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Yee WX, Yasir M, Turner AK, Baker DJ, Cehovin A, Tang CM. Evolution, persistence, and host adaption of a gonococcal AMR plasmid that emerged in the pre-antibiotic era. PLoS Genet 2023; 19:e1010743. [PMID: 37186602 DOI: 10.1371/journal.pgen.1010743] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/25/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Plasmids are diverse extrachromosomal elements significantly contributing to interspecies dissemination of antimicrobial resistance (AMR) genes. However, within clinically important bacteria, plasmids can exhibit unexpected narrow host ranges, a phenomenon that has scarcely been examined. Here we show that pConj is largely restricted to the human-specific pathogen, Neisseria gonorrhoeae. pConj can confer tetracycline resistance and is central to the dissemination of other AMR plasmids. We tracked pConj evolution from the pre-antibiotic era 80 years ago to the modern day and demonstrate that, aside from limited gene acquisition and loss events, pConj is remarkably conserved. Notably, pConj has remained prevalent in gonococcal populations despite cessation of tetracycline use, thereby demonstrating pConj adaptation to its host. Equally, pConj imposes no measurable fitness costs and is stably inherited by the gonococcus. Its maintenance depends on the co-operative activity of plasmid-encoded Toxin:Antitoxin (TA) and partitioning systems rather than host factors. An orphan VapD toxin encoded on pConj forms a split TA with antitoxins expressed from an ancestral co-resident plasmid or a horizontally-acquired chromosomal island, potentially explaining pConj's limited distribution. Finally, ciprofloxacin can induce loss of this highly stable plasmid, reflecting epidemiological evidence of transient local falls in pConj prevalence when fluoroquinolones were introduced to treat gonorrhoea.
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Affiliation(s)
- Wearn-Xin Yee
- Sir William Dunn School of Pathology, University of Oxford, OXFORD, United Kingdom
| | | | | | | | - Ana Cehovin
- Sir William Dunn School of Pathology, University of Oxford, OXFORD, United Kingdom
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, OXFORD, United Kingdom
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2
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Tibayrenc M, Ayala FJ. Models in parasite and pathogen evolution: Genomic analysis reveals predominant clonality and progressive evolution at all evolutionary scales in parasitic protozoa, yeasts and bacteria. ADVANCES IN PARASITOLOGY 2021; 111:75-117. [PMID: 33482977 DOI: 10.1016/bs.apar.2020.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The predominant clonal evolution (PCE) model of pathogenic microorganisms postulates that the impact of genetic recombination in those pathogens' natural populations is not enough to erase a persistent phylogenetic signal at all evolutionary scales from microevolution till geological times in the whole ecogeographical range of the species considered. We have tested this model with a set of representative parasitic protozoa, yeasts and bacteria in the light of the most recent genomic data. All surveyed species, including those that were considered as highly recombining, exhibit similar PCE patterns above and under the species level, from macro- to micro-evolutionary scales (Russian doll pattern), suggesting gradual evolution. To our knowledge, it is the first time that such a strong common evolutionary feature among very diverse pathogens has been evidenced. The implications of this model for basic biology and applied research are exposed. These implications include our knowledge on the pathogens' reproductive mode, their population structure, the possibility to type strain and to follow up epidemics (molecular epidemiology) and to revisit pathogens' taxonomy through a flexible use of the phylogenetic species concept (Cracraft, 1983).
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Affiliation(s)
- Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Institut de recherche pour le développement, Montpellier Cedex 5, France.
| | - Francisco J Ayala
- Catedra Francisco Jose Ayala of Science, Technology, and Religion, University of Comillas, Madrid, Spain; 2 Locke Court, Irvine, CA, United States
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Juscamayta-López E, Valdivia F, Morales S, Donaires LF, Fiestas-Solórzano V, Oré M, Pachas P, León-Janampa N, Gavilán R. Emergence of ciprofloxacin-resistant Neisseria meningitidis B from asymptomatic carriers during an outbreak in Peru, 2017. J Med Microbiol 2020; 70. [PMID: 33196407 DOI: 10.1099/jmm.0.001245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Asymptomatic carriers are a likely source of transmission of Neisseria meningitidis to close contacts who are placed at a higher risk for invasive meningococcal disease (IMD). Although N. meningitidis ciprofloxacin-resistance is rare, there have been an increase in the reports of resistant isolates mainly in patients diagnosed with IMD, and little is known about the N. meningitidis ciprofloxacin-resistance in the carrier populations. We performed a pharyngeal carriage study during a 2017 military setting outbreak in Peru, caused by a ciprofloxacin-resistant N. meningitidis B. The isolates analysed came from two hospitalized cases and six asymptomatic carriers. Whole-genome sequence-based analysis was performed and showed that strains carrying the Thr91Ile mutation, in the gene encoding for subunit A of DNA gyrase (gyrA), were responsible for the fluoroquinolone resistance (MICs ≥0.256 µg ml-1) and were closely related to highly virulent strains from France, Norway and the UK. Phylogenetic analysis of the gyrA gene revealed that likely these Peruvian isolates acquired resistance through horizontal gene transfer from Neisseria lactamica. Our study provides evidence for the emergence and propagation of ciprofloxacin-resistant N. meningitidis B from asymptomatic carriers, and recommends the introduction of serogroup B vaccines for high-risk populations.
