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Ceyhan M, Ozsurekci Y, Lucidarme J, Borrow R. Characterization of invasive Neisseria meningitidis isolates recovered from children in Turkey during a period of increased serogroup B disease, 2013-2017. Vaccine 2020; 38:3545-3552. [PMID: 32199701 DOI: 10.1016/j.vaccine.2020.03.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/03/2020] [Accepted: 03/09/2020] [Indexed: 01/24/2023]
Abstract
Diverse Neisseria meningitidis strains belonging to various serogroups and clonal complexes cause epidemic and endemic life-threatening disease worldwide. This study aimed to investigate the genetic diversity of recent invasive meningococci in Turkey with respect to multilocus sequence type (MLST) and also meningococcal serogroup B (MenB) vaccine antigens to enable assessment of potential MenB strain coverage using the genetic Meningococcal Antigen Typing System (gMATS). Fifty-four isolates, representing 37.5% of all pediatric (ages 0-18 years) invasive meningococcal disease cases in Turkey from January 2013 to December 2017, underwent genome sequence analysis. Thirty-six (66.7%) isolates were MenB, 10 (18.5%) were serogroup W (MenW), 4 (7.4%) were serogroup A (MenA), 3 (5.6%) were serogroup Y (MenY) and 1 (1.8%) was serogroup X (MenX). The MenB isolates were diverse with cc35 (19.4%), cc41/44 (19.4%) and cc32 (13.8%) as the most prevalent clonal complexes. The MenW isolates (n = 10) comprised cc11 (n = 5), ST-2754 (cc-unassigned; n = 4) and cc22 (n = 1). gMATS was indicative of high 4CMenB coverage (72.2-79.1%) of Turkish invasive MenB strains from pediatric patients. Strain coverage of several clonal complexes differed from that seen elsewhere in Europe highlighting the importance of performing local assessments and also the use of phenotypic methods, i.e. MATS, where possible. All of the isolates possessed in-frame fhbp alleles and so were potentially covered by MenB-fHbp. Continued surveillance is essential to guide recommendations for current and future vaccines as well as understanding changes in epidemiology.
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Affiliation(s)
- Mehmet Ceyhan
- Hacettepe University, Faculty of Medicine, Department of Pediatric Infectious Diseases, Ankara, Turkey
| | - Yasemin Ozsurekci
- Hacettepe University, Faculty of Medicine, Department of Pediatric Infectious Diseases, Ankara, Turkey.
| | - Jay Lucidarme
- Meningococcal Reference Unit, Public Health England, Manchester, United Kingdom
| | - Ray Borrow
- Meningococcal Reference Unit, Public Health England, Manchester, United Kingdom
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2
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Bennett DE, Meyler KL, Cafferkey MT, Cunney RJ. Diversity of meningococci associated with invasive meningococcal disease in the Republic of Ireland over a 19 year period, 1996-2015. PLoS One 2020; 15:e0228629. [PMID: 32053601 PMCID: PMC7018037 DOI: 10.1371/journal.pone.0228629] [Citation(s) in RCA: 4] [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: 07/22/2019] [Accepted: 01/20/2020] [Indexed: 12/19/2022] Open
Abstract
This study examined the capsular phenotype and genotype of invasive meningococcal disease (IMD)-associated Neisseria meningitidis recovered in the Republic of Ireland (RoI) between 1996 and 2015. This time period encompasses both pre- (when IMD was hyperendemic in the RoI) and post- meningococcal serogroup C conjugate (MCC) vaccine introduction. In total, 1327 isolates representing over one-third of all laboratory-confirmed cases of IMD diagnosed each epidemiological year (EY), were characterised. Serogroups B (menB) and C (menC) predominated throughout, although their relative abundance changed; with an initial increase in the proportion of menC in the late 1990s followed by their dramatic reduction post-MCC vaccine implementation and a concomitant dominance of menB, despite an overall decline in IMD incidence. While the increase in menC was associated with expansion of specific clonal-complexes (cc), cc11 and cc8; the dominance of menB was not. There was considerable variation in menB-associated cc with declines in cc41/44 and cc32, and increases in cc269 and cc461, contributing to a significant increase in the clonal diversity of menB isolates over the study. This increase in diversity was also displayed among the serosubtyping data, with significant declines in proportions of menB isolates expressing p1.4 and p1.15 antigens. These data highlight the changing diversity of IMD-associated meningococci since 1996 in the RoI and emphasise the need for on-going surveillance particularly in view of the recent introduction of a menB vaccine.
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Affiliation(s)
- Désirée E. Bennett
- Irish Meningitis and Sepsis Reference Laboratory, Children’s Health Ireland, Dublin, Ireland
- * E-mail:
| | - Kenneth L. Meyler
- Irish Meningitis and Sepsis Reference Laboratory, Children’s Health Ireland, Dublin, Ireland
| | - Mary T. Cafferkey
- Irish Meningitis and Sepsis Reference Laboratory, Children’s Health Ireland, Dublin, Ireland
- Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Robert J. Cunney
- Irish Meningitis and Sepsis Reference Laboratory, Children’s Health Ireland, Dublin, Ireland
- Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Clinical Microbiology, Children’s Health Ireland, Dublin, Ireland
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3
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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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4
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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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5
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Andreae CA, Sessions RB, Virji M, Hill DJ. Bioinformatic analysis of meningococcal Msf and Opc to inform vaccine antigen design. PLoS One 2018; 13:e0193940. [PMID: 29547646 PMCID: PMC5856348 DOI: 10.1371/journal.pone.0193940] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/21/2018] [Indexed: 11/19/2022] Open
Abstract
Neisseria meningitidis is an antigenically and genetically variable Gram-negative bacterium and a causative agent of meningococcal meningitis and septicaemia. Meningococci encode many outer membrane proteins, including Opa, Opc, Msf, fHbp and NadA, identified as being involved in colonisation of the host and evasion of the immune response. Although vaccines are available for the prevention of some types of meningococcal disease, none currently offer universal protection. We have used sequences within the Neisseria PubMLST database to determine the variability of msf and opc in 6,500 isolates. In-silico analysis revealed that although opc is highly conserved, it is not present in all isolates, with most isolates in clonal complex ST-11 lacking a functional opc. In comparison, msf is found in all meningococcal isolates, and displays diversity in the N-terminal domain. We identified 20 distinct Msf sequence variants (Msf SV), associated with differences in number of residues within the putative Vn binding motifs. Moreover, we showed distinct correlations with certain Msf SVs and isolates associated with either hyperinvasive lineages or those clonal complexes associated with a carriage state. We have demonstrated differences in Vn binding between three Msf SVs and generated a cross reactive Msf polyclonal antibody. Our study has highlighted the importance of using large datasets to inform vaccine development and provide further information on the antigenic diversity exhibited by N. meningitidis.
