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Shevtsov A, Aushakhmetova Z, Amirgazin A, Khegay O, Kamalova D, Sanakulova B, Abdaliyev A, Bayesheva D, Seidullayeva A, Ramankulov Y, Shustov A, Vergnaud G. Whole genome sequence analysis of Neisseria meningitidis strains circulating in Kazakhstan, 2017-2018. PLoS One 2022; 17:e0279536. [PMID: 36576937 PMCID: PMC9797059 DOI: 10.1371/journal.pone.0279536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 12/11/2022] [Indexed: 12/29/2022] Open
Abstract
Neisseria meningitidis (meningococcus) is a cosmopolitan bacterium that is often found in the upper respiratory tract of asymptomatic humans. However, N. meningitidis also causes meningeal inflammation and/or sepsis in humans with a periodic resurgence in incidence and high mortality rates. The pathogen is highly diverse genetically and antigenically, so that genotyping is considered important for vaccine matching to circulating strains. Annual incidence of meningococcal disease in Kazakhstan ranges between 0.2 and 2.5 cases per 100 thousand population. In total, 78 strains of N. meningitidis were isolated from clinical patients and contact persons during the years 2017-2018 in Kazakhstan. Of these, 41 strains including four from the patients and 37 from contacts, were sequenced using Illumina MiSeq. In silico typing was completed using the Neisseria pipeline 1.2 on the Galaxy Workflow Management System and PubMLST. Whole genome SNP (single nucleotide polymorphisms) trees were built using BioNumerics 8. Seven-gene multilocus sequence typing (MLST) identified ten sequence types (ST), two of which have not been previously described (ST-16025; ST-16027). ST-16025 was detected in two patients with invasive meningococcal disease in 2017 and 2018 in Akmola region and 16 contacts in 2017 in Turkistan region. This prevalent type ST-16025 demonstrates considerable intertypic diversity as it consists of three subcomplexes with a distance of more than 2000 SNPs. Invasive and carrier strains belong to different serogroups (MenB and MenC), PorA and FetA_VR. Two invasive strains were MenB, one MenC and one MenW (Hajj lineage). The strains from the contact persons were: MenC (n = 18), cnl (n = 9), MenY (n = 7), MenW (n = 1), MenB (n = 1) and one unidentifiable. Different numbers of alleles were present: 12, 11, 7, and 7 alleles for PorA, FetA, fHbp, and NHBA, respectively. This study is the first report of the genetic diversity of N. meningitidis strains in Kazakhstan. Despite limitations with the studied sample size, important conclusions can be drawn based on data produced. This study provides evidence for regulatory authorities with regard to changing routine diagnostic protocols to increase the collecting of samples for WGS.
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Affiliation(s)
| | | | | | - Olga Khegay
- National Centre of expertise CSEC MN RK, Astana, Kazakhstan
| | | | | | | | - Dinagul Bayesheva
- Medical University Astana, Astana, Kazakhstan
- Multidisciplinary City Children’s Hospital №3, Astana, Kazakhstan
| | - Aliya Seidullayeva
- Medical University Astana, Astana, Kazakhstan
- Multidisciplinary City Children’s Hospital №3, Astana, Kazakhstan
| | - Yerlan Ramankulov
- National Center for Biotechnology, Astana, Kazakhstan
- School of Science and Humanities Nazarbayev University, Astana, Kazakhstan
| | | | - Gilles Vergnaud
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
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Ruiz García Y, Sohn WY, Seib KL, Taha MK, Vázquez JA, de Lemos APS, Vadivelu K, Pizza M, Rappuoli R, Bekkat-Berkani R. Looking beyond meningococcal B with the 4CMenB vaccine: the Neisseria effect. NPJ Vaccines 2021; 6:130. [PMID: 34716336 PMCID: PMC8556335 DOI: 10.1038/s41541-021-00388-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/01/2021] [Indexed: 11/30/2022] Open
Abstract
Infections with Neisseria meningitidis and Neisseria gonorrhoeae have different clinical manifestations, but the bacteria share up to 80-90% genome sequence identity. The recombinant meningococcal serogroup B (MenB) vaccine 4CMenB consists of four antigenic components that can be present in non-B meningococcal and gonococcal strains. This comprehensive review summarizes scientific evidence on the genotypic and phenotypic similarities between vaccine antigens and their homologs expressed by non-B meningococcal and gonococcal strains. It also includes immune responses of 4CMenB-vaccinated individuals and effectiveness and impact of 4CMenB against these strains. Varying degrees of strain coverage were estimated depending on the non-B meningococcal serogroup and antigenic repertoire. 4CMenB elicits immune responses against non-B meningococcal serogroups and N. gonorrhoeae. Real-world evidence showed risk reductions of 69% for meningococcal serogroup W clonal complex 11 disease and 40% for gonorrhea after 4CMenB immunization. In conclusion, functional antibody activity and real-world evidence indicate that 4CMenB has the potential to provide some protection beyond MenB disease.
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Affiliation(s)
| | - Woo-Yun Sohn
- grid.418019.50000 0004 0393 4335GSK, Rockville, MD USA
| | - Kate L. Seib
- grid.1022.10000 0004 0437 5432Institute for Glycomics, Griffith University, Gold Coast, QLD Australia
| | | | - Julio A. Vázquez
- grid.413448.e0000 0000 9314 1427National Centre of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
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de Lemos APS, Sacchi CT, Gonçalves CR, Camargo CH, Andrade AL. Genomic surveillance of Neisseria meningitidis serogroup B invasive strains: Diversity of vaccine antigen types, Brazil, 2016-2018. PLoS One 2020; 15:e0243375. [PMID: 33347452 PMCID: PMC7751880 DOI: 10.1371/journal.pone.0243375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/19/2020] [Indexed: 11/19/2022] Open
Abstract
Background Neisseria meningitidis serogroup B remains a prominent cause of invasive meningococcal disease (IMD) in Brazil. Because two novel protein-based vaccines against serogroup B are available, the main purpose of this study was to provide data on the diversity and distribution of meningococcal vaccine antigen types circulating in Brazil. Methodology Genetic lineages, vaccine antigen types, and allele types of antimicrobial-associated resistance genes based on whole-genome sequencing of a collection of 145 Neisseria meningitidis serogroup B invasive strains recovered in Brazil from 2016 to 2018 were collected. Results A total of 11 clonal complexes (ccs) were identified among the 145 isolates, four of which were predominant, namely, cc461, cc35, cc32, and cc213, accounting for 72.0% of isolates. The most prevalent fHbp peptides were 24 (subfamily A/variant 2), 47 (subfamily A/variant 3), 1 (subfamily B/variant 1) and 45 (subfamily A/variant 3), which were predominantly associated with cc35, cc461, cc32, and cc213, respectively. The NadA peptide was detected in only 26.2% of the isolates. The most frequent NadA peptide 1 was found almost exclusively in cc32. We found seven NHBA peptides that accounted for 74.5% of isolates, and the newly described peptide 1390 was the most prevalent peptide exclusively associated with cc461. Mutated penA alleles were detected in 56.5% of the isolates, whereas no rpoB and gyrA mutant alleles were found. Conclusion During the study period, changes in the clonal structure of circulating strains were observed, without a predominance of a single hyperinvasive lineage, indicating that an epidemiologic shift has occurred that led to a diversity of vaccine antigen types in recent years in Brazil.