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Affiliation(s)
| | - Faviola Valdivia
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Sara Morales
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | | | | | - Marianela Oré
- Epidemiología, Comando de Salud del Ejército, Lima, Peru
| | - Paul Pachas
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Nancy León-Janampa
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Ronnie Gavilán
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
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Cehovin A, Jolley KA, Maiden MCJ, Harrison OB, Tang CM. Association of Neisseria gonorrhoeae Plasmids With Distinct Lineages and The Economic Status of Their Country of Origin. J Infect Dis 2020; 222:1826-1836. [PMID: 32163577 PMCID: PMC7653084 DOI: 10.1093/infdis/jiaa003] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 01/09/2020] [Indexed: 12/29/2022] Open
Abstract
Plasmids are vehicles for horizontal gene transfer between bacteria, and in Neisseria gonorrhoeae plasmids can mediate high-level antimicrobial resistance (AMR). Using genomic and phylogenetic analyses, we show that plasmids are widespread in a collection of 3724 gonococcal isolates from 56 countries, and characterized the conjugative, β-lactamase and cryptic plasmids. We found that variants of the conjugative plasmid (which can mediate tetracycline resistance) and the β-lactamase plasmid expressing TEM-135 are associated with distinct gonococcal lineages. Furthermore, AMR plasmids are significantly more prevalent in gonococci from less wealthy countries, highlighting the need for further studies. More than 94% of gonococci possess the cryptic plasmid, with its absence correlated with the presence of a novel chromosomal type IV secretion system. Our results reveal the extent of plasmid-mediated AMR in the gonococcus, particularly in less wealthy countries, where diagnostic and therapeutic options can be limited, and highlight the risk of their global spread.
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Affiliation(s)
- Ana Cehovin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Odile B Harrison
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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5
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Moreno J, Alarcon Z, Parra E, Duarte C, Sanabria O, Prada D, Gabastou JM. Molecular characterization of Neisseria meningitidis isolates recovered from patients with invasive meningococcal disease in Colombia from 2013 to 2016. PLoS One 2020; 15:e0234475. [PMID: 32663215 PMCID: PMC7360035 DOI: 10.1371/journal.pone.0234475] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 05/26/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Neisseria meningitidis is a significant cause of morbidity and mortality worldwide. Meningococcal isolates have a highly dynamic population structure and can be phenotypically and genetically differentiated into serogroups and clonal complexes. The aim of this study was to describe the phenotypic and genotypic characteristics of invasive isolates recovered in Colombia from 2013 to 2016. METHODOLOGY A total of 193 invasive isolates were analyzed. Phenotypic and genotypic characteristics were determined by serotyping, antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. RESULTS Based on the results, meningococcal serogroups C, B and Y were responsible for 47.9%, 41.7%, and 9.4% of cases, respectively, and the distribution of serogroups B and C changed over time. Fifteen clonal groups and 14 clonal complexes (cc) were identified by PFGE and genome sequencing. The main clonal group included serogroup B isolates with sequence type (ST)-9493 and its four single-locus variants, which has only been identified in Colombian isolates. The clonal population structure demonstrates that the isolates in this study mainly belong to four clonal complexes: ST-11 cc, ST-32 cc, ST-35 cc and ST-41/44 cc. Thirty-eight penA alleles were identified, but no correlation between MICs and specific sequences was observed. CONCLUSION This study shows that most meningococcal isolates recovered from patients with invasive meningococcal disease in Colombia are strains associated with distinct globally disseminated hyperinvasive clones.