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Affiliation(s)
- Clio A. Andreae
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | | | - Mumtaz Virji
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Darryl. J. Hill
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- * E-mail:
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6
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Mowlaboccus S, Mullally CA, Richmond PC, Howden BP, Stevens K, Speers DJ, Keil AD, Bjørnstad ON, Perkins TT, Kahler CM. Differences in the population structure of Neisseria meningitidis in two Australian states: Victoria and Western Australia. PLoS One 2017; 12:e0186839. [PMID: 29065137 PMCID: PMC5655437 DOI: 10.1371/journal.pone.0186839] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/09/2017] [Indexed: 01/06/2023] Open
Abstract
Neisseria meningitidis is the causative agent of invasive meningococcal disease (IMD). A recombinant vaccine called Bexsero® incorporates four subcapsular antigens (fHbp, NHBA, NadA and PorA) which are used to assign a Bexsero® antigen sequence type (BAST) to each meningococcal strain. The vaccine elicits an immune response against combinations of variants of these antigens which have been grouped into specific BAST profiles that have been shown to have different distributions within geographical locations thus potentially affecting the efficacy of the vaccine. In this study, invasive meningococcal disease isolates from the western seaboard of Australia (Western Australia; WA) were compared to those from the south-eastern seaboard (Victoria; VIC) from 2008 to 2012. Whole-genome sequencing (WGS) of 131 meningococci from VIC and 70 meningococci from WA were analysed for MLST, FetA and BAST profiling. Serogroup B predominated in both jurisdictions and a total of 10 MLST clonal complexes (cc) were shared by both states. Isolates belonging to cc22, cc103 and cc1157 were unique to VIC whilst isolates from cc60 and cc212 were unique to WA. Clonal complex 41/44 represented one-third of the meningococcal population in each state but the predominant ST was locally different: ST-6058 in VIC and ST-146 in WA. Of the 108 BAST profiles identified in this collection, only 9 BASTs were simultaneously observed in both states. A significantly larger proportion of isolates in VIC harboured alleles for the NHBA-2 peptide and fHbp-1, antigenic variants predicted to be covered by the Bexsero® vaccine. The estimate for vaccine coverage in WA (47.1% [95% CI: 41.1-53.1%]) was significantly lower than that in VIC (66.4% [95% CI: 62.3-70.5%]). In conclusion, the antigenic structure of meningococci causing invasive disease in two geographically distinct states of Australia differed significantly during the study period which may affect vaccine effectiveness and highlights the need for representative surveillance when predicting potential impact of meningococcal B vaccines.
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Affiliation(s)
- Shakeel Mowlaboccus
- Marshall Center for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Christopher A. Mullally
- Marshall Center for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Peter C. Richmond
- Division of Paediatrics, School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
- Telethon Kids Institute, Perth, Western Australia, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - David J. Speers
- Department of Microbiology, QEII Medical Centre, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Perth, Western Australia, Australia
| | - Anthony D. Keil
- Department of Microbiology, Princess Margaret Hospital for Children, PathWest Laboratory Medicine WA, Perth, Australia
| | - Ottar N. Bjørnstad
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Timothy T. Perkins
- Marshall Center for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Charlene M. Kahler
- Marshall Center for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Telethon Kids Institute, Perth, Western Australia, Australia
- * E-mail:
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7
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Metabolic shift in the emergence of hyperinvasive pandemic meningococcal lineages. Sci Rep 2017; 7:41126. [PMID: 28112239 PMCID: PMC5282872 DOI: 10.1038/srep41126] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 12/15/2016] [Indexed: 12/15/2022] Open
Abstract
Hyperinvasive lineages of Neisseria meningitidis, which persist despite extensive horizontal genetic exchange, are a major cause of meningitis and septicaemia worldwide. Over the past 50 years one such lineage of meningococci, known as serogroup A, clonal complex 5 (A:cc5), has caused three successive pandemics, including epidemics in sub-Saharan Africa. Although the principal antigens that invoke effective immunity have remained unchanged, distinct A:cc5 epidemic clones have nevertheless emerged. An analysis of whole genome sequence diversity among 153 A:cc5 isolates identified eleven genetic introgression events in the emergence of the epidemic clones, which primarily involved variants of core genes encoding metabolic processes. The acquired DNA was identical to that found over many years in other, unrelated, hyperinvasive meningococci, suggesting that the epidemic clones emerged by acquisition of pre-existing metabolic gene variants, rather than ‘virulence’ associated or antigen-encoding genes. This is consistent with mathematical models which predict the association of transmission fitness with the emergence and maintenance of virulence in recombining commensal organisms.
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Serogroup and Clonal Characterization of Czech Invasive Neisseria meningitidis Strains Isolated from 1971 to 2015. PLoS One 2016; 11:e0167762. [PMID: 27936105 PMCID: PMC5147975 DOI: 10.1371/journal.pone.0167762] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/18/2016] [Indexed: 01/03/2023] Open
Abstract
Background This study presents antigenic and genetic characteristics of Neisseria meningitidis strains recovered from invasive meningococcal disease (IMD) in the Czech Republic in 1971–2015. Material and Methods A total of 1970 isolates from IMD, referred to the National Reference Laboratory for Meningococcal Infections in 1971–2015, were studied. All isolates were identified and characterized by conventional biochemical and serological tests. Most isolates (82.5%) were characterized by multilocus sequence typing method. Results In the study period 1971–2015, the leading serogroup was B (52.4%), most often assigned to clonal complexes cc32, cc41/44, cc18, and cc269. A significant percentage of strains were of serogroup C (41.4%), with high clonal homogeneity due to hyperinvasive complex cc11, which played an important role in IMD in the Czech Republic in the mid-1990s. Serogroup Y isolates, mostly assigned to cc23, and isolates of clonally homogeneous serogroup W have also been recovered more often over the last years. Conclusion The incidence of IMD and distribution of serogroups and clonal complexes of N. meningitidis in the Czech Republic varied over time, as can be seen from the long-term monitoring, including molecular surveillance data. Data from the conventional and molecular IMD surveillance are helpful in refining the antimeningococcal vaccination strategy in the Czech Republic.
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Agier L, Martiny N, Thiongane O, Mueller JE, Paireau J, Watkins ER, Irving TJ, Koutangni T, Broutin H. Towards understanding the epidemiology of Neisseria meningitidis in the African meningitis belt: a multi-disciplinary overview. Int J Infect Dis 2016; 54:103-112. [PMID: 27826113 DOI: 10.1016/j.ijid.2016.10.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/21/2016] [Accepted: 10/29/2016] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVES Neisseria meningitidis is the major cause of seasonal meningitis epidemics in the African meningitis belt. In the changing context of a reduction in incidence of serogroup A and an increase in incidence of serogroups W and C and of Streptococcus pneumoniae, a better understanding of the determinants driving the disease transmission dynamics remains crucial to improving bacterial meningitis control. METHODS The literature was searched to provide a multi-disciplinary overview of the determinants of meningitis transmission dynamics in the African meningitis belt. RESULTS Seasonal hyperendemicity is likely predominantly caused by increased invasion rates, sporadic localized epidemics by increased transmission rates, and larger pluri-annual epidemic waves by changing population immunity. Carriage likely involves competition for colonization and cross-immunity. The duration of immunity likely depends on the acquisition type. Major risk factors include dust and low humidity, and presumably human contact rates and co-infections; social studies highlighted environmental and dietary factors, with supernatural explanations. CONCLUSIONS Efforts should focus on implementing multi-country, longitudinal seroprevalence and epidemiological studies, validating immune markers of protection, and improving surveillance, including more systematic molecular characterizations of the bacteria. Integrating climate and social factors into disease control strategies represents a high priority for optimizing the public health response and anticipating the geographic evolution of the African meningitis belt.
