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Tayimetha CY, Njunda LA, Akenji B, Founou RC, Feteh V, Zofou D, Chafa A, Oyono Y, Etogo B, Tseuko D, Fonkoua MC, Harrison OB. Phenotypic and genotypic characterization of Neisseria gonorrhoeae isolates from Yaoundé, Cameroon, 2019 to 2020. Microb Genom 2023; 9:mgen001091. [PMID: 37590058 PMCID: PMC10483411 DOI: 10.1099/mgen.0.001091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
This study investigated antimicrobial resistance (AMR) phenotypes and genotypes exhibited by Neisseria gonorrhoeae from Yaoundé, Cameroon. AMR to tetracycline, penicillin and ciprofloxacin was observed although none of the isolates had reduced susceptibility to azithromycin, cefixime or ceftriaxone. Whole genome sequence (WGS) data were obtained and, using a threshold of 300 or fewer locus differences in the N. gonorrhoeae core gene multilocus sequence typing (cgMLST) scheme, four distinct core genome lineages were identified. Publicly available WGS data from 1355 gonococci belonging to these four lineages were retrieved from the PubMLST database, allowing the Cameroonian isolates to be examined in the context of existing data and compared with related gonococci. Examination of AMR genotypes in this dataset found an association between the core genome and AMR with, for example, isolates belonging to the core genome group, Ng_cgc_300 : 21, possessing GyrA and ParC alleles with amino acid substitutions conferring high-level resistance to ciprofloxacin while lineages Ng_cgc_300 : 41 and Ng_cgc_300 : 243 were predicted to be susceptible to several antimicrobials. A core genome lineage, Ng_cgc_300 : 498, was observed which largely consisted of gonococci originating from Africa. Analyses from this study demonstrate the advantages of using the N. gonorrhoeae cgMLST scheme to find related gonococci to carry out genomic analyses that enhance our understanding of the population biology of this important pathogen.
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Affiliation(s)
- Carolle Yanique Tayimetha
- Faculty of Health Sciences of the University of Buea, Buea, Cameroon
- National Public Health Laboratory, Yaounde, Cameroon
| | | | - Blaise Akenji
- National Public Health Laboratory, Yaounde, Cameroon
| | - Raspail Carrel Founou
- Department of Microbiology, Haematology and Immunology of University of Dschang, Dschang, Cameroon
| | - Vitalis Feteh
- Faculty of Health Sciences of the University of Buea, Buea, Cameroon
| | - Denis Zofou
- Faculty of Health Sciences of the University of Buea, Buea, Cameroon
| | - Anicet Chafa
- Medical Bacteriology Laboratory of University Hospital Center, Yaoundé, Cameroon
| | - Yannick Oyono
- Faculty of Health Sciences of the University of Buea, Buea, Cameroon
| | | | - Dorine Tseuko
- National Public Health Laboratory, Yaounde, Cameroon
| | - Marie Christine Fonkoua
- Centre Pasteur du Cameroon, Yaoundé, Cameroon
- Cameroonian Society of Microbiology, Yaoundé, Cameroon
| | - Odile B. Harrison
- Department of Biology, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
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Kurzyp K, Harrison OB. Bacterium of one thousand and one variants: genetic diversity of Neisseria gonorrhoeae pathogenicity. Microb Genom 2023; 9. [PMID: 37285200 DOI: 10.1099/mgen.0.001040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023] Open
Abstract
The bacterium Neisseria gonorrhoeae causes the sexually transmitted infection gonorrhoea. Although diverse clinical manifestations are associated with gonorrhoea, ranging from asymptomatic through to localized and disseminated infection, very little is known about the bacterial determinants implicated in causing such different clinical symptoms. In particular, virulence factors, although defined and investigated in particular strains, often lack comprehensive analysis of their genetic diversity and how this relates to particular disease states. This review examines the clinical manifestations of gonorrhoea and discusses them in relation to disease severity and association with expression of particular virulence factors including PorB, lipooligosaccharide (LOS) and Opa, both in terms of their mechanisms of action and inter- and intra-strain variation. Particular attention is paid to phase variation as a key mechanism of genetic variation in the gonococcus and the impact of this during infection. We describe how whole-genome-sequence-based approaches that focus on virulence factors can be employed for vaccine development and discuss whether whole-genome-sequence data can be used to predict the severity of gonococcal infection.