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Affiliation(s)
- Jaime Moreno
- Grupo de Microbiología, Instituto Nacional de Salud (INS), Bogotá, Colombia
- * E-mail:
| | - Zonia Alarcon
- Grupo de Microbiología, Instituto Nacional de Salud (INS), Bogotá, Colombia
| | - Eliana Parra
- Grupo de Microbiología, Instituto Nacional de Salud (INS), Bogotá, Colombia
| | - Carolina Duarte
- Grupo de Microbiología, Instituto Nacional de Salud (INS), Bogotá, Colombia
| | - Olga Sanabria
- Grupo de Microbiología, Instituto Nacional de Salud (INS), Bogotá, Colombia
| | - Diego Prada
- Grupo de Microbiología, Instituto Nacional de Salud (INS), Bogotá, Colombia
| | - Jean Marc Gabastou
- Panamerican Health Organization/World Health Organization (PAHO/WHO), Washington, DC, United States of America
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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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Bratcher HB, Brehony C, Heuberger S, Pieridou-Bagatzouni D, Křížová P, Hoffmann S, Toropainen M, Taha MK, Claus H, Tzanakaki G, Erdôsi T, Galajeva J, van der Ende A, Skoczyńska A, Pana M, Vaculíková A, Paragi M, Maiden MC, Caugant DA. Establishment of the European meningococcal strain collection genome library (EMSC-GL) for the 2011 to 2012 epidemiological year. ACTA ACUST UNITED AC 2019; 23. [PMID: 29790460 PMCID: PMC6152424 DOI: 10.2807/1560-7917.es.2018.23.20.17-00474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Invasive meningococcal disease surveillance in Europe combines isolate characterisation and epidemiological data to support public health intervention. A representative European Meningococcal Strain Collection (EMSC) of IMD isolates was obtained, and whole genome sequenced to characterise 799 EMSC isolates from the epidemiological year July 2011-June 2012. To establish a genome library (GL), the isolate information was deposited in the pubMLST.org/neisseria database. Genomes were curated and annotated at 2,429 meningococcal loci, including those defining clonal complex, capsule, antigens, and antimicrobial resistance. Most genomes contained genes encoding B (n = 525; 65.7%) or C (n = 163; 20.4%) capsules; isolates were genetically highly diverse, with >20 genomic lineages, five of which comprising 60.7% (n = 485) of isolates. There were >350 antigenic fine-types: 307 were present once, the most frequent (P1.7-2,4:F5-1) comprised 8% (n = 64) of isolates. Each genome was characterised for Bexsero Antigen Sequence Typing (BAST): 25.5% (n = 204) of isolates contained alleles encoding the fHbp and/or the PorA VR1 vaccine component, but most genomes (n = 513; 64.2%) did not contain the NadA component. EMSC-GL will support an integrated surveillance of disease-associated genotypes in Europe, enabling the monitoring of hyperinvasive lineages, outbreak identification, and supporting vaccine programme implementation.
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Affiliation(s)
- Holly B Bratcher
- University of Oxford, Department of Zoology, Oxford, United Kingdom
| | - Carina Brehony
- Clinical Science Institute, National University of Ireland, Galway, Republic of Ireland.,University of Oxford, Department of Zoology, Oxford, United Kingdom
| | | | | | - Pavla Křížová
- National Institute of Public Health, Prague, Czech Republic
| | | | | | | | | | | | - Tímea Erdôsi
- National Center for Epidemiology, Budapest, Hungary
| | | | | | | | - Marina Pana
- National Institute of Research and Development for Microbiology and Immunology, Bucharest, Romania
| | - Alena Vaculíková
- Public Health Authority of the Slovak Republic, Bratislava, Slovakia
| | - Metka Paragi
- National Institute of Public Health, Ljubljana, Slovenia
| | - Martin Cj Maiden
- University of Oxford, Department of Zoology, Oxford, United Kingdom
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8
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León ME, Kawabata A, Nagai M, Rojas L, Chamorro G. [Genotypes of Neisseria meningitidis isolates in patients with meningococcal meningitis in Paraguay, 1996-2015Genótipos de Neisseria meningitidis isolados de pacientes com doença meningocócica no Paraguai, 1996-2015]. Rev Panam Salud Publica 2019; 43:e10. [PMID: 31093234 PMCID: PMC6393723 DOI: 10.26633/rpsp.2019.10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 07/04/2018] [Indexed: 11/26/2022] Open