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Affiliation(s)
- Lydiane Agier
- Combining Health Information, Computation and Statistics, Lancaster Medical School, Lancaster University, Lancaster, UK.
| | - Nadège Martiny
- Centre de Recherches de Climatologie (CRC), UMR 6282 CNRS Biogeosciences, Université de Bourgogne, Dijon, France
| | - Oumy Thiongane
- Institut de Recherche pour le Développement, UMR INTERTRYP IRD-CIRAD, Antenne IRD Bobo Dioulasso, Bobo, Burkina Faso
| | - Judith E Mueller
- EHESP French School of Public Health, Sorbonne Paris Cité, Rennes, France; Unité de l'Epidémiologie des Maladies Emergentes, Institut Pasteur, Paris, France
| | - Juliette Paireau
- Unité de l'Epidémiologie des Maladies Emergentes, Institut Pasteur, Paris, France; Department of Ecology and Evolutionary Biology, Princeton Environmental Institute, Princeton University, Princeton, New Jersey, USA
| | | | - Tom J Irving
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Thibaut Koutangni
- EHESP French School of Public Health, Sorbonne Paris Cité, Rennes, France; Unité de l'Epidémiologie des Maladies Emergentes, Institut Pasteur, Paris, France
| | - Hélène Broutin
- MIVEGEC, UMR 590CNRS/224IRD/UM, Montpellier, France; Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta Diop, Fann, Dakar, Senegal
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10
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Watkins ER, Maiden MC, Gupta S. Metabolic competition as a driver of bacterial population structure. Future Microbiol 2016; 11:1339-1357. [PMID: 27660887 DOI: 10.2217/fmb-2016-0079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Understanding the processes whereby diversity arises and is maintained in pathogen populations is pivotal for designing disease control interventions. A particular problem is the maintenance of strain structure in bacterial pathogen populations despite frequent genetic exchange. Although several theoretical frameworks have been put forward to explain this widespread phenomenon, few have focused on the role of genes encoding metabolic functions, despite an increasing recognition of their importance in pathogenesis and transmission. In this article, we review the literature for evidence of metabolic niches within the host and discuss theoretical frameworks which examine ecological interactions between metabolic genes. We contend that metabolic competition is an important phenomenon which contributes to the maintenance of population structure and diversity of many bacterial pathogens.
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Affiliation(s)
- Eleanor R Watkins
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Martin Cj Maiden
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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11
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Stefanelli P, Miglietta A, Pezzotti P, Fazio C, Neri A, Vacca P, Voller F, D'Ancona FP, Guerra R, Iannazzo S, Pompa MG, Rezza G. Increased incidence of invasive meningococcal disease of serogroup C / clonal complex 11, Tuscany, Italy, 2015 to 2016. ACTA ACUST UNITED AC 2016; 21:30176. [PMID: 27035155 DOI: 10.2807/1560-7917.es.2016.21.12.30176] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 03/24/2016] [Indexed: 11/20/2022]
Abstract
We report an increase of serogroup C Neisseria meningitidis invasive meningococcal disease in Tuscany. From January 2015 to end February 2016, 43 cases were reported, among which 10 were fatal, compared to two cases caused by serogroup C recorded in 2014 and three in 2013. No secondary cases occurred. Thirty-five strains belonged to C:P1.5-1,10-8:F3-6:ST-11(cc11). Control measures have been adopted and immunisation campaigns implemented. Studies on risk factors and carriage are ongoing.
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Affiliation(s)
- Paola Stefanelli
- Department of Infectious, Parasitic & Immuno-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
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12
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Mowlaboccus S, Perkins TT, Smith H, Sloots T, Tozer S, Prempeh LJ, Tay CY, Peters F, Speers D, Keil AD, Kahler CM. Temporal Changes in BEXSERO® Antigen Sequence Type Associated with Genetic Lineages of Neisseria meningitidis over a 15-Year Period in Western Australia. PLoS One 2016; 11:e0158315. [PMID: 27355628 PMCID: PMC4927168 DOI: 10.1371/journal.pone.0158315] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 06/14/2016] [Indexed: 12/12/2022] Open
Abstract
Neisseria meningitidis is the causative agent of invasive meningococcal disease (IMD). The BEXSERO® vaccine which is used to prevent serogroup B disease is composed of four sub-capsular protein antigens supplemented with an outer membrane vesicle. Since the sub-capsular protein antigens are variably expressed and antigenically variable amongst meningococcal isolates, vaccine coverage can be estimated by the meningococcal antigen typing system (MATS) which measures the propensity of the strain to be killed by vaccinated sera. Whole genome sequencing (WGS) which identifies the alleles of the antigens that may be recognised by the antibody response could represent, in future, an alternative estimate of coverage. In this study, WGS of 278 meningococcal isolates responsible for 62% of IMD in Western Australia from 2000–2014 were analysed for association of genetic lineage (sequence type [ST], clonal complex [cc]) with BEXSERO® antigen sequence type (BAST) and MATS to predict the annual vaccine coverage. A hyper-endemic period of IMD between 2000–05 was caused by cc41/44 with the major sequence type of ST-146 which was not predicted by MATS or BAST to be covered by the vaccine. An increase in serogroup diversity was observed between 2010–14 with the emergence of cc11 serogroup W in the adolescent population and cc23 serogroup Y in the elderly. BASTs were statistically associated with clonal complex although individual antigens underwent antigenic drift from the major type. BAST and MATS predicted an annual range of 44–91% vaccine coverage. Periods of low vaccine coverage in years post-2005 were not a result of the resurgence of cc41/44:ST-146 but were characterised by increased diversity of clonal complexes expressing BASTs which were not predicted by MATS to be covered by the vaccine. The driving force behind the diversity of the clonal complex and BAST during these periods of low vaccine coverage is unknown, but could be due to immune selection and inter-strain competition with carriage of non-disease causing meningococci.