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Affiliation(s)
| | | | | | | | - Ana Lúcia Andrade
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Brazil
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Carr J, Plested E, Aley P, Camara S, Davis K, MacLennan JM, Gray S, Faust SN, Borrow R, Christensen H, Trotter C, Maiden MCJ, Finn A, Snape MD. 'Be on the TEAM' Study (Teenagers Against Meningitis): protocol for a controlled clinical trial evaluating the impact of 4CMenB or MenB-fHbp vaccination on the pharyngeal carriage of meningococci in adolescents. BMJ Open 2020; 10:e037358. [PMID: 33093030 PMCID: PMC7583083 DOI: 10.1136/bmjopen-2020-037358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
INTRODUCTION Capsular group B Neisseria meningitidis (MenB) is the most common cause of invasive meningococcal disease (IMD) in many parts of the world. A MenB vaccine directed against the polysaccharide capsule remains elusive due to poor immunogenicity and safety concerns. The vaccines licensed for the prevention of MenB disease, 4CMenB (Bexsero) and MenB-fHbp (Trumenba), are serogroup B 'substitute' vaccines, comprised of subcapsular proteins and are designed to provide protection against most MenB disease-causing strains. In many high-income countries, such as the UK, adolescents are at increased risk of IMD and have the highest rates of meningococcal carriage. Beginning in the late 1990s, immunisation of this age group with the meningococcal group C conjugate vaccine reduced asymptomatic carriage and disrupted transmission of this organism, resulting in lower group C IMD incidence across all age groups. Whether vaccinating teenagers with the novel 'MenB' protein-based vaccines will prevent acquisition or reduce duration of carriage and generate herd protection was unknown at the time of vaccine introduction and could not be inferred from the effects of the conjugate vaccines. 4CMenB and MenB-fHbp may also impact on non-MenB disease-causing capsular groups as well as commensal Neisseria spp. This study will evaluate the impact of vaccination with 4CMenB or MenB-fHbp on oropharyngeal carriage of pathogenic meningococci in teenagers, and consequently the potential for these vaccines to provide broad community protection against MenB disease. METHODS AND ANALYSIS The 'Be on the TEAM' (Teenagers Against Meningitis) Study is a pragmatic, partially randomised controlled trial of 24 000 students aged 16-19 years in their penultimate year of secondary school across the UK with regional allocation to a 0+6 month schedule of 4CMenB or MenB-fHbp or to a control group. Culture-confirmed oropharyngeal carriage will be assessed at baseline and at 12 months, following which the control group will be eligible for 4CMenB vaccination. The primary outcome is the carriage prevalence of potentially pathogenic meningococci (defined as those with genogroups B, C, W, Y or X), in each vaccine group compared separately to the control group at 12 months post-enrolment, that is, 12 months after the first vaccine dose and 6 months after the second vaccine dose. Secondary outcomes include impact on carriage of: genogroup B meningococci; hyperinvasive meningococci; all meningococci; those meningococci expressing vaccine antigens and; other Neisseria spp. A sample size of 8000 in each arm will provide 80% power to detect a 30% reduction in meningococcal carriage, assuming genogroup B, C, W, Y or X meningococci carriage of 3.43%, a design effect of 1.5, a retention rate of 80% and a significance level of 0.05. Study results will be available in 2021 and will inform the UK and international immunisation policy and future vaccine development. ETHICS AND DISSEMINATION This study is approved by the National Health Service South Central Research Ethics Committee (18/SC/0055); the UK Health Research Authority (IRAS ID 239091) and the UK Medicines and Healthcare products Regulatory Agency. Publications arising from this study will be submitted to peer-reviewed journals. Study results will be disseminated in public forums, online, presented at local and international conferences and made available to the participating schools. TRIAL REGISTRATION NUMBERS ISRCTN75858406; Pre-results, EudraCT 2017-004609-42.