Abstract
Objetivo Describir las características fenotípicas y genotípicas de cepas de Neisseria meningitidis aisladas de enfermedad meningocócica en Paraguay entre 1996 y 2015. Métodos Se estudiaron por métodos microbiológicos convencionales y técnicas moleculares 114 aislamientos de N. meningitidis y 12 muestras clínicas sin aislamiento confirmadas por reacción en cadena de la polimerasa (PCR) que fueron remitidas por los diferentes centros centinelas y centros colaboradores de Paraguay. Resultados El grupo de edad más afectado fue el de menores de 1 año (19,0%), seguido por el de 1 a 5 años (17,5%). Un mayor porcentaje de las cepas se aisló de casos de meningitis (81,7%) y el serogrupo B se encontró en 60,3% de los casos. Los fenotipos más frecuentes fueron B:4:P1.14 (16,0%), B:15:P1.5, C:NT:NST y W:NT:P1.2 (10,5%), respectivamente. Los complejos clonales prevalentes fueron ST-11/ET37 complex 29,6% (8/27) con predominio del serogrupo W (6/8), ST-35 complex 18,5% (5/27) en el serogrupo B (4/4), y ST-32/ET5 complex 14,8% (4/16) en el serogrupo B (5/5). Conclusiones En Paraguay la enfermedad meningocócica es relativamente infrecuente. Los análisis de distribución de serogrupo muestran que el más frecuente es el B y en los últimos dos años aumentaron los casos de enfermedad meningocócica por C y W. Los complejos clonales encontrados se correlacionan con los hallados en la región del Cono Sur. Debido al alto nivel de virulencia de N. meningitidis, su vigilancia debe constituir una prioridad estratégica de los sistemas de salud pública nacionales y regionales para prevenir brotes epidémicos y apoyar la toma de decisiones en salud pública.
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Affiliation(s)
- María Eugenia León
- Laboratorio Central de Salud Pública, Ministerio de Salud Pública y Bienestar Social, Asunción, Paraguay
| | - Aníbal Kawabata
- Laboratorio Central de Salud Pública, Ministerio de Salud Pública y Bienestar Social, Asunción, Paraguay
| | - Minako Nagai
- Laboratorio Central de Salud Pública, Ministerio de Salud Pública y Bienestar Social, Asunción, Paraguay
| | - Liliana Rojas
- Laboratorio Central de Salud Pública, Ministerio de Salud Pública y Bienestar Social, Asunción, Paraguay
| | - Gustavo Chamorro
- Laboratorio Central de Salud Pública, Ministerio de Salud Pública y Bienestar Social, Asunción, Paraguay
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Whaley MJ, Joseph SJ, Retchless AC, Kretz CB, Blain A, Hu F, Chang HY, Mbaeyi SA, MacNeil JR, Read TD, Wang X. Whole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis. Sci Rep 2018; 8:15803. [PMID: 30361650 PMCID: PMC6202316 DOI: 10.1038/s41598-018-33622-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/13/2018] [Indexed: 01/14/2023] Open
Abstract
Although rare in the U.S., outbreaks due to Neisseria meningitidis do occur. Rapid, early outbreak detection is important for timely public health response. In this study, we characterized U.S. meningococcal isolates (N = 201) from 15 epidemiologically defined outbreaks (2009-2015) along with temporally and geographically matched sporadic isolates using multilocus sequence typing, pulsed-field gel electrophoresis (PFGE), and six whole genome sequencing (WGS) based methods. Recombination-corrected maximum likelihood (ML) and Bayesian phylogenies were reconstructed to identify genetically related outbreak isolates. All WGS analysis methods showed high degree of agreement and distinguished isolates with similar or indistinguishable PFGE patterns, or the same strain genotype. Ten outbreaks were caused by a single strain; 5 were due to multiple strains. Five sporadic isolates were phylogenetically related to 2 outbreaks. Analysis of 9 outbreaks using timed phylogenies identified the possible origin and estimated the approximate time that the most recent common ancestor emerged for outbreaks analyzed. U.S. meningococcal outbreaks were caused by single- or multiple-strain introduction, with organizational outbreaks mainly caused by a clonal strain and community outbreaks by divergent strains. WGS can infer linkage of meningococcal cases when epidemiological links are uncertain. Accurate identification of outbreak-associated cases requires both WGS typing and epidemiological data.