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Affiliation(s)
- Shakeel Mowlaboccus
- Marshall Centre for Infectious Disease Research and Training, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia
| | - Timothy T. Perkins
- Marshall Centre for Infectious Disease Research and Training, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia
| | - Helen Smith
- Public Health Microbiology, Forensic and Scientific Services, Health Support Queensland Department of Health, Brisbane, Australia
| | - Theo Sloots
- Sir Albert Sakzewski Virus Research Centre, Queensland Paediatric Infectious Diseases Laboratory, Royal Children’s Hospital, Brisbane, Australia
| | - Sarah Tozer
- Sir Albert Sakzewski Virus Research Centre, Queensland Paediatric Infectious Diseases Laboratory, Royal Children’s Hospital, Brisbane, Australia
| | - Lydia-Jessica Prempeh
- Marshall Centre for Infectious Disease Research and Training, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia
| | - Chin Yen Tay
- Marshall Centre for Infectious Disease Research and Training, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia
| | - Fanny Peters
- Marshall Centre for Infectious Disease Research and Training, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia
| | - David Speers
- Department of Microbiology, QEII Medical Centre, PathWest Laboratory Medicine WA, Perth, Australia
| | - Anthony D. Keil
- Department of Microbiology, Princess Margaret Hospital for Children, PathWest Laboratory Medicine WA, Perth, Australia
| | - Charlene M. Kahler
- Marshall Centre for Infectious Disease Research and Training, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia
- Telethon Kids Institute, Perth, WA, Australia
- * E-mail:
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Brehony C, Hill DM, Lucidarme J, Borrow R, Maiden MC. Meningococcal vaccine antigen diversity in global databases. ACTA ACUST UNITED AC 2016; 20:30084. [PMID: 26676305 DOI: 10.2807/1560-7917.es.2015.20.49.30084] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 07/09/2015] [Indexed: 11/20/2022]
Abstract
The lack of an anti-capsular vaccine against serogroup B meningococcal disease has necessitated the exploration of alternative vaccine candidates, mostly proteins exhibiting varying degrees of antigenic variation. Analysis of variants of antigen-encoding genes is facilitated by publicly accessible online sequence repositories, such as the Neisseria PubMLST database and the associated Meningitis Research Foundation Meningococcus Genome Library (MRF-MGL). We investigated six proposed meningococcal vaccine formulations by deducing the prevalence of their components in the isolates represented in these repositories. Despite high diversity, a limited number of antigenic variants of each of the vaccine antigens were prevalent, with strong associations of particular variant combinations with given serogroups and genotypes. In the MRF-MGL and globally, the highest levels of identical sequences were observed with multicomponent/multivariant vaccines. Our analyses further demonstrated that certain combinations of antigen variants were prevalent over periods of decades in widely differing locations, indicating that vaccine formulations containing a judicious choice of antigen variants have potential for long-term protection across geographic regions. The data further indicated that formulations with multiple variants would be especially relevant at times of low disease incidence, as relative diversity was higher. Continued surveillance is required to monitor the changing prevalence of these vaccine antigens.
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Affiliation(s)
- Carina Brehony
- Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
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Abstract
Rapid low-cost whole-genome sequencing (WGS) is revolutionizing microbiology; however, complementary advances in accessible, reproducible, and rapid analysis techniques are required to realize the potential of these data. Here, investigations of the genus Neisseria illustrated the gene-by-gene conceptual approach to the organization and analysis of WGS data. Using the gene and its link to phenotype as a starting point, the BIGSdb database, which powers the PubMLST databases, enables the assembly of large open-access collections of annotated genomes that provide insight into the evolution of the Neisseria, the epidemiology of meningococcal and gonococcal disease, and mechanisms of Neisseria pathogenicity.
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Sanders H, Norheim G, Chan H, Dold C, Vipond C, Derrick JP, Pollard AJ, Maiden MCJ, Feavers IM. FetA Antibodies Induced by an Outer Membrane Vesicle Vaccine Derived from a Serogroup B Meningococcal Isolate with Constitutive FetA Expression. PLoS One 2015; 10:e0140345. [PMID: 26466091 PMCID: PMC4605655 DOI: 10.1371/journal.pone.0140345] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 09/24/2015] [Indexed: 02/06/2023] Open
Abstract
Invasive meningococcal disease causes over 3500 cases each year in Europe, with particularly high incidence among young children. Among serogroup B meningococci, which cause most of the cases, high diversity in the outer membrane proteins (OMPs) is observed in endemic situations; however, comprehensive molecular epidemiological data are available for the diversity and distribution of the OMPs PorA and FetA and these can be used to rationally design a vaccine with high coverage of the case isolates. The aim of this study was to determine whether outer membrane vesicles (OMVs) derived from an isolate with constitutive FetA expression (MenPF-1 vaccine) could be used to induce antibodies against both the PorA and FetA antigens. The immunogenicity of various dose levels and number of doses was evaluated in mice and rabbits, and IgG antibody responses tested against OMVs and recombinant PorA and FetA proteins. A panel of four isogenic mutants was generated and used to evaluate the relative ability of the vaccine to induce serum bactericidal activity (SBA) against FetA and PorA. Sera from mice were tested in SBA against the four target strains. Results demonstrated that the MenPF-1 OMVs were immunogenic against PorA and FetA in both animal models. Furthermore, the murine antibodies induced were bactericidal against isogenic mutant strains, suggesting that antibodies to both PorA and FetA were functional. The data presented indicate that the MenPF-1 vaccine is a suitable formulation for presenting PorA and FetA OMPs in order to induce bactericidal antibodies, and that proceeding to a Phase I clinical trial with this vaccine candidate is justified.
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Affiliation(s)
- Holly Sanders
- National Institute of Biological Standards and Control, South Mimms, Potters Bar, United Kingdom
| | - Gunnstein Norheim
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
- Division of Infectious Disease Control, Norwegian Institute of Public Health, Oslo, Norway Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Hannah Chan
- National Institute of Biological Standards and Control, South Mimms, Potters Bar, United Kingdom
- * E-mail:
| | - Christina Dold
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Caroline Vipond
- National Institute of Biological Standards and Control, South Mimms, Potters Bar, United Kingdom
| | - Jeremy P. Derrick
- Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, United Kingdom
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | | | - Ian M. Feavers
- National Institute of Biological Standards and Control, South Mimms, Potters Bar, United Kingdom
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Besbes A, Le Goff S, Antunes A, Terrade A, Hong E, Giorgini D, Taha MK, Deghmane AE. Hyperinvasive Meningococci Induce Intra-nuclear Cleavage of the NF-κB Protein p65/RelA by Meningococcal IgA Protease. PLoS Pathog 2015; 11:e1005078. [PMID: 26241037 PMCID: PMC4524725 DOI: 10.1371/journal.ppat.1005078] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 07/10/2015] [Indexed: 11/30/2022] Open
Abstract
Differential modulation of NF-κB during meningococcal infection is critical in innate immune response to meningococcal disease. Non-invasive isolates of Neisseria meningitidis provoke a sustained NF-κB activation in epithelial cells. However, the hyperinvasive isolates of the ST-11 clonal complex (ST-11) only induce an early NF-κB activation followed by a sustained activation of JNK and apoptosis. We show that this temporal activation of NF-κB was caused by specific cleavage at the C-terminal region of NF-κB p65/RelA component within the nucleus of infected cells. This cleavage was mediated by the secreted 150 kDa meningococcal ST-11 IgA protease carrying nuclear localisation signals (NLS) in its α-peptide moiety that allowed efficient intra-nuclear transport. In a collection of non-ST-11 healthy carriage isolates lacking NLS in the α-peptide, secreted IgA protease was devoid of intra-nuclear transport. This part of iga polymorphism allows non-invasive isolates lacking NLS, unlike hyperinvasive ST-11 isolates of N. meningitides habouring NLS in their α-peptide, to be carried asymptomatically in the human nasopharynx through selective eradication of their ability to induce apoptosis in infected epithelial cells.