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Affiliation(s)
- Jeremy Carr
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Emma Plested
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, Oxfordshire, UK
| | - Parvinder Aley
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, Oxfordshire, UK
| | - Susana Camara
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, Oxfordshire, UK
| | - Kimberly Davis
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Steve Gray
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, UK
| | - Saul N Faust
- NIHR Southampton Clinical Research Facility and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Faculty of Medicine and Institute of Life Sciences, University of Southampton, Southampton, UK
| | - Ray Borrow
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, UK
| | - Hannah Christensen
- School of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline Trotter
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Adam Finn
- School of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Matthew D Snape
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, Oxfordshire, UK
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Predicted coverage by 4CMenB vaccine against invasive meningococcal disease cases in the Netherlands. Vaccine 2020; 38:7850-7857. [PMID: 33097311 DOI: 10.1016/j.vaccine.2020.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 11/23/2022]
Abstract
Neisseria meningitidis serogroup B is a major cause of invasive meningococcal disease in Europe. In the absence of a conjugate serogroup B vaccine, a subcapsular 4CMenB vaccine was developed. Data on 4CMenB vaccine efficacy is still limited. Recently, genomic MATS (Meningococcal Antigen Typing System) was developed as a tool to predict strain coverage, using vaccine antigens sequence data. We characterized all invasive meningococcal isolates received by the Netherlands Reference Laboratory for Bacterial Meningitis (NRLBM) in two epidemiological years 2017-2019 using whole-genome sequencing and determined serogroup, clonal complex (cc) and estimated 4CMenB vaccine coverage by gMATS. Of 396 cases of invasive meningococcal disease, corresponding to an incidence of 1.22 cases/105 inhabitants, 180 (45%) were serogroup W, 155 (39%) serogroup B, 46 (12%) serogroup Y, 10 (3%) serogroup C, 2 non-groupable (0.5%) and 3 (0.7%) unknown. The incidence was the highest among 0-4 years olds (4 cases/105 inhabitants), and 57/72 (79%) of these cases were serogroup B. Serogroup W predominated among persons 45 years of age or older with 110/187 (59%) cases. Serogroup B isolates comprised 11 different clonal complexes, with 103/122 (84%) isolates belonging to 4 clonal complexes: cc32, cc41/44, cc269 and cc213. In contrast, serogroup W isolates were genetically similar with 95% belonging to cc11. Of 122 serogroup B isolates, 89 (73%; 95% CI: 64-80%) were estimated to be covered by 4CMenB and the degree of coverage varied largely by clonal complex and age. Among the 0-4 year olds, 25 of 43 (58%; 95% CI: 43-72%) MenB isolates were estimated to be covered. Since the coverage of the 4CMenB vaccine is dependent on circulating clonal complexes, our findings emphasize the need for surveillance of circulating meningococcal strains. In addition, estimation of age specific coverage is relevant to determine the right target age group for vaccination.
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Rodgers E, Bentley SD, Borrow R, Bratcher HB, Brisse S, Brueggemann AB, Caugant DA, Findlow J, Fox L, Glennie L, Harrison LH, Harrison OB, Heyderman RS, van Rensburg MJ, Jolley KA, Kwambana-Adams B, Ladhani S, LaForce M, Levin M, Lucidarme J, MacAlasdair N, Maclennan J, Maiden MCJ, Maynard-Smith L, Muzzi A, Oster P, Rodrigues CMC, Ronveaux O, Serino L, Smith V, van der Ende A, Vázquez J, Wang X, Yezli S, Stuart JM. The global meningitis genome partnership. J Infect 2020; 81:510-520. [PMID: 32615197 DOI: 10.1016/j.jinf.2020.06.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 10/24/2022]
Abstract
Genomic surveillance of bacterial meningitis pathogens is essential for effective disease control globally, enabling identification of emerging and expanding strains and consequent public health interventions. While there has been a rise in the use of whole genome sequencing, this has been driven predominately by a subset of countries with adequate capacity and resources. Global capacity to participate in surveillance needs to be expanded, particularly in low and middle-income countries with high disease burdens. In light of this, the WHO-led collaboration, Defeating Meningitis by 2030 Global Roadmap, has called for the establishment of a Global Meningitis Genome Partnership that links resources for: N. meningitidis (Nm), S. pneumoniae (Sp), H. influenzae (Hi) and S. agalactiae (Sa) to improve worldwide co-ordination of strain identification and tracking. Existing platforms containing relevant genomes include: PubMLST: Nm (31,622), Sp (15,132), Hi (1935), Sa (9026); The Wellcome Sanger Institute: Nm (13,711), Sp (> 24,000), Sa (6200), Hi (1738); and BMGAP: Nm (8785), Hi (2030). A steering group is being established to coordinate the initiative and encourage high-quality data curation. Next steps include: developing guidelines on open-access sharing of genomic data; defining a core set of metadata; and facilitating development of user-friendly interfaces that represent publicly available data.
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Affiliation(s)
- Elizabeth Rodgers
- Meningitis Research Foundation, Newminster House, 27-29 Newminster House, Baldwin Street, Bristol BS1 1LT, UK.
| | - Stephen D Bentley
- Wellcome Sanger Institute, Parasites and microbes, Hinxton CB10 1SA, UK
| | - Ray Borrow
- Public Health England, Meningococcal Reference Unit, Manchester Royal Infirmary, Manchester M13 9WZ, UK
| | | | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Angela B Brueggemann
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Dominique A Caugant
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jamie Findlow
- Pfizer Limited, Walton Oaks, Dorking Road, Tadworth, Surrey KT20 7NS, UK
| | - LeAnne Fox
- Meningitis and Vaccine Preventable Disease Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, United States
| | - Linda Glennie
- Meningitis Research Foundation, Newminster House, 27-29 Newminster House, Baldwin Street, Bristol BS1 1LT, UK
| | - Lee H Harrison
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, PA, United States
| | | | - Robert S Heyderman
- NIHR Global Health Mucosal Pathogens Research Unit, Division of Infection & Immunity, University College London, London, UK
| | | | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | - Brenda Kwambana-Adams
- NIHR Global Health Mucosal Pathogens Research Unit, Division of Infection & Immunity, University College London, London, UK
| | - Shamez Ladhani
- Public Health England, Immunisation and Countermeasures Division, 61 Colindale Avenue, London NW9 5EQ, UK; Paediatric Infectious Diseases Research Group (PIDRG), St. George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | | | | | - Jay Lucidarme
- Public Health England, Meningococcal Reference Unit, Manchester Royal Infirmary, Manchester M13 9WZ, UK
| | - Neil MacAlasdair
- Wellcome Sanger Institute, Parasites and microbes, Hinxton CB10 1SA, UK
| | - Jenny Maclennan
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | | | | | | | | | | | | | | | - Vinny Smith
- Meningitis Research Foundation, Newminster House, 27-29 Newminster House, Baldwin Street, Bristol BS1 1LT, UK
| | - Arie van der Ende
- Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam UMC and, the Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam, the Netherlands
| | | | - Xin Wang
- Meningitis and Vaccine Preventable Disease Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, United States
| | - Saber Yezli
- Ministry of Health, The Global Centre for Mass Gatherings Medicine, Riyadh, Saudi Arabia
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Leo S, Lazarevic V, Girard M, Getaz-Jimenez Velasco GC, Gaïa N, Renzi G, Cherkaoui A, Hong E, Taha MK, Schrenzel J. Strain coverage of Bexsero vaccine assessed by whole-genome sequencing over a cohort of invasive meningococci of serogroups B and W isolated in Switzerland. Vaccine 2020; 38:5324-5331. [PMID: 32561121 DOI: 10.1016/j.vaccine.2020.05.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 12/27/2022]
Abstract
Invasive meningococcal disease (IMD), caused by Neisseria meningitidis (Nm) strains, is a life-threatening but vaccine-preventable condition. Bexsero is a four-component vaccine that offers broad protection against Nm of serogroup B (NmB), particularly common in Europe. In Switzerland, Bexsero has not yet been licensed and no information is available concerning the predicted vaccine coverage on isolates of circulating Nm. We performed genotyping of Bexsero antigen loci by whole-genome sequencing (WGS) on 104 NmB collected in Switzerland in the 2010-2015 period. We searched for antigen variants previously defined as predictors of strain coverage and estimated that 50% of IMD NmB strains were potentially covered by the vaccine. Clonal complexes (cc) 32, 41/44 and 269, considered the best covered lineages, were further sub-typed according to Bexsero Antigen Sequence Type (BAST) scheme. We also genotyped by WGS 40 Nm of serogroup W (NmW) collected in the country between 2010 and 2016. NmW cc22 isolates appeared to be covered by the vaccine, which was not the case for cc11 isolates, whose incidence has recently increased in Switzerland and all over Europe. Our work underlines the benefit of using WGS for surveillance of vaccine antigen variant distribution in local Nm population and taking proper measures to prevent the spread of NmB.