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Affiliation(s)
- Kacper Kurzyp
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Odile B Harrison
- Department of Biology, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
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Maynard-Smith L, Derrick JP, Borrow R, Lucidarme J, Maiden MCJ, Heyderman RS, Harrison OB. Genome-Wide Association Studies Identify an Association of Transferrin Binding Protein B Variation and Invasive Serogroup Y Meningococcal Disease in Older Adults. J Infect Dis 2022; 226:2204-2214. [PMID: 36322504 PMCID: PMC9748998 DOI: 10.1093/infdis/jiac430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/24/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Neisseria meningitidis serogroup Y, especially ST-23 clonal complex (Y:cc23), represents a larger proportion of invasive meningococcal disease (IMD) in older adults compared to younger individuals. This study explored the meningococcal genetic variation underlying this association. METHODS Maximum-likelihood phylogenies and the pangenome were analyzed using whole-genome sequence (WGS) data from 200 Y:cc23 isolates in the Neisseria PubMLST database. Genome-wide association studies (GWAS) were performed on WGS data from 250 Y:cc23 isolates from individuals with IMD aged ≥65 years versus < 65 years. RESULTS Y:cc23 meningococcal variants did not cluster by age group or disease phenotype in phylogenetic analyses. Pangenome comparisons found no differences in presence or absence of genes in IMD isolates from the different age groups. GWAS identified differences in nucleotide polymorphisms within the transferrin-binding protein B (tbpB) gene in isolates from individuals ≥65 years of age. TbpB structure modelling suggests these may impact binding of human transferrin. CONCLUSIONS These data suggest differential iron scavenging capacity amongst Y:cc23 meningococci isolated from older compared to younger patients. Iron acquisition is essential for many bacterial pathogens including the meningococcus. These polymorphisms may facilitate colonization, thereby increasing the risk of disease in vulnerable older people with altered nasopharyngeal microbiomes and nutritional status.
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Affiliation(s)
- Laura Maynard-Smith
- Correspondence: Laura Maynard-Smith, MBBS, Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK ()
| | - Jeremy P Derrick
- Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, United Kingdom
| | - Ray Borrow
- Meningococcal Reference Unit, UK Health Security Agency, Manchester, United Kingdom
| | - Jay Lucidarme
- Meningococcal Reference Unit, UK Health Security Agency, Manchester, United Kingdom
| | | | - Robert S Heyderman
- Division of Infection and Immunity, University College London, London, United Kingdom
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Carr JP, MacLennan JM, Plested E, Bratcher HB, Harrison OB, Aley PK, Bray JE, Camara S, Rodrigues CMC, Davis K, Bartolf A, Baxter D, Cameron JC, Cunningham R, Faust SN, Fidler K, Gowda R, Heath PT, Hughes S, Khajuria S, Orr D, Raman M, Smith A, Turner DP, Whittaker E, Williams CJ, Zipitis CS, Pollard AJ, Oliver J, Morales-Aza B, Lekshmi A, Clark SA, Borrow R, Christensen H, Trotter C, Finn A, Maiden MCJ, Snape MD. Impact of meningococcal ACWY conjugate vaccines on pharyngeal carriage in adolescents: evidence for herd protection from the UK MenACWY programme. Clin Microbiol Infect 2022; 28:1649.e1-1649.e8. [PMID: 35840033 DOI: 10.1016/j.cmi.2022.