compared to 053442, virulence protein species were less in 053426, with lower express volumes too. No Opa and Opc were detected in 053426.

CONCLUSIONS

The different protein expression profiles of the clinical strain 053442 and carrier strain 053426 in the present study provide some clues of the different pathogenicity of the two strains, which may account for result in the final epidemics.

Distribution of surface-protein variants of hyperinvasive meningococci in China

OBJECTIVE

Information regarding the different types of FetA and PorB meningococci that circulate in various regions of the world is still scarce. The present study investigated the distribution of FetA and PorB variable region (VR) types among meningococci belonging to hyperinvasive lineages circulating in China.

METHODS

The approach consisted of genotypic analysis of 201 Neisseria meningitidis strains belonging to hyperinvasive lineages isolated in China during the period 1956-2006.

RESULTS

Sixteen different PorB types were found, 8 of which were newly identified. Of the 24 different FetA VR types, 3 were determined to be novel. Particular combinations of FetA and PorB types associated with distinct clonal complexes were also observed. Most cases of invasive disease were caused by five individual clones: A: P1.7-1,10: F5-5: ST-3 (cc1) with P3.6,11,10,7 (class 3 PorB protein; VR1-6, VR2-11, VR3-10, and VR4-7); A: P1.20,9: F3-1: ST-5 (cc5) with P3.4,11,10,7; A: P1.20,9: F3-1: ST-5 (cc5) with P3.9,11,10,7; A: P1.20,9: F3-1: ST-7 (cc5) with P3.4,11,10,7; and C: P1.7-2,14: F3-3: ST-4821 (cc4821) with P3.9,15,6,7.

CONCLUSION

A number of antigen-gene variants and combinations exhibited broad temporal and geographic distributions, although several invasive clones were mainly associated with a specified timeframe. The changes that are increasingly emerging in circulating strains and the prevalent clone replacement describe the molecular epidemiology of meningococcal disease in China. Our findings have implications for both public-health monitoring and further study of this organism.

Multilocus sequence typing

Multilocus sequence typing (MLST) was first proposed in 1998 as a typing approach that enables the unambiguous characterization of bacterial isolates in a standardized, reproducible, and portable manner using the human pathogen Neisseria meningitidis as the exemplar organism. Since then, the approach has been applied to a large and growing number of organisms by public health laboratories and research institutions. MLST data, shared by investigators over the world via the Internet, have been successfully exploited in applications ranging from molecular epidemiological investigations to population biology and evolutionary analyses. This chapter describes the practical steps in the development and application of an MLST scheme and some of the common tools and techniques used to obtain the maximum benefit from the data. Considerations pertinent to the implementation of high-capacity MLST projects (i.e., those involving thousands of isolates) are discussed.