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Affiliation(s)
- Stefano Leo
- Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Vladimir Lazarevic
- Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Myriam Girard
- Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Gisela C Getaz-Jimenez Velasco
- Swiss National Reference Center for Meningococci (www.meningo.ch), Bacteriology Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Nadia Gaïa
- Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Gesuele Renzi
- Swiss National Reference Center for Meningococci (www.meningo.ch), Bacteriology Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Abdessalam Cherkaoui
- Swiss National Reference Center for Meningococci (www.meningo.ch), Bacteriology Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Eva Hong
- Invasive Bacterial Infection and National Reference Centre for Meningococci, Institut Pasteur, Paris, France
| | - Muhamed-Kheir Taha
- Invasive Bacterial Infection and National Reference Centre for Meningococci, Institut Pasteur, Paris, France
| | - Jacques Schrenzel
- Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Geneva, Switzerland; Swiss National Reference Center for Meningococci (www.meningo.ch), Bacteriology Laboratory, Geneva University Hospitals, Geneva, Switzerland.
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Azevedo AC, Franco NEC, de Carvalho Rocha MR, Andrade C, Torres MC, de Filippis I. Molecular surveillance of brazilian meningococcal isolates serogroup c in the pre and post-men-c-vaccination period: Emergence of ST-3780. INFECTION GENETICS AND EVOLUTION 2020; 78:104079. [DOI: 10.1016/j.meegid.2019.104079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/16/2019] [Accepted: 10/20/2019] [Indexed: 12/15/2022]
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Waśko I, Gołębiewska A, Kiedrowska M, Ronkiewicz P, Wróbel-Pawelczyk I, Kuch A, Hong E, Skoczyńska A. Genetic variability of Polish serogroup B meningococci (2010-2016) including the 4CMenB vaccine component genes. Vaccine 2020; 38:1943-1952. [PMID: 31980191 DOI: 10.1016/j.vaccine.2020.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 12/20/2019] [Accepted: 01/07/2020] [Indexed: 01/25/2023]
Abstract
Neisseria meningitidis serogroup B (MenB) has recently become the major cause of invasive meningococcal disease in Poland. Therefore, the purpose of this study was to characterize MenB isolates, responsible for invasive meningococcal disease in 2010-2016, by MLST and sequencing of genes encoding proteins used as 4CMenB vaccine antigens. Two methods of coverage estimation were performed: extrapolation of MATS results of Polish meningococci 2010-2011 (exMATS) and gMATS, which combines genotyping and MATS results. Among 662 isolates 20 clonal complexes (CC) were detected, of which the most frequent were CC32, CC41/44 and CC18, accounting for 31.9%, 16.5% and 12.7%, respectively. A total of 111 combinations of PorA variable regions (VR1/VR2) were found, with P1.7,16 (15.0%) and P1.22,14 (13.6%) being prevalent. Vaccine variant VR2:4 was detected in 7.3% of isolates, mainly representing CC41/44 and non-assigned CC. Eighty five fHbp alleles encoding 74 peptide subvariants were revealed. Subvariant 1.1, a component of 4CMenB, was prevalent (24.2%) and found generally in CC32. Typing of the nhba gene revealed 102 alleles encoding 87 peptides. The most frequent was peptide 3 (22.4%), whereas vaccine peptide 2 was detected in 9.8%, mostly among CC41/44. The nadA gene was detected in 34.0% of isolates and the most prevalent was peptide 1 (variant NadA-1; 71.6%), found almost exclusively in CC32 meningococci. Vaccine peptide 8 (variant NadA-2/3) was identified once. Consequently, 292 completed BAST profiles were revealed. Regarding vaccine coverage, 39.7% of isolates had at least one 4CMenB vaccine variant, but according to exMATS and gMATS the coverage was 83.3% and 86.6%, respectively. In conclusion, Polish MenB (2010-2016) was highly diverse according to MLST and gene alleles encoding 4CMenB vaccine antigens. Some correlations between clonal complexes and variants of examined proteins/BAST profiles were revealed and a high coverage of 4CMenB vaccine was estimated.