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Serogroup W and Y invasive meningococcal disease (IMD) increased globally from 2000 onwards. Responding to a rapid increase in serogroup W clonal complex 11 (W:cc11) IMD, the UK replaced an adolescent booster dose of meningococcal C conjugate vaccine with quadrivalent MenACWY conjugate vaccine in 2015. By 2018, vaccine coverage in the eligible school cohorts aged 14-19 years-old was 84%. We assessed the impact of the MenACWY vaccination programme on meningococcal carriage. METHODS An observational study of culture-defined oropharyngeal meningococcal carriage prevalence before and after the start of the MenACWY vaccination programme in UK school students, aged 15-19 years, using two cross-sectional studies: 2014-15 "UKMenCar4" and 2018 "Be on the TEAM" (ISRCTN75858406). RESULTS A total of 10625 participants pre-implementation and 13434 post-implementation were included. Carriage of genogroups C, W, and Y (combined) decreased from 2·03% to 0·71% (OR 0·34 [95% CI 0·27-0·44] p<0·001). Carriage of genogroup B meningococci did not change (1·26% vs 1·23% [95% CI 0.77-1.22] p=0·80) and genogroup C remained rare (n = 7/10625 vs 17/13488, p=0·135). The proportion of serogroup positive isolates, i.e., those expressing capsule, decreased for genogroup W by 53.8% (95% CI -5.0%-79.8%, p=0·016) and for genogroup Y by 30·1% (95% CI 8·9%-46·3%, p=0·0025). CONCLUSIONS The UK MenACWY vaccination programme reduced carriage acquisition of genogroup and serogroup Y and W meningococci and sustained low levels of genogroup C carriage. These data support the use of quadrivalent MenACWY conjugate vaccine for indirect (herd) protection.
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Affiliation(s)
- Jeremy P Carr
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK; Monash University, Melbourne, Australia; Monash Children's Hospital, Melbourne, Australia
| | | | - Emma Plested
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | | | | | - Parvinder K Aley
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | | | - Susana Camara
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | - Charlene M C Rodrigues
- Department of Zoology, University of Oxford, UK; Department of Paediatric Infectious Diseases, Great Ormond Street Hospital for Children NHS Foundation Trust, UK
| | - Kimberly Davis
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | - Angela Bartolf
- St George's Vaccine Institute, Institute of Infection & Immunity; St George's University of London, UK
| | | | | | | | - Saul N Faust
- NIHR Southampton Clinical Research Facility and NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust; and Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Katy Fidler
- Brighton and Sussex Medical School, UK; Royal Alexandra Children's Hospital, University Hospital Sussex NHS Foundation Trust, Brighton, UK
| | | | - Paul T Heath
- St George's Vaccine Institute, Institute of Infection & Immunity; St George's University of London, UK
| | - Stephen Hughes
- Royal Manchester Children's Hospital; Manchester University NHS Foundation Trust, UK
| | | | - David Orr
- Lancashire Teaching Hospitals NHS Foundation Trust, UK
| | - Mala Raman
- University Hospitals Plymouth NHS Foundation Trust, UK
| | - Andrew Smith
- Glasgow Dental Hospital & School, College of Medical, Veterinary & Life Sciences, University of Glasgow, UK
| | - David Pj Turner
- School of Life Sciences, University of Nottingham & Nottingham University Hospitals NHS Trust, UK
| | - Elizabeth Whittaker
- Imperial College London, UK; Imperial College Healthcare NHS Trust, London, UK
| | | | - Christos S Zipitis
- Wrightington, Wigan and Leigh Teaching Hospitals NHS Foundation Trust, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | - Jennifer Oliver
- Bristol Children's Vaccine Centre, University of Bristol, UK
| | | | - Aiswarya Lekshmi
- UK Health Security Agency Meningococcal Reference Unit, Manchester Royal Infirmary Manchester, UK
| | - Stephen A Clark
- UK Health Security Agency Meningococcal Reference Unit, Manchester Royal Infirmary Manchester, UK
| | - Ray Borrow
- UK Health Security Agency Meningococcal Reference Unit, Manchester Royal Infirmary Manchester, UK
| | - Hannah Christensen
- School of Population Health Sciences, Bristol Medical School, University of Bristol, UK
| | | | - Adam Finn
- School of Population Health Sciences, Bristol Medical School, University of Bristol, UK
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, United Kingdom.