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Affiliation(s)
- Melissa J Whaley
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sandeep J Joseph
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Adam C Retchless
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Cecilia B Kretz
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amy Blain
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Fang Hu
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - How-Yi Chang
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sarah A Mbaeyi
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica R MacNeil
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Timothy D Read
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Xin Wang
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
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10
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Molecular Characterization of Invasive Isolates of Neisseria meningitidis in Casablanca, Morocco. J Clin Microbiol 2018; 56:JCM.00445-18. [PMID: 29743304 DOI: 10.1128/jcm.00445-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/23/2018] [Indexed: 11/20/2022] Open
Abstract
Meningococcal epidemiology may change unpredictably, and typing of Neisseria meningitidis isolates is crucial for the surveillance of invasive meningococcal disease (IMD). Few data are available regarding the meningococcal epidemiology in countries of North Africa. We aimed to explore invasive meningococcal isolates from the Casablanca region in Morocco. We used whole-genome sequencing (WGS) to characterize 105 isolates from this region during the period of 2011 to 2016. Our data showed that the majority (n = 100) of the isolates belonged to serogroup B. Genotyping indicated that most of the isolates (n = 62) belonged to sequence type 33 of clonal complex 32. The isolates also showed the same PorA and FetA markers and clustered together on the basis of WGS phylogenetic analysis; they seemed to correspond to an expansion of local isolates in the Casablanca region, as reported for similar isolates in several other countries. These data suggest that serogroup B isolates may predominate in Morocco, which may have an important impact in the design of vaccination strategies.
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11
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Harrison OB, Schoen C, Retchless AC, Wang X, Jolley KA, Bray JE, Maiden MCJ. Neisseria genomics: current status and future perspectives. Pathog Dis 2018; 75:3861976. [PMID: 28591853 PMCID: PMC5827584 DOI: 10.1093/femspd/ftx060] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/05/2017] [Indexed: 12/17/2022] Open
Abstract
High-throughput whole genome sequencing has unlocked a multitude of possibilities enabling members of the Neisseria genus to be examined with unprecedented detail, including the human pathogens Neisseria meningitidis and Neisseria gonorrhoeae. To maximise the potential benefit of this for public health, it is becoming increasingly important to ensure that this plethora of data are adequately stored, disseminated and made readily accessible. Investigations facilitating cross-species comparisons as well as the analysis of global datasets will allow differences among and within species and across geographic locations and different times to be identified, improving our understanding of the distinct phenotypes observed. Recent advances in high-throughput platforms that measure the transcriptome, proteome and/or epigenome are also becoming increasingly employed to explore the complexities of Neisseria biology. An integrated approach to the analysis of these is essential to fully understand the impact these may have in the Neisseria genus. This article reviews the current status of some of the tools available for next generation sequence analysis at the dawn of the ‘post-genomic’ era.
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Affiliation(s)
| | - Christoph Schoen
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg 97080, Germany
| | - Adam C Retchless
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Xin Wang
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | - James E Bray
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
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12
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Dretler AW, Rouphael NG, Stephens DS. Progress toward the global control of Neisseria meningitidis: 21st century vaccines, current guidelines, and challenges for future vaccine development. Hum Vaccin Immunother 2018; 14:1146-1160. [PMID: 29543582 PMCID: PMC6067816 DOI: 10.1080/21645515.2018.1451810] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/21/2018] [Accepted: 03/09/2018] [Indexed: 12/21/2022] Open
Abstract
The control of meningitis, meningococcemia and other infections caused by Neisseria meningitidis is a significant global health challenge. Substantial progress has occurred in the last twenty years in meningococcal vaccine development and global implementation. Meningococcal protein-polysaccharide conjugate vaccines to serogroups A, C, W, and Y (modeled after the Haemophilus influenzae b conjugate vaccines) provide better duration of protection and immunologic memory, and overcome weak immune responses in infants and young children and hypo-responsive to repeated vaccine doses seen with polysaccharide vaccines. ACWY conjugate vaccines also interfere with transmission and reduce nasopharyngeal colonization, thus resulting in significant herd protection. Advances in serogroup B vaccine development have also occurred using conserved outer membrane proteins with or without OMV as vaccine targets. Challenges for meningococcal vaccine research remain including developing combination vaccines containing ACYW(X) and B, determining the ideal booster schedules for the conjugate and MenB vaccines, and addressing issues of waning effectiveness.