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Affiliation(s)
- Anissa Besbes
- Institut Pasteur, Invasive Bacterial Infections Unit, Paris, France
| | - Salomé Le Goff
- Institut Pasteur, Invasive Bacterial Infections Unit, Paris, France
| | - Ana Antunes
- Institut Pasteur, Invasive Bacterial Infections Unit, Paris, France
| | - Aude Terrade
- Institut Pasteur, Invasive Bacterial Infections Unit, Paris, France
| | - Eva Hong
- Institut Pasteur, Invasive Bacterial Infections Unit, Paris, France
| | - Dario Giorgini
- Institut Pasteur, Invasive Bacterial Infections Unit, Paris, France
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Poolman JT, Richmond P. Multivalent meningococcal serogroup B vaccines: challenges in predicting protection and measuring effectiveness. Expert Rev Vaccines 2015. [PMID: 26204792 DOI: 10.1586/14760584.2015.1071670] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Vaccines targeting Neisseria meningitidis serogroup B (MenB) have been attempted for 40 years. Monovalent outer membrane vesicle vaccines targeted at epidemic outbreaks have been successfully developed. Newer vaccines aim to induce antibodies to cross-reactive antigens, such as factor H binding protein (rLP2086) or a mix of outer membrane vesicle, factor H binding protein and other minor antigens (4CMenB). The true protective coverage among circulating MenB isolates afforded by these vaccines is unknown. Carefully conducted Phase IV post-implementation evaluations designed to measure specific effectiveness against major circulating MenB clonal lineages are needed to address the critical question of which antigens are linked to protection. Progress with whole-genome sequencing and bio-informatics may allow the composition of antigen mozaics based on two major outer membrane proteins: PorA and FetA.
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Affiliation(s)
- Jan T Poolman
- Bacterial Vaccine Discovery & Early Development, Janssen, Zernikedreef 9; 2333 CK Leiden, The Netherlands
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18
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Lourenço J, Wikramaratna PS, Gupta S. MANTIS: an R package that simulates multilocus models of pathogen evolution. BMC Bioinformatics 2015; 16:176. [PMID: 26017358 PMCID: PMC4445977 DOI: 10.1186/s12859-015-0598-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/27/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In host-pathogen systems the development of immunity by the host places pressure on pathogens, by setting up competition between genetic variants due to the establishment of cross-protective responses. These pressures can lead to pathogen-specific, ubiquitous dynamic behaviours. Understanding the evolutionary forces that shape these patterns is one of the key goals of computationally simulated epidemiological models. Despite the contribution of such research methods in recent years to our current understanding of pathogen evolution, the availability of free software tools for the general public remains scarce. RESULTS We developed the Multilocus ANTIgenic Simulator (MANTIS) software package for the R statistical environment. MANTIS can simulate and analyse epidemiological time-series generated under the biological assumptions of the strain theory of host-pathogen systems by Gupta et al. CONCLUSIONS MANTIS wraps a C/C++ ordinary-differential equations system and Runge-Kutta solver into a set of user-friendly R functions. These include routines to numerically simulate the system and others to analyse, visualize and export results. For this, the package offers its own set of time-series plotting and exportation functions. MANTIS's main goal is to serve as a free, ready-to-use academic software tool. Its open source nature further provides an opportunity for users with advanced programming skills to expand its capabilities. Here, we describe the background theory, implementation, basic functionality and usage of this package. MANTIS is freely available from http://www.eeid.ox.ac.uk/mantis under the GPL license.
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Affiliation(s)
- José Lourenço
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK.
| | | | - Sunetra Gupta
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK.
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19
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Marsay L, Dold C, Green CA, Rollier CS, Norheim G, Sadarangani M, Shanyinde M, Brehony C, Thompson AJ, Sanders H, Chan H, Haworth K, Derrick JP, Feavers IM, Maiden MC, Pollard AJ. A novel meningococcal outer membrane vesicle vaccine with constitutive expression of FetA: A phase I clinical trial. J Infect 2015; 71:326-37. [PMID: 25982025 PMCID: PMC4535279 DOI: 10.1016/j.jinf.2015.05.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/05/2015] [Accepted: 05/09/2015] [Indexed: 12/01/2022]
Abstract
Objectives Outer membrane vesicle (OMV) vaccines are used against outbreaks of capsular group B Neisseria meningitidis (MenB) caused by strains expressing particular PorA outer membrane proteins (OMPs). Ferric enterobactin receptor (FetA) is another variable OMP that induces type-specific bactericidal antibodies, and the combination of judiciously chosen PorA and FetA variants in vaccine formulations is a potential approach to broaden protection of such vaccines. Methods The OMV vaccine MenPF-1 was generated by genetically modifying N. meningitidis strain 44/76 to constitutively express FetA. Three doses of 25 μg or 50 μg of MenPF-1 were delivered intra-muscularly to 52 healthy adults. Results MenPF-1 was safe and well tolerated. Immunogenicity was measured by serum bactericidal assay (SBA) against wild-type and isogenic mutant strains. After 3 doses, the proportion of volunteers with SBA titres ≥1:4 (the putative protective titre) was 98% for the wild-type strain, and 77% for the strain 44/76 FetAonPorAoff compared to 51% in the strain 44/76 FetAoffPorAoff, demonstrating that vaccination with MenPF-1 simultaneously induced FetA and PorA bactericidal antibodies. Conclusion This study provides a proof-of-concept for generating bactericidal antibodies against FetA after OMV vaccination in humans. Prevalence-based choice of PorA and FetA types can be used to formulate a vaccine for broad protection against MenB disease. MenB OMV vaccines' efficacy is strain-restricted by the variable antigen PorA. FetA is another variable antigen, but has iron-dependent expression. The combination of only a few PorA and FetA can induce broad-protection. A mutated OMV was created containing one PorA and one FetA. FetA induces bactericidal antibody response in addition to the PorA response in a Phase I trial.