| | - Matthew D Snape
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
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de Korne-Elenbaas J, Bruisten SM, van Dam AP, Maiden MCJ, Harrison OB. The Neisseria gonorrhoeae Accessory Genome and Its Association with the Core Genome and Antimicrobial Resistance. Microbiol Spectr 2022; 10:e0265421. [PMID: 35604129 PMCID: PMC9241924 DOI: 10.1128/spectrum.02654-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/14/2022] [Indexed: 01/22/2023] Open
Abstract
The bacterial accessory genome provides the genetic flexibility needed to facilitate environment and host adaptation. In Neisseria gonorrhoeae, known accessory elements include plasmids which can transfer and mediate antimicrobial resistance (AMR); however, chromosomal accessory genes could also play a role in AMR. Here, the gonococcal accessory genome was characterized using gene-by-gene approaches and its association with the core genome and AMR were assessed. The gonococcal accessory gene pool consisted of 247 genes, which were mainly genes located on large mobile genetic elements, phage associated genes, or genes encoding putative secretion systems. Accessory elements showed similar synteny across genomes, indicating either a predisposition for particular genomic locations or ancestral inheritance that are conserved during strain expansion. Significant associations were found between the prevalence of accessory elements and core genome multi-locus sequence types (cgMLST), consistent with a structured gonococcal population despite frequent horizontal gene transfer (HGT). Increased prevalence of putative DNA exchange regulators was significantly associated with AMR, which included a putative secretion system, methyltransferases and a toxin-antitoxin system. Although frequent HGT results in high genetic diversity in the gonococcus, we found that this is mediated by a small gene pool. In fact, a highly organized genome composition was identified with a strong association between the accessory and core genome. Increased prevalence of DNA exchange regulators in antimicrobial resistant isolates suggests that genetic material exchange plays a role in the development or maintenance of AMR. These findings enhance our understanding of gonococcal genome architecture and have important implications for gonococcal population biology. IMPORTANCE The emergence of antimicrobial resistance (AMR) against third generation cephalosporins in Neisseria gonorrhoeae is a major public health concern, as these are antibiotics of last resort for the effective treatment of gonorrhea. Although the resistance mechanisms against this class of antibiotics have not been entirely resolved, resistance against other classes of antibiotics, such as tetracyclines, is known to be mediated through plasmids, which are known gonococcal extra-chromosomal accessory elements. A complete assessment of the chromosomal accessory genome content and its role in AMR has not yet been undertaken. Here, we comprehensively characterize the gonococcal accessory genome to better understand genome architecture as well as the evolution and mechanisms of AMR in this species.
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Affiliation(s)
- Jolinda de Korne-Elenbaas
- Public Health Laboratory, Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity (AI&II), Academic Medical Center, Amsterdam, the Netherlands
| | - Sylvia M. Bruisten
- Public Health Laboratory, Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands
- Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity (AI&II), Amsterdam, the Netherlands
| | - Alje P. van Dam
- Public Health Laboratory, Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity (AI&II), Academic Medical Center, Amsterdam, the Netherlands
| | - Martin C. J. Maiden
- Department of Zoology, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Odile B. Harrison
- Department of Zoology, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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Cehovin A, Jolley KA, Maiden MCJ, Harrison OB, Tang CM. Mobile antimicrobial resistance in Neisseria gonorrhoeae. Access Microbiol 2022. [DOI: 10.1099/acmi.ac2021.po0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neisseria gonorrhoeae (the gonococcus) is the causative agent of the sexually-transmitted infection gonorrhoea, and has developed resistance to all classes of antimicrobials. In gonococci, plasmids can mediate high-level antimicrobial resistance (AMR) to tetracyclines and ß-lactams. Plasmids can spread through bacterial populations by transformation and conjugation, resulting in the rapid dissemination of traits. Characterisation of plasmids, including understanding their