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Affiliation(s)
- A. W. Dretler
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - N. G. Rouphael
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - D. S. Stephens
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
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13
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Marin MA, Fonseca E, Encinas F, Freitas F, Camargo DA, Coimbra RS, de Filippis I, Vicente AC. The invasive Neisseria meningitidis MenC CC103 from Brazil is characterized by an accessory gene repertoire. Sci Rep 2017; 7:1617. [PMID: 28487566 PMCID: PMC5431661 DOI: 10.1038/s41598-017-01671-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 03/30/2017] [Indexed: 12/21/2022] Open
Abstract
Neisseria meningitidis infections are a major issue for global health. The invasive MenC ST-103 clonal complex (CC103) has been the most prevalent in meningococcal outbreaks in Brazil, occurring also in several countries worldwide. Here we have analysed the population structure and accessory genome of MenC CC103 strains from a global perspective. An in-depth phylogenomic analysis revealed a lineage of N. meningitidis causing meningitis in Brazil and the United Kingdom. This lineage was also characterized as harbouring a particular accessory genome composed of CRISPR/Cas and restriction modification systems. This lineage was also characterized by a genomic island resembling an integrative and conjugative element. This island carried genes potentially associated with virulence and fitness. We propose this accessory gene repertoire could be contributing to the spatial-temporal persistence of the invasive MenC CC103 lineage.
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Affiliation(s)
- Michel Abanto Marin
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC) - Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brazil.
| | - Erica Fonseca
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC) - Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brazil
| | - Fernando Encinas
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC) - Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brazil
| | - Fernanda Freitas
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC) - Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brazil
| | | | - Roney Santos Coimbra
- Neurogenômica, Centro de Pesquisas René Rachou (CPqRR), Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, MG, Brazil
| | - Ivano de Filippis
- Instituto Nacional de Controle de Qualidade em Saúde (INCQS), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Ana Carolina Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC) - Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brazil
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14
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Bartley SN, Mowlaboccus S, Mullally CA, Stubbs KA, Vrielink A, Maiden MCJ, Harrison OB, Perkins TT, Kahler CM. Acquisition of the capsule locus by horizontal gene transfer in Neisseria meningitidis is often accompanied by the loss of UDP-GalNAc synthesis. Sci Rep 2017; 7:44442. [PMID: 28290510 PMCID: PMC5349592 DOI: 10.1038/srep44442] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/08/2017] [Indexed: 12/27/2022] Open
Abstract
Pathogenic meningococci have acquired a 24 kb capsule synthesis island (cps) by horizontal gene transfer which consists of a synthetic locus and associated capsule transport genes flanked by repetitive Regions D and D'. Regions D and D' contain an intact gene encoding a UDP-galactose epimerase (galE1) and a truncated remnant (galE2), respectively. In this study, GalE protein alleles were shown to be either mono-functional, synthesising UDP-galactose (UDP-Gal), or bi-functional, synthesising UDP-Gal and UDP-galactosamine (UDP-GalNAc). Meningococci possessing a capsule null locus (cnl) typically possessed a single bi-functional galE. Separation of functionality between galE1 and galE2 alleles in meningococcal isolates was retained for all serogroups except serogroup E which has a synthetic requirement for UDP-GalNAc. The truncated galE2 remnant in Region D' was also phylogenetically related to the bi-functional galE of the cnl locus suggesting common ancestry. A model is proposed in which the illegitimate recombination of the cps island into the galE allele of the cnl locus results in the formation of Region D' containing the truncated galE2 locus and the capture of the cps island en bloc. The retention of the duplicated Regions D and D' enables inversion of the synthetic locus within the cps island during bacterial growth.