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Affiliation(s)
- Izabela Waśko
- National Reference Centre for Bacterial Meningitis, National Medicines Institute, Warsaw, Poland
| | - Agnieszka Gołębiewska
- National Reference Centre for Bacterial Meningitis, National Medicines Institute, Warsaw, Poland
| | - Marlena Kiedrowska
- National Reference Centre for Bacterial Meningitis, National Medicines Institute, Warsaw, Poland
| | - Patrycja Ronkiewicz
- National Reference Centre for Bacterial Meningitis, National Medicines Institute, Warsaw, Poland
| | - Izabela Wróbel-Pawelczyk
- National Reference Centre for Bacterial Meningitis, National Medicines Institute, Warsaw, Poland
| | - Alicja Kuch
- National Reference Centre for Bacterial Meningitis, National Medicines Institute, Warsaw, Poland
| | - Eva Hong
- Institute Pasteur, Invasive Bacterial Infections Unit, Paris, France
| | - Anna Skoczyńska
- National Reference Centre for Bacterial Meningitis, National Medicines Institute, Warsaw, Poland
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Caugant DA, Brynildsrud OB. Neisseria meningitidis: using genomics to understand diversity, evolution and pathogenesis. Nat Rev Microbiol 2019; 18:84-96. [PMID: 31705134 DOI: 10.1038/s41579-019-0282-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2019] [Indexed: 01/30/2023]
Abstract
Meningococcal disease remains an important cause of morbidity and death worldwide despite the development and increasing implementation of effective vaccines. Elimination of the disease is hampered by the enormous diversity and antigenic variability of the causative agent, Neisseria meningitidis, one of the most variable bacteria in nature. These features are attained mainly through high rates of horizontal gene transfer and alteration of protein expression through phase variation. The recent availability of whole-genome sequencing (WGS) of large-scale collections of N. meningitidis isolates from various origins, databases to facilitate storage and sharing of WGS data and the concomitant development of effective bioinformatics tools have led to a much more thorough understanding of the diversity of the species, its evolution and population structure and how virulent traits may emerge. Implementation of WGS is already contributing to enhanced epidemiological surveillance and is essential to ascertain the impact of vaccination strategies. This Review summarizes the recent advances provided by WGS studies in our understanding of the biology of N. meningitidis and the epidemiology of meningococcal disease.
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Affiliation(s)
- Dominique A Caugant
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway. .,Department of Community Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Ola B Brynildsrud
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Food Safety and Infection Biology, Faculty of Veterinary Science, Norwegian University of Life Science, Oslo, Norway
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11
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Bratcher HB, Rodrigues CMC, Finn A, Wootton M, Cameron JC, Smith A, Heath P, Ladhani S, Snape MD, Pollard AJ, Cunningham R, Borrow R, Trotter C, Gray SJ, Maiden MCJ, MacLennan JM. UKMenCar4: A cross-sectional survey of asymptomatic meningococcal carriage amongst UK adolescents at a period of low invasive meningococcal disease incidence. Wellcome Open Res 2019; 4:118. [PMID: 31544158 PMCID: PMC6749934 DOI: 10.12688/wellcomeopenres.15362.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2019] [Indexed: 01/02/2023] Open
Abstract
Carriage of
Neisseria meningitidis, the meningococcus, is a prerequisite for invasive meningococcal disease (IMD), a potentially devastating infection that disproportionately afflicts infants and children. Humans are the sole known reservoir for the meningococcus, and it is carried asymptomatically in the nasopharynx of ~10% of the population. Rates of carriage are dependent on age of the host and social and behavioural factors. In the UK, meningococcal carriage has been studied through large, multi-centre carriage surveys of adolescents in 1999, 2000, and 2001, demonstrating carriage can be affected by immunisation with the capsular group C meningococcal conjugate vaccine, inducing population immunity against carriage. Fifteen years after these surveys were carried out, invasive meningococcal disease incidence had declined from a peak in 1999. The UKMenCar4 study was conducted in 2014/15 to investigate rates of carriage amongst the adolescent population during a period of low disease incidence. The protocols and methodology used to perform UKMenCar4, a large carriage survey, are described here.
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Affiliation(s)
- Holly B Bratcher
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK
| | - Charlene M C Rodrigues
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK
| | - Adam Finn
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS2 8AE, UK
| | - Mandy Wootton
- Division of Public Health Wales, Cardiff, CF10 3NW, UK
| | - J Claire Cameron
- NHS National Services Scotland, Health Protection Scotland, Glasgow, G2 6QE, UK
| | - Andrew Smith
- University of Glasgow Dental School, Glasgow, G2 3JZ, UK.,Scottish Microbiology Reference Laboratory, NHS Greater Glasgow & Clyde, Glasgow, G2 6QE, UK
| | - Paul Heath
- Paediatric Infectious Diseases Research Group, St George's, University of London, London, SW17 0QT, UK
| | - Shamez Ladhani
- Paediatric Infectious Diseases Research Group, St George's, University of London, London, SW17 0QT, UK.,Immunisation Department, Public Health England, London, UK
| | - Matthew D Snape
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford Biomedical Research Centre, Oxford, OX3 7LE, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford Biomedical Research Centre, Oxford, OX3 7LE, UK
| | - Richard Cunningham
- Microbiology Department, University Hospitals Plymouth NHS Trust, Plymouth, PL6 8DH, UK
| | - Raymond Borrow
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, M13 9WL, UK
| | - Caroline Trotter
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Stephen J Gray
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, M13 9WL, UK
| | - Martin C J Maiden
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK
| | - Jenny M MacLennan
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK
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12
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Bratcher HB, Rodrigues CMC, Finn A, Wootton M, Cameron JC, Smith A, Heath P, Ladhani S, Snape MD, Pollard AJ, Cunningham R, Borrow R, Trotter C, Gray SJ, Maiden MCJ, MacLennan JM. UKMenCar4: A cross-sectional survey of asymptomatic meningococcal carriage amongst UK adolescents at a period of low invasive meningococcal disease incidence. Wellcome Open Res 2019; 4:118. [PMID: 31544158 DOI: 10.12688/wellcomeopenres.15362.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2019] [Indexed: 11/20/2022] Open
Abstract
Carriage of Neisseria meningitidis, the meningococcus, is a prerequisite for invasive meningococcal disease (IMD), a potentially devastating infection that disproportionately afflicts infants and children. Humans are the sole known reservoir for the meningococcus, and it is carried asymptomatically in the nasopharynx of ~10% of the population. Rates of carriage are dependent on age of the host and social and behavioural factors. In the UK, meningococcal carriage has been studied through large, multi-centre carriage surveys of adolescents in 1999, 2000, and 2001, demonstrating carriage can be affected by immunisation with the capsular group C meningococcal conjugate vaccine, inducing population immunity against carriage. Fifteen years after these surveys were carried out, invasive meningococcal disease incidence had declined from a peak in 1999. The UKMenCar4 study was conducted in 2014/15 to investigate rates of carriage amongst the adolescent population during a period of low disease incidence. The protocols and methodology used to perform UKMenCar4, a large carriage survey, are described here.