distribution in bacterial populations, is therefore key to understanding bacterial evolution, and in particular the spread of AMR. N. gonorrhoeae can harbour three plasmids, conjugative (pConj), ß-lactamase (pbla) and cryptic (pCryp). Using genomic and phylogenetic analyses, we show that plasmids are widespread in a large collection of gonococcal isolates from 56 countries. We found that variants of pConj (which can mediate tetracycline resistance) and pbla expressing TEM-135 ß-lactamase are associated with distinct gonococcal lineages. Furthermore, AMR plasmids are significantly more prevalent in gonococci from less wealthy countries. Over 94% of gonococci possess the cryptic plasmid (pCryp), and its absence can be 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
- University of Oxford, Sir William Dunn School of Pathology, United Kingdom
| | - Keith A Jolley
- University of Oxford, Department of Zoology, United Kingdom
| | | | | | - Christoph M Tang
- University of Oxford, Sir William Dunn School of Pathology, United Kingdom
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Earle SG, Lobanovska M, Lavender H, Tang C, Exley RM, Ramos-Sevillano E, Browning DF, Kostiou V, Harrison OB, Bratcher HB, Varani G, Tang CM, Wilson DJ, Maiden MCJ. Genome-wide association studies reveal the role of polymorphisms affecting factor H binding protein expression in host invasion by Neisseria meningitidis. PLoS Pathog 2021; 17:e1009992. [PMID: 34662348 PMCID: PMC8553145 DOI: 10.1371/journal.ppat.1009992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/28/2021] [Accepted: 09/29/2021] [Indexed: 11/18/2022] Open
Abstract
Many invasive bacterial diseases are caused by organisms that are ordinarily harmless components of the human microbiome. Effective interventions against these microbes require an understanding of the processes whereby symbiotic or commensal relationships transition into pathology. Here, we describe bacterial genome-wide association studies (GWAS) of Neisseria meningitidis, a common commensal of the human respiratory tract that is nevertheless a leading cause of meningitis and sepsis. An initial GWAS discovered bacterial genetic variants, including single nucleotide polymorphisms (SNPs), associated with invasive meningococcal disease (IMD) versus carriage in several loci across the meningococcal genome, encoding antigens and other extracellular components, confirming the polygenic nature of the invasive phenotype. In particular, there was a significant peak of association around the fHbp locus, encoding factor H binding protein (fHbp), which promotes bacterial immune evasion of human complement by recruiting complement factor H (CFH) to the meningococcal surface. The association around fHbp with IMD was confirmed by a validation GWAS, and we found that the SNPs identified in the validation affected the 5' region of fHbp mRNA, altering secondary RNA structures, thereby increasing fHbp expression and enhancing bacterial escape from complement-mediated killing. This finding is consistent with the known link between complement deficiencies and CFH variation with human susceptibility to IMD. These observations demonstrate the importance of human and bacterial genetic variation across the fHbp:CFH interface in determining IMD susceptibility, the transition from carriage to disease.
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Affiliation(s)
- Sarah G. Earle
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
| | - Mariya Lobanovska
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Hayley Lavender
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Changyan Tang
- Department of Chemistry, University of Washington, Seattle, Washington United States of America
| | - Rachel M. Exley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | - Douglas F. Browning
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Vasiliki Kostiou
- Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, Oxford, United Kingdom
| | | | | | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington United States of America
- * E-mail: (GV); (CMT); (DJW); (MCJM)
| | - Christoph M. Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- * E-mail: (GV); (CMT); (DJW); (MCJM)
| | - Daniel J. Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
- Department for Continuing Education, University of Oxford, Oxford, United Kingdom
- * E-mail: (GV); (CMT); (DJW); (MCJM)
| | - Martin C. J. Maiden
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (GV); (CMT); (DJW); (MCJM)
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Abstract
The sexually transmitted infection (STI) gonorrhoea remains a major global public health concern. The World Health Organization (WHO) estimates