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Affiliation(s)
- Stephanie N. Bartley
- School of Biomedical Sciences, University of Western Australia, Perth, Australia
- The Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Perth, Australia
- School of Molecular Sciences, University of Western Australia, Perth, Australia
| | - Shakeel Mowlaboccus
- School of Biomedical Sciences, University of Western Australia, Perth, Australia
- The Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Perth, Australia
| | - Christopher A. Mullally
- School of Biomedical Sciences, University of Western Australia, Perth, Australia
- The Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Perth, Australia
| | - Keith A. Stubbs
- School of Molecular Sciences, University of Western Australia, Perth, Australia
| | - Alice Vrielink
- School of Molecular Sciences, University of Western Australia, Perth, Australia
| | - Martin C. J. Maiden
- University of Oxford, Department of Zoology, South Parks Road, Oxford OX1 3PS, United Kingdom
| | - Odile B. Harrison
- University of Oxford, Department of Zoology, South Parks Road, Oxford OX1 3PS, United Kingdom
| | - Timothy T. Perkins
- School of Biomedical Sciences, University of Western Australia, Perth, Australia
- The Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Perth, Australia
| | - Charlene M. Kahler
- School of Biomedical Sciences, University of Western Australia, Perth, Australia
- The Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Perth, Australia
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15
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Simonis A, Schubert-Unkmeir A. Interactions of meningococcal virulence factors with endothelial cells at the human blood-cerebrospinal fluid barrier and their role in pathogenicity. FEBS Lett 2016; 590:3854-3867. [PMID: 27498906 DOI: 10.1002/1873-3468.12344] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/08/2016] [Accepted: 07/31/2016] [Indexed: 01/06/2023]
Abstract
The Gram-negative extracellular bacterium Neisseria meningitidis is one of the most common aetiological agents of bacterial meningitis affecting predominantly young children worldwide. This bacterium is normally a quiescent coloniser of the upper respiratory tract, but in some individuals it enters the blood stream and causes invasive diseases, such as septicaemia and meningitis. Interactions of N. meningitidis with human endothelial cells are crucially involved in pathogencitiy, and great efforts have been made to understand these molecular interactions. The aim of this review article is to provide an overview of the interactions of meningococcal virulence factors with host endothelial cells at the blood-cerebrospinal fluid barrier.
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Affiliation(s)
- Alexander Simonis
- Division of Hematology, University Hospital Zurich, Switzerland.,Institute of Hygiene and Microbiology, University of Wuerzburg, Germany
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16
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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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17
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Mustapha MM, Marsh JW, Harrison LH. Global epidemiology of capsular group W meningococcal disease (1970-2015): Multifocal emergence and persistence of hypervirulent sequence type (ST)-11 clonal complex. Vaccine 2016; 34:1515-1523. [PMID: 26876439 DOI: 10.1016/j.vaccine.2016.02.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 01/28/2016] [Accepted: 02/02/2016] [Indexed: 12/21/2022]
Abstract
Following an outbreak in Mecca Saudi Arabia in 2000, meningococcal strains expressing capsular group W (W) emerged as a major cause of invasive meningococcal disease (IMD) worldwide. The Saudi Arabian outbreak strain (Hajj clone) belonging to the ST-11 clonal complex (cc11) is similar to W cc11 causing occasional sporadic disease before 2000. Since 2000, W cc11 has caused large meningococcal disease epidemics in the African meningitis belt and endemic disease in South America, Europe and China. Traditional molecular epidemiologic typing suggested that a majority of current W cc11 burden represented global spread of the Hajj clone. However, recent whole genome sequencing (WGS) analyses revealed significant genetic heterogeneity among global W cc11 strains. While continued spread of the Hajj clone occurs in the Middle East, the meningitis belt and South Africa have co-circulation of the Hajj clone and other unrelated W cc11 strains. Notably, South America, the UK, and France share a genetically distinct W cc11 strain. Other W lineages persist in low numbers in Europe, North America and the meningitis belt. In summary, WGS is helping to unravel the complex genomic epidemiology of group W meningococcal strains. Wider application of WGS and strengthening of global IMD surveillance is necessary to monitor the continued evolution of group W lineages.
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Affiliation(s)
- Mustapha M Mustapha
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, A525 Crabtree Hall,130 Desoto Street, Pittsburgh, PA 15261,USA
| | - Jane W Marsh
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, A525 Crabtree Hall,130 Desoto Street, Pittsburgh, PA 15261,USA
| | - Lee H Harrison
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, A525 Crabtree Hall,130 Desoto Street, Pittsburgh, PA 15261,USA.
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18
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Oldfield NJ, Harrison OB, Bayliss CD, Maiden MCJ, Ala'Aldeen DAA, Turner DPJ. Genomic Analysis of Serogroup Y Neisseria meningitidis Isolates Reveals Extensive Similarities Between Carriage-Associated and Disease-Associated Organisms. J Infect Dis 2016; 213:1777-85. [PMID: 26747709 DOI: 10.1093/infdis/jiw008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/18/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Neisseria meningitidis is a frequent colonizer of the human nasopharynx, with asymptomatic carriage providing the reservoir for invasive, disease-causing strains. Serogroup Y (MenY) strains are a major cause of meningococcal disease. High-resolution genetic analyses of carriage and disease isolates can establish epidemiological relationships and identify potential virulence factors. METHODS Whole-genome sequence data were obtained for 99 MenY carriage isolates recovered in the United Kingdom during 1997-2010. Sequences were compared to those of 73 MenY invasive isolates recovered during 2010-2011, using a gene-by-gene approach. RESULTS Comparisons across 1605 core genes resolved 91% of isolates into one of 8 clusters containing closely related disease and carriage isolates. Six clusters contained carried meningococci isolated during 1997-2001, suggesting temporal stability. One cluster of isolates, predominately sharing the designation Y: P1.5-1,10-1: F4-1: ST-1655 (cc23), was resolved into one subcluster with 86% carriage isolates and a second with 90% invasive isolates. These subclusters were defined by specific allelic differences in 5 core genes encoding glycerate kinase (glxK), valine-pyruvate transaminase (avtA), superoxide dismutase (sodB), and 2 hypothetical proteins. CONCLUSIONS High-resolution genetic analyses detected long-term temporal stability and temporally overlapping carriage and disease populations for MenY clones but also evidence of a disease-associated clone.