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Affiliation(s)
- Holly B Bratcher
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK
| | - Charlene M C Rodrigues
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK
| | - Adam Finn
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS2 8AE, UK
| | - Mandy Wootton
- Division of Public Health Wales, Cardiff, CF10 3NW, UK
| | - J Claire Cameron
- NHS National Services Scotland, Health Protection Scotland, Glasgow, G2 6QE, UK
| | - Andrew Smith
- University of Glasgow Dental School, Glasgow, G2 3JZ, UK.,Scottish Microbiology Reference Laboratory, NHS Greater Glasgow & Clyde, Glasgow, G2 6QE, UK
| | - Paul Heath
- Paediatric Infectious Diseases Research Group, St George's, University of London, London, SW17 0QT, UK
| | - Shamez Ladhani
- Paediatric Infectious Diseases Research Group, St George's, University of London, London, SW17 0QT, UK.,Immunisation Department, Public Health England, London, UK
| | - Matthew D Snape
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford Biomedical Research Centre, Oxford, OX3 7LE, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford Biomedical Research Centre, Oxford, OX3 7LE, UK
| | - Richard Cunningham
- Microbiology Department, University Hospitals Plymouth NHS Trust, Plymouth, PL6 8DH, UK
| | - Raymond Borrow
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, M13 9WL, UK
| | - Caroline Trotter
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Stephen J Gray
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, M13 9WL, UK
| | - Martin C J Maiden
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK
| | - Jenny M MacLennan
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK
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13
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Van Goethem N, Descamps T, Devleesschauwer B, Roosens NHC, Boon NAM, Van Oyen H, Robert A. Status and potential of bacterial genomics for public health practice: a scoping review. Implement Sci 2019; 14:79. [PMID: 31409417 PMCID: PMC6692930 DOI: 10.1186/s13012-019-0930-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/26/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist's perspective. METHODS In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. RESULTS Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. CONCLUSIONS For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist's perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance.
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Affiliation(s)
- Nina Van Goethem
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Woluwe-Saint-Lambert, Belgium
| | - Tine Descamps
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Brecht Devleesschauwer
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Nele A. M. Boon
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Herman Van Oyen
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Public Health and Primary Care, Faculty of Medicine, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Annie Robert
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Woluwe-Saint-Lambert, Belgium
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14
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Krizova P, Honskus M. Genomic surveillance of invasive meningococcal disease in the Czech Republic, 2015-2017. PLoS One 2019; 14:e0219477. [PMID: 31295279 PMCID: PMC6622526 DOI: 10.1371/journal.pone.0219477] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/25/2019] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION The study presents the results of the genomic surveillance of invasive meningococcal disease (IMD) in the Czech Republic for the period of 2015-2017. MATERIAL AND METHODS The study set includes all available IMD isolates recovered in the Czech Republic and referred to the National Reference Laboratory for Meningococcal Infections in 2015-2017, a total of 89 Neissseria meningitidis isolates-from 2015 (n = 20), 2016 (n = 27), and from 2017 (n = 42). All isolates were studied by whole genome sequencing (WGS). RESULTS Serogroup B (MenB) was the most common, followed by serogroups C, W, and Y. Altogether 17 clonal complexes were identified, the most common of which was hypervirulent complex cc11, followed by complexes cc32, cc41/44, cc269, and cc865. Over the three study years, hypervirulent cc11 (MenC) showed an upward trend. The WGS method showed two clearly differentiated clusters of N. meningitidis C: P1.5,2:F3-3:ST-11 (cc11). The first cluster is represented by nine isolates, all of which are from 2017. The second cluster consisted of five isolates from 2016 and eight isolates from 2017. Their genetic discordance is illustrated by the changing nadA allele and subsequently by the variance in BAST type. Clonal complex cc269 (MenB) also increased over the time frame. WGS identified the presence of MenB vaccine antigen genes in all B and non-B isolates of N. meningitidis. Altogether 49 different Bexsero antigen sequence types (BAST) were identified and 10 combinations of these have not been previously described in the PubMLST database. CONCLUSIONS The genomic surveillance of IMD in the Czech Republic provides data needed to update immunisation guidelines for this disease. WGS showed a higher discrimination power and provided more accurate data on molecular characteristics and genetic relationships among invasive N. meningitidis isolates.
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Affiliation(s)
- Pavla Krizova
- National Reference Laboratory for Meningococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
- * E-mail:
| | - Michal Honskus
- National Reference Laboratory for Meningococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
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15
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Rodrigues CMC, Chan H, Vipond C, Jolley K, Harrison OB, Wheeler J, Whiting G, Feavers IM, Maiden MCJ. Typing complex meningococcal vaccines to understand diversity and population structure of key vaccine antigens. Wellcome Open Res 2019; 3:151. [PMID: 30687793 DOI: 10.12688/wellcomeopenres.14859.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2018] [Indexed: 11/20/2022] Open
Abstract
Background: Protein-conjugate capsular polysaccharide vaccines can potentially control invasive meningococcal disease (IMD) caused by five (A, C, W, X, Y) of the six IMD-associated serogroups. Concerns raised by immunological similarity of the serogroup B capsule to human neural cell carbohydrates, meant that 'serogroup B substitute' vaccines target more variable subcapsular protein antigens. A successful approach using outer membrane vesicles (OMVs) as major vaccine components had limited strain coverage. In 4CMenB (Bexsero ®), recombinant proteins have been added to ameliorate this problem. Methods: Scalable, portable, genomic techniques were used to investigate the Bexsero ® OMV protein diversity in meningococcal populations. Shotgun proteomics identified 461 proteins in the OMV, defining a complex proteome. Amino acid sequences for the 24 proteins most likely to be involved in cross-protective immune responses were catalogued within the PubMLST.org/neisseria database using a novel OMV peptide Typing (OMVT) scheme. Results: Among these proteins there was variation in the extent of diversity and association with meningococcal lineages, identified as clonal complexes (ccs), ranging from the most conserved peptides (FbpA, NEISp0578, and putative periplasmic protein, NEISp1063) to the most diverse (TbpA, NEISp1690). There were 1752 unique OMVTs identified amongst 2492/3506 isolates examined by whole-genome sequencing (WGS). These OMVTs were grouped into clusters (sharing ≥18 identical OMVT peptides), with 45.3% of isolates assigned to one of 27 OMVT clusters. OMVTs and OMVT clusters were strongly associated with cc, genogroup, and Bexsero ® antigen variants, demonstrating that combinations of OMV proteins exist in discrete, non-overlapping combinations associated with genogroup and Bexsero ® Antigen Sequence Type. This highly structured population of IMD-associated meningococci is consistent with strain structure models invoking host immune and/or metabolic selection. Conclusions: The OMVT scheme facilitates region-specific WGS investigation of meningococcal diversity and is an open-access, portable tool with applications for vaccine development, especially in the choice of antigen combinations, assessment and implementation.