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Affiliation(s)
- L Marsay
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, CCVTM, Churchill Lane, Oxford OX37LE, United Kingdom
| | - C Dold
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, CCVTM, Churchill Lane, Oxford OX37LE, United Kingdom
| | - C A Green
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, CCVTM, Churchill Lane, Oxford OX37LE, United Kingdom
| | - C S Rollier
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, CCVTM, Churchill Lane, Oxford OX37LE, United Kingdom.
| | - G Norheim
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, CCVTM, Churchill Lane, Oxford OX37LE, United Kingdom
| | - M Sadarangani
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, CCVTM, Churchill Lane, Oxford OX37LE, United Kingdom
| | - M Shanyinde
- Nuffield Department of Primary Health Care Sciences, Primary Care Clinical Trials Unit, University of Oxford, 23-38 Hythe Bridge Street, Oxford, United Kingdom
| | - C Brehony
- Department of Zoology, University of Oxford, South Parks Road, United Kingdom
| | - A J Thompson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, CCVTM, Churchill Lane, Oxford OX37LE, United Kingdom
| | - H Sanders
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, United Kingdom
| | - H Chan
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, United Kingdom
| | - K Haworth
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, CCVTM, Churchill Lane, Oxford OX37LE, United Kingdom
| | - J P Derrick
- Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - I M Feavers
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, United Kingdom
| | - M C Maiden
- Department of Zoology, University of Oxford, South Parks Road, United Kingdom
| | - A J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, CCVTM, Churchill Lane, Oxford OX37LE, United Kingdom
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Abstract
Background The predominant model for bacterial pandemics is the emergence of a virulent variant that diversifies as it spreads in human populations. We investigated a 40-year meningococcal disease pandemic caused by the hyper-invasive ET-5/ST-32 complex. Methods A global collection of Neisseria meningitidis isolates dating from 1969 to 2008 was whole genome sequenced (WGS) and analysed using a gene-by-gene approach at http://pubmlst.org/neisseria. Findings Analysis of WGS data identified a ‘Lineage 5 pan genome’ of 1940 genes, 1752 (92%) of which were present in all isolates (Lineage 5 ‘core genome’). Genetic diversity, which was mostly generated by horizontal gene transfer, was unevenly distributed in the genome; however, genealogical analysis of diverse and conserved core genes, accessory genes, and antigen encoding genes, robustly identified a star phylogeny with a number of sub-lineages. Most European and American isolates belonged to one of two closely related sub-lineages, which had diversified before the identification of the pandemic in the 1970s. A third, genetically more diverse sub-lineage, was associated with Asian isolates. Several isolates had acquired DNA from the related gonococcus. Interpretation These data were inconsistent with a single point of origin followed by pandemic spread, rather suggesting that the sub-lineages had diversified and spread by asymptomatic transmission, with multiple distinct strains causing localised hyperendemic outbreaks. Genomic analysis of hyper-invasive N. meningitidis lineage 5 distinguishing sub-lineages and localised outbreaks. Identification of a gonococcal conjugative plasmid consistent with horizontal genetic transfer. Discovery of a distinct type 4 secretion system previously unidentified in Neisseria. Gene-by-gene analysis of conserved and diverse loci providing essential tools in serogroup B vaccine development.
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21
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Abstract
Neisseria meningitidis, the cause of meningococcal disease, has been the subject of sophisticated molecular epidemiological investigation as a consequence of the significant public health threat posed by this organism. The use of multilocus sequence typing and whole genome sequencing classifies the organism into clonal complexes. Extensive phenotypic, genotypic and epidemiological information is available on the PubMLST website. The human nasopharynx is the sole ecological niche of this species, and carrier isolates show extensive genetic diversity as compared with hyperinvasive lineages. Horizontal gene exchange and recombinant events within the meningococcal genome during residence in the human nasopharynx result in antigenic diversity even within clonal complexes, so that individual clones may express, for example, more than one capsular polysaccharide (serogroup). Successful clones are capable of wide global dissemination, and may be associated with explosive epidemics of invasive disease.
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Affiliation(s)
- R C Read
- Clinical and Experimental Sciences and NIHR Respiratory Biomedical Research Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
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22
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Whelan J, Bambini S, Biolchi A, Brunelli B, Robert–Du Ry van Beest Holle M. Outbreaks of meningococcal B infection and the 4CMenB vaccine: historical and future perspectives. Expert Rev Vaccines 2015; 14:713-36. [DOI: 10.1586/14760584.2015.1004317] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Wang X, Shutt KA, Vuong JT, Cohn A, MacNeil J, Schmink S, Plikaytis B, Messonnier NE, Harrison LH, Clark TA, Mayer LW. Changes in the Population Structure of Invasive Neisseria meningitidis in the United States After Quadrivalent Meningococcal Conjugate Vaccine Licensure. J Infect Dis 2015; 211:1887-94. [PMID: 25556253 DOI: 10.1093/infdis/jiu842] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 12/22/2014] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Meningococcal conjugate vaccines against serogroups A, C, W, and Y (MenACWY) are recommended for routine use in adolescents aged 11-18 years. The impact of these vaccines on the meningococcal population structure in the United States have yet to be evaluated. METHODS Meningococcal isolates recovered during 2006-2010 (ie, after introduction of MenACWY) collected through Active Bacterial Core surveillance (ABCs) were characterized; serogroup distribution and molecular features of these isolates were compared to previously published data on ABCs isolates recovered from 2000 to 2005 (ie, before introduction of MenACWY). P values were generated using χ(2) statistics and exact methods. RESULTS There was a significant change (P < .05) in serogroup distribution among all age groups between the 2 periods. A small proportion of isolates showed evidence of capsular switching in both periods. Between the 2 periods, significant changes were observed in the distribution of porin A, ferric enterobactin transport, and strain genotypes among vaccine and nonvaccine serogroups. CONCLUSIONS The population structure of US meningococcal isolates is dynamic; some changes occurred over time, but the basic structure remained. Vaccine-induced serogroup replacement was not observed, although a small proportion of isolates had undergone capsule switching, possibly driven by non-vaccine-mediated selection. Changes in the distribution of molecular features are likely due to horizontal gene transfer and changes in serogroup distribution.