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Hill DMC, Lucidarme J, Gray SJ, Newbold LS, Ure R, Brehony C, Harrison OB, Bray JE, Jolley KA, Bratcher HB, Parkhill J, Tang CM, Borrow R, Maiden MCJ. Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study. THE LANCET. INFECTIOUS DISEASES 2015; 15:1420-8. [PMID: 26515523 PMCID: PMC4655307 DOI: 10.1016/s1473-3099(15)00267-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 08/09/2015] [Accepted: 08/11/2015] [Indexed: 11/24/2022]
Abstract
Background Invasive meningococcal disease (IMD) is a worldwide health issue that is potentially preventable with vaccination. In view of its sporadic nature and the high diversity of Neisseria meningitidis, epidemiological surveillance incorporating detailed isolate characterisation is crucial for effective control and understanding the evolving epidemiology of IMD. The Meningitis Research Foundation Meningococcus Genome Library (MRF-MGL) exploits whole-genome sequencing (WGS) for this purpose and presents data on a comprehensive and coherent IMD isolate collection from England and Wales via the internet. We assessed the contribution of these data to investigating IMD epidemiology. Methods WGS data were obtained for all 899 IMD isolates available for England and Wales in epidemiological years 2010–11 and 2011–12. The data had been annotated at 1720 loci, analysed, and disseminated online. Information was also available on meningococcal population structure and vaccine (Bexsero, GlaxoSmithKline, Brentford, Middlesex, UK) antigen variants, which enabled the investigation of IMD-associated genotypes over time and by patients' age groups. Population genomic analyses were done with a hierarchical gene-by-gene approach. Findings The methods used by MRF-MGL efficiently characterised IMD isolates and information was provided in plain language. At least 20 meningococcal lineages were identified, three of which (hyperinvasive clonal complexes 41/44 [lineage 3], 269 [lineage 2], and 23 [lineage 23]) were responsible for 528 (59%) of IMD isolates. Lineages were highly diverse and showed evidence of extensive recombination. Specific lineages were associated with IMD in particular age groups, with notable diversity in the youngest and oldest individuals. The increased incidence of IMD from 1984 to 2010 in England and Wales was due to successive and concurrent epidemics of different lineages. Genetically, 74% of isolates were characterised as encoding group B capsules: 16% group Y, 6% group W, and 3% group C. Exact peptide matches for individual Bexsero vaccine antigens were present in up to 26% of isolates. Interpretation The MRF-MGL represents an effective, broadly applicable model for the storage, analysis, and dissemination of WGS data that can facilitate real-time genomic pathogen surveillance. The data revealed information crucial to effective deployment and assessment of vaccines against N meningitidis. Funding Meningitis Research Foundation, Wellcome Trust, Public Health England, European Union.
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Affiliation(s)
| | - Jay Lucidarme
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, UK
| | - Stephen J Gray
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, UK
| | - Lynne S Newbold
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, UK
| | - Roisin Ure
- Scottish Haemophilus, Legionella, Meningococcus and Pneumococcus Reference Laboratory, Glasgow Royal Infirmary, Glasgow, UK
| | | | | | - James E Bray
- Department of Zoology, University of Oxford, Oxford, UK
| | | | | | | | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ray Borrow
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, UK
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20
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Golparian D, Unemo M. Will Genome Analysis Elucidate Evolution, Global Transmission and Virulence of Neisseria Meningitidis Lineages? EBioMedicine 2015; 2:186-7. [PMID: 26137558 PMCID: PMC4484816 DOI: 10.1016/j.ebiom.2015.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 02/02/2015] [Accepted: 02/02/2015] [Indexed: 11/25/2022] Open
Affiliation(s)
- Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden
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