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Affiliation(s)
| | - Hannah Chan
- Division of Bacteriology, National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Caroline Vipond
- Division of Bacteriology, National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Keith Jolley
- Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK
| | - Odile B Harrison
- Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK
| | - Jun Wheeler
- Division of Bacteriology, National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Gail Whiting
- Division of Bacteriology, National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Ian M Feavers
- Division of Bacteriology, National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
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16
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Rodrigues CMC, Chan H, Vipond C, Jolley K, Harrison OB, Wheeler J, Whiting G, Feavers IM, Maiden MCJ. Typing complex meningococcal vaccines to understand diversity and population structure of key vaccine antigens. Wellcome Open Res 2019; 3:151. [PMID: 30687793 PMCID: PMC6338130 DOI: 10.12688/wellcomeopenres.14859.2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2019] [Indexed: 01/09/2023] Open
Abstract
Background: Protein-conjugate capsular polysaccharide vaccines can potentially control invasive meningococcal disease (IMD) caused by five (A, C, W, X, Y) of the six IMD-associated serogroups. Concerns raised by immunological similarity of the serogroup B capsule to human neural cell carbohydrates, meant that ‘serogroup B substitute’ vaccines target more variable subcapsular protein antigens. A successful approach using outer membrane vesicles (OMVs) as major vaccine components had limited strain coverage. In 4CMenB (Bexsero
®), recombinant proteins have been added to ameliorate this problem. Methods: Scalable, portable, genomic techniques were used to investigate the Bexsero
® OMV protein diversity in meningococcal populations. Shotgun proteomics identified 461 proteins in the OMV, defining a complex proteome. Amino acid sequences for the 24 proteins most likely to be involved in cross-protective immune responses were catalogued within the
PubMLST.org/neisseria database using a novel OMV peptide Typing (OMVT) scheme. Results: Among these proteins there was variation in the extent of diversity and association with meningococcal lineages, identified as clonal complexes (ccs), ranging from the most conserved peptides (FbpA, NEISp0578, and putative periplasmic protein, NEISp1063) to the most diverse (TbpA, NEISp1690). There were 1752 unique OMVTs identified amongst 2492/3506 isolates examined by whole-genome sequencing (WGS). These OMVTs were grouped into clusters (sharing ≥18 identical OMVT peptides), with 45.3% of isolates assigned to one of 27 OMVT clusters. OMVTs and OMVT clusters were strongly associated with cc, genogroup, and Bexsero
® antigen variants, demonstrating that combinations of OMV proteins exist in discrete, non-overlapping combinations associated with genogroup and Bexsero
® Antigen Sequence Type. This highly structured population of IMD-associated meningococci is consistent with strain structure models invoking host immune and/or metabolic selection. Conclusions:The OMVT scheme facilitates region-specific WGS investigation of meningococcal diversity and is an open-access, portable tool with applications for vaccine development, especially in the choice of antigen combinations, assessment and implementation.
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Affiliation(s)
| | - Hannah Chan
- Division of Bacteriology, National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Caroline Vipond
- Division of Bacteriology, National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Keith Jolley
- Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK
| | - Odile B Harrison
- Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK
| | - Jun Wheeler
- Division of Bacteriology, National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Gail Whiting
- Division of Bacteriology, National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Ian M Feavers
- Division of Bacteriology, National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
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17
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Kesanopoulos K, Bratcher HB, Hong E, Xirogianni A, Papandreou A, Taha MK, Maiden MCJ, Tzanakaki G. Characterization of meningococcal carriage isolates from Greece by whole genome sequencing: Implications for 4CMenB vaccine implementation. PLoS One 2018; 13:e0209919. [PMID: 30592763 PMCID: PMC6310245 DOI: 10.1371/journal.pone.0209919] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 12/13/2018] [Indexed: 12/21/2022] Open
Abstract
Herd protection, resulting from the interruption of transmission and asymptomatic carriage, is an important element of the effectiveness of vaccines against the meningococcus. Whilst this has been well established for conjugate polysaccharide vaccines directed against the meningococcal capsule, two uncertainties surround the potential herd protection provided by the novel protein-based vaccines that are used in place of serogroup B (MenB) polysaccharide vaccines (i) the strain coverage of such vaccines against carried meningococci, which are highly diverse; and (ii) the generation of a protective immune response in the mucosa. These considerations are essential for realistic estimates of cost-effectiveness of new MenB vaccines. Here the first of these questions is addressed by the whole genome sequence (WGS) analysis of meningococci isolated from healthy military recruits and university students in Greece. The study included a total of 71 MenB isolates obtained from 1420 oropharyngeal single swab samples collected from military recruits and university students on voluntary basis, aged 18-26 years. In addition to WGS analysis to identify genetic lineage and vaccine antigen genes, including the Bexsero Antigen Sequence Type (BAST), the isolates were examined with the serological Meningococcal antigen Typing System (MATS) assay. Comparison of these data demonstrated that the carried meningococcal population was highly diverse with 38% of the carriage isolates showed expression of antigens matching those included in the 4CMenB vaccine. Our data may suggest a limited potential herd immunity to be expected and be driven by an impact on a subset of carriage isolates.