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Affiliation(s)
- Xin Wang
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Kathleen A Shutt
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pennsylvania
| | - Jeni T Vuong
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Amanda Cohn
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jessica MacNeil
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Susanna Schmink
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Brian Plikaytis
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Lee H Harrison
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pennsylvania
| | - Thomas A Clark
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Leonard W Mayer
- Centers for Disease Control and Prevention, Atlanta, Georgia
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Bratcher HB, Corton C, Jolley KA, Parkhill J, Maiden MCJ. A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. BMC Genomics 2014; 15:1138. [PMID: 25523208 PMCID: PMC4377854 DOI: 10.1186/1471-2164-15-1138] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/04/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Highly parallel, 'second generation' sequencing technologies have rapidly expanded the number of bacterial whole genome sequences available for study, permitting the emergence of the discipline of population genomics. Most of these data are publically available as unassembled short-read sequence files that require extensive processing before they can be used for analysis. The provision of data in a uniform format, which can be easily assessed for quality, linked to provenance and phenotype and used for analysis, is therefore necessary. RESULTS The performance of de novo short-read assembly followed by automatic annotation using the pubMLST.org Neisseria database was assessed and evaluated for 108 diverse, representative, and well-characterised Neisseria meningitidis isolates. High-quality sequences were obtained for >99% of known meningococcal genes among the de novo assembled genomes and four resequenced genomes and less than 1% of reassembled genes had sequence discrepancies or misassembled sequences. A core genome of 1600 loci, present in at least 95% of the population, was determined using the Genome Comparator tool. Genealogical relationships compatible with, but at a higher resolution than, those identified by multilocus sequence typing were obtained with core genome comparisons and ribosomal protein gene analysis which revealed a genomic structure for a number of previously described phenotypes. This unified system for cataloguing Neisseria genetic variation in the genome was implemented and used for multiple analyses and the data are publically available in the PubMLST Neisseria database. CONCLUSIONS The de novo assembly, combined with automated gene-by-gene annotation, generates high quality draft genomes in which the majority of protein-encoding genes are present with high accuracy. The approach catalogues diversity efficiently, permits analyses of a single genome or multiple genome comparisons, and is a practical approach to interpreting WGS data for large bacterial population samples. The method generates novel insights into the biology of the meningococcus and improves our understanding of the whole population structure, not just disease causing lineages.
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Neri A, Fazio C, Ciammaruconi A, Anselmo A, Fortunato A, Palozzi A, Vacca P, Fillo S, Lista F, Stefanelli P. Draft Genome Sequence of C:P1.5-1,10-8:F3-6:ST-11 Meningococcal Clinical Isolate Associated with a Cluster on a Cruise Ship. GENOME ANNOUNCEMENTS 2014; 2:e01263-14. [PMID: 25477415 PMCID: PMC4256196 DOI: 10.1128/genomea.01263-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 10/24/2014] [Indexed: 11/20/2022]
Abstract
Meningococcal serogroup C strains, in particular those belonging to the ST-11 clonal complex, are known to cause invasive diseases worldwide. We report the genome sequence of a Neisseria meningitidis strain linked to a cluster of cases of invasive meningococcal disease on a cruise ship that was described in 2012.
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Affiliation(s)
- A Neri
- Department of Infectious, Parasitic & Immuno-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - C Fazio
- Department of Infectious, Parasitic & Immuno-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - A Ciammaruconi
- Army Medical and Veterinary Research Center, Rome, Italy
| | - A Anselmo
- Army Medical and Veterinary Research Center, Rome, Italy
| | - A Fortunato
- Army Medical and Veterinary Research Center, Rome, Italy
| | - A Palozzi
- Army Medical and Veterinary Research Center, Rome, Italy
| | - P Vacca
- Department of Infectious, Parasitic & Immuno-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - S Fillo
- Army Medical and Veterinary Research Center, Rome, Italy
| | - F Lista
- Army Medical and Veterinary Research Center, Rome, Italy
| | - P Stefanelli
- Department of Infectious, Parasitic & Immuno-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
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Contrasting within- and between-host immune selection shapes Neisseria Opa repertoires. Sci Rep 2014; 4:6554. [PMID: 25296566 PMCID: PMC4894414 DOI: 10.1038/srep06554] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 09/08/2014] [Indexed: 11/30/2022] Open
Abstract
Pathogen evolution is influenced strongly by the host immune response. Previous studies of the effects of herd immunity on the population structure of directly transmitted, short-lived pathogens have primarily focused on the impact of competition for hosts. In contrast, for long-lived infections like HIV, theoretical work has focused on the mechanisms promoting antigenic variation within the host. In reality, successful transmission requires that pathogens balance both within- and between-host immune selection. The Opa adhesins in the bacterial Neisseria genus provide a unique system to study the evolution of the same antigens across two major pathogens: while N. meningitidis is an airborne, respiratory pathogen colonising the nasopharynx relatively transiently, N. gonorrhoeae can cause sexually transmitted, long-lived infections. We use a simple mathematical model and genomic data to show that trade-offs between immune selection pressures within- and between-hosts can explain the contrasting Opa repertoires observed in meningococci and gonococci.
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Implications of differential age distribution of disease-associated meningococcal lineages for vaccine development. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2014; 21:847-53. [PMID: 24695776 PMCID: PMC4054250 DOI: 10.1128/cvi.00133-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
New vaccines targeting meningococci expressing serogroup B polysaccharide have been developed, with some being licensed in Europe. Coverage depends on the distribution of disease-associated genotypes, which may vary by age. It is well established that a small number of hyperinvasive lineages account for most disease, and these lineages are associated with particular antigens, including vaccine candidates. A collection of 4,048 representative meningococcal disease isolates from 18 European countries, collected over a 3-year period, were characterized by multilocus sequence typing (MLST). Age data were available for 3,147 isolates. The proportions of hyperinvasive lineages, identified as particular clonal complexes (ccs) by MLST, differed among age groups. Subjects <1 year of age experienced lower risk of sequence type 11 (ST-11) cc, ST-32 cc, and ST-269 cc disease and higher risk of disease due to unassigned STs, 1- to 4-year-olds experienced lower risk of ST-11 cc and ST-32 cc disease, 5- to 14-year-olds were less likely to experience ST-11 cc and ST-269 cc disease, and ≥25-year-olds were more likely to experience disease due to less common ccs and unassigned STs. Younger and older subjects were vulnerable to a more diverse set of genotypes, indicating the more clonal nature of genotypes affecting adolescents and young adults. Knowledge of temporal and spatial diversity and the dynamics of meningococcal populations is essential for disease control by vaccines, as coverage is lineage specific. The nonrandom age distribution of hyperinvasive lineages has consequences for the design and implementation of vaccines, as different variants, or perhaps targets, may be required for different age groups.
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Wörmann ME, Horien CL, Bennett JS, Jolley KA, Maiden MCJ, Tang CM, Aho EL, Exley RM. Sequence, distribution and chromosomal context of class I and class II pilin genes of Neisseria meningitidis identified in whole genome sequences. BMC Genomics 2014; 15:253. [PMID: 24690385 PMCID: PMC4023411 DOI: 10.1186/1471-2164-15-253] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 03/25/2014] [Indexed: 12/05/2022] Open
Abstract
Background Neisseria meningitidis expresses type four pili (Tfp) which are important for colonisation and virulence. Tfp have been considered as one of the most variable structures on the bacterial surface due to high frequency gene conversion, resulting in amino acid sequence variation of the major pilin subunit (PilE). Meningococci express either a class I or a class II pilE gene and recent work has indicated that class II pilins do not undergo antigenic variation, as class II pilE genes encode conserved pilin subunits. The purpose of this work was to use whole genome sequences to further investigate the frequency and variability of the class II pilE genes in meningococcal isolate collections. Results We analysed over 600 publically available whole genome sequences of N. meningitidis isolates to determine the sequence and genomic organization of pilE. We confirmed that meningococcal strains belonging to a limited number of clonal complexes (ccs, namely cc1, cc5, cc8, cc11 and cc174) harbour a class II pilE gene which is conserved in terms of sequence and chromosomal context. We also identified pilS cassettes in all isolates with class II pilE, however, our analysis indicates that these do not serve as donor sequences for pilE/pilS recombination. Furthermore, our work reveals that the class II pilE locus lacks the DNA sequence motifs that enable (G4) or enhance (Sma/Cla repeat) pilin antigenic variation. Finally, through analysis of pilin genes in commensal Neisseria species we found that meningococcal class II pilE genes are closely related to pilE from Neisseria lactamica and Neisseria polysaccharea, suggesting horizontal transfer among these species. Conclusions Class II pilins can be defined by their amino acid sequence and genomic context and are present in meningococcal isolates which have persisted and spread globally. The absence of G4 and Sma/Cla sequences adjacent to the class II pilE genes is consistent with the lack of pilin subunit variation in these isolates, although horizontal transfer may generate class II pilin diversity. This study supports the suggestion that high frequency antigenic variation of pilin is not universal in pathogenic Neisseria.
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Affiliation(s)
| | | | | | | | | | | | - Ellen L Aho
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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Norheim G, Sadarangani M, Omar O, Yu LM, Mølbak K, Howitz M, Olcén P, Haglund M, van der Ende A, Pollard AJ. Association between population prevalence of smoking and incidence of meningococcal disease in Norway, Sweden, Denmark and the Netherlands between 1975 and 2009: a population-based time series analysis. BMJ Open 2014; 4:e003312. [PMID: 24513866 PMCID: PMC3927814 DOI: 10.1136/bmjopen-2013-003312] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE To investigate the relationship between the prevalence of smoking in the population and incidence of invasive meningococcal disease (IMD) among children under 5 years of age. DESIGN Retrospective, longitudinal, observational study. Poisson regression controlled for confounding factors. SETTING Norway, Sweden, Denmark and the Netherlands between 1975 and 2009. POPULATION Total population of approximately 35 million people in these four countries. DATA SOURCES Data were collected from the Ministries of Health, National Statistics Bureaus and other relevant national institutes. RESULTS In Norway, there was a significant positive relationship between the annual prevalence of daily smokers among individuals aged 25-49 years and the incidence of IMD in children under 5 years of age, unadjusted (RR=1.04-1.06, 95% CI 1.02 to 1.07, p<0.001) and after adjustment for time of year (quarter), incidence of influenza-like illness and household crowding (RR=1.05-1.07, 95% CI 1.03 to 1.09, p<0.001). Depending on age group, the risk of IMD increased by 5.2-6.9% per 1% increase in smoking prevalence among individuals aged 25-49 years in adjusted analyses. Using limited datasets from the three other countries, unadjusted analysis showed positive associations between IMD in children related to older smokers in Sweden and the Netherlands and negative associations related to younger smokers in Sweden. However, there were no demonstrable associations between incidence of IMD and prevalence of smoking, after adjustment for the same confounding variables. CONCLUSIONS The reduced incidence of IMD in Norway between 1975 and 2009 may partly be explained by the reduced prevalence of smoking during this period. High-quality surveillance data are required to confirm this in other countries. Strong efforts to reduce smoking in the whole population including targeted campaigns to reduce smoking among adults may have a role to play in the prevention of IMD in children.
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Affiliation(s)
- Gunnstein Norheim
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
- Norwegian Institute of Public Health, Oslo, Norway
| | - Manish Sadarangani
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Omar Omar
- Centre for Statistics in Medicine, University of Oxford, Oxford, UK
| | - Ly-Mee Yu
- Centre for Statistics in Medicine, University of Oxford, Oxford, UK
| | - Kåre Mølbak
- Department of Infectious Disease Epidemiology, Statens Serum Institut, Copenhagen S, Denmark
| | - Michael Howitz
- Department of Infectious Disease Epidemiology, Statens Serum Institut, Copenhagen S, Denmark
| | - Per Olcén
- University of Örebro, Örebro, Sweden
| | | | - Arie van der Ende
- Department of Medical Microbiology, The Netherlands Reference Laboratory for Bacterial Meningitis, Academic Center, Amsterdam, The Netherlands
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
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Otete EH, Ahankari AS, Jones H, Bolton KJ, Jordan CW, Boswell TC, Wilcox MH, Ferguson NM, Beck CR, Puleston RL. Parameters for the mathematical modelling of Clostridium difficile acquisition and transmission: a systematic review. PLoS One 2013; 8:e84224. [PMID: 24376797 PMCID: PMC3869946 DOI: 10.1371/journal.pone.0084224] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 11/12/2013] [Indexed: 01/05/2023] Open
Abstract
INTRODUCTION Mathematical modelling of Clostridium difficile infection dynamics could contribute to the optimisation of strategies for its prevention and control. The objective of this systematic review was to summarise the available literature specifically identifying the quantitative parameters required for a compartmental mathematical model of Clostridium difficile transmission. METHODS Six electronic healthcare databases were searched and all screening, data extraction and study quality assessments were undertaken in duplicate. Results were synthesised using a narrative approach. RESULTS Fifty-four studies met the inclusion criteria. Reproduction numbers for hospital based epidemics were described in two studies with a range from 0.55 to 7. Two studies provided consistent data on incubation periods. For 62% of cases, symptoms occurred in less than 4 weeks (3-28 days) after infection. Evidence on contact patterns was identified in four studies but with limited data reported for populating a mathematical model. Two studies, including one without clinically apparent donor-recipient pairs, provided information on serial intervals for household or ward contacts, showing transmission intervals of <1 week in ward based contacts compared to up to 2 months for household contacts. Eight studies reported recovery rates of between 75%-100% for patients who had been treated with either metronidazole or vancomycin. Forty-nine studies gave recurrence rates of between 3% and 49% but were limited by varying definitions of recurrence. No study was found which specifically reported force of infection or net reproduction numbers. CONCLUSIONS There is currently scant literature overtly citing estimates of the parameters required to inform the quantitative modelling of Clostridium difficile transmission. Further high quality studies to investigate transmission parameters are required, including through review of published epidemiological studies where these quantitative estimates may not have been explicitly estimated, but that nonetheless contain the relevant data to allow their calculation.
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Affiliation(s)
- Eroboghene H. Otete
- School of Community Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Anand S. Ahankari
- School of Community Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Helen Jones
- School of Community Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Kirsty J. Bolton
- Melbourne School of Population and Global Health , University of Melbourne, Melbourne, Australia
- School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Caroline W. Jordan
- NHS England Area Team Derbyshire, Nottingham and Nottinghamshire, United Kingdom
| | - Tim C. Boswell
- Department of Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Mark H. Wilcox
- Department of Microbiology, University of Leeds, Leeds, United Kingdom
| | - Neil M. Ferguson
- School of Public Health, Imperial College London, London, United Kingdom
| | - Charles R. Beck
- School of Community Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Richard L. Puleston
- School of Community Health Sciences, University of Nottingham, Nottingham, United Kingdom
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