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Affiliation(s)
- Konstantinos Kesanopoulos
- National Meningitis Reference Laboratory (NMRL), Dept of Public Health, National School of Public Health, Athens, Greece
| | - Holly B. Bratcher
- Department of Zoology, Peter Medawar Building, University of Oxford, Oxford, United Kingdom
| | - Eva Hong
- Institute Pasteur, Invasive Bacterial Infections Unit, Paris, France
| | - Athanasia Xirogianni
- National Meningitis Reference Laboratory (NMRL), Dept of Public Health, National School of Public Health, Athens, Greece
| | - Anastasia Papandreou
- National Meningitis Reference Laboratory (NMRL), Dept of Public Health, National School of Public Health, Athens, Greece
| | | | - Martin C. J. Maiden
- Department of Zoology, Peter Medawar Building, University of Oxford, Oxford, United Kingdom
| | - Georgina Tzanakaki
- National Meningitis Reference Laboratory (NMRL), Dept of Public Health, National School of Public Health, Athens, Greece
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18
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Stein-Zamir C, Shoob H, Abramson N, Block C, Keller N, Jaffe J, Valinsky L. Invasive meningococcal disease epidemiology and characterization of Neisseria meningitidis serogroups, sequence types, and clones; implication for use of meningococcal vaccines. Hum Vaccin Immunother 2018; 15:242-248. [PMID: 30156954 DOI: 10.1080/21645515.2018.1507261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND AND AIMS Neisseria meningitidis (N. meningitidis) is a Gram-negative bacterium that can cause life-threatening invasive infections referred to as invasive meningococcal disease (IMD). In the last decade the incidence of IMD in Israel is about 1/100,000 population annually. We aimed to describe the epidemiology of IMD in Israel combining epidemiological data and characterization of N. meningitidis isolates. METHODS Invasive infection caused by N. meningitidis is a notifiable disease in Israel. Data were collected by epidemiological investigations and control measures were employed. Laboratory work-up included serogrouping, N. meningitides molecular characterization and whole-genome sequencing. RESULTS During 1998-2017, 1349 cases of IMD were notified in Israel (mean annual incidence rate 0.94/100,000). The peak incidence rates were observed in infants under 1 year of age (10.9/100,000). Case fatality rate was 9.7%. The majority of the N. meningitidis isolates were of serogroup B (67.9%). During 2007-2017, three clonal complexes (CC) 32, 41/44 and 23 (hyper-invasive clonal complexes) were the leading CC (61%). CC32 was the leading CC causing meningococcemia and mortality. In 2017, 35 isolates were tested for 4CMenB antigens variants; of the serogroup B isolates tested 46.7% showed a match to one or more antigens (fHbp or PorA:VR1), most were ST32 (CC32). CONCLUSIONS Preliminary analysis based on limited number of samples suggests that the 4CMenB coverage would be about half the strains; further research is necessary. Integration of clinical, epidemiological and laboratory data is essential to support decision-making on the introduction of the novel MENB vaccines in Israel.
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Affiliation(s)
- Chen Stein-Zamir
- a Ministry of Health , Jerusalem District Health Office , Jerusalem , Israel.,b The Hebrew University of Jerusalem, Faculty of Medicine , The Hebrew University and Hadassah Braun School of Public and Community Medicine , Jerusalem , Israel
| | - Hanna Shoob
- a Ministry of Health , Jerusalem District Health Office , Jerusalem , Israel
| | - Nitza Abramson
- a Ministry of Health , Jerusalem District Health Office , Jerusalem , Israel
| | - Colin Block
- c Department of Clinical Microbiology and Infectious Diseases , Hadassah-Hebrew University Medical Centre , Jerusalem , Israel
| | - Natan Keller
- d Ministry of Health , National Reference Center for Meningococci, Microbiology Laboratory, Sheba Medical Center , Ramat-Gan , Israel
| | - Joseph Jaffe
- e Ministry of Health , Government Central Laboratories , Jerusalem , Israel
| | - Lea Valinsky
- e Ministry of Health , Government Central Laboratories , Jerusalem , Israel
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19
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Invasive meningococcal disease in Shanghai, China from 1950 to 2016: implications for serogroup B vaccine implementation. Sci Rep 2018; 8:12334. [PMID: 30120257 PMCID: PMC6098053 DOI: 10.1038/s41598-018-30048-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/23/2018] [Indexed: 11/24/2022] Open
Abstract
Serogroup B invasive meningococcal disease (IMD) is increasing in China, but little is known about the causative meningococci. Here, IMD and carriage isolates in Shanghai characterised and the applicability of different vaccines assessed. Seven IMD epidemic periods have been observed in Shanghai since 1950, with 460 isolates collected including 169 from IMD and 291 from carriage. Analyses were divided according to the period of meningococcal polysaccharide vaccine (MPV) introduction: (i) pre-MPV-A, 1965–1980; (ii) post-MPV-A, 1981–2008; and (iii) post-MPV-A + C, 2009–2016. Over this period, IMD incidence decreased from 55.4/100,000 to 0.71 then to 0.02, corresponding to successive changes in meningococcal type from serogroup A ST-5 complex (MenA:cc5) to MenC:cc4821, and finally MenB:cc4821. MenB IMD became predominant (63.2%) in the post-MPV-A + C period, and 50% of cases were caused by cc4821, with the highest incidence in infants (0.45/100,000) and a case-fatality rate of 9.5%. IMD was positively correlated with population carriage rates. Using the Bexsero Antigen Sequence Type (BAST) system, fewer than 25% of MenB isolates in the post-MPV-A + C period contained exact or predicted cross reactive matches to the vaccines Bexsero, Trumenba, or an outer membrane vesicle (OMV)-based vaccine, NonaMen. A unique IMD epidemiology was seen in China, changing periodically from epidemic to hyperepidemic and low-level endemic disease. At the time of writing, MenB IMD dominated IMD in Shanghai, with isolates potentially beyond coverage with licenced OMV- and protein-based MenB vaccines.
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Rodrigues CMC, Maiden MCJ. A world without bacterial meningitis: how genomic epidemiology can inform vaccination strategy. F1000Res 2018; 7:401. [PMID: 29636909 PMCID: PMC5871810 DOI: 10.12688/f1000research.13793.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/21/2018] [Indexed: 11/20/2022] Open
Abstract
Bacterial meningitis remains an important cause of global morbidity and mortality. Although effective vaccinations exist and are being increasingly used worldwide, bacterial diversity threatens their impact and the ultimate goal of eliminating the disease. Through genomic epidemiology, we can appreciate bacterial population structure and its consequences for transmission dynamics, virulence, antimicrobial resistance, and development of new vaccines. Here, we review what we have learned through genomic epidemiological studies, following the rapid implementation of whole genome sequencing that can help to optimise preventative strategies for bacterial meningitis.
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Affiliation(s)
- Charlene M C Rodrigues
- Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, UK
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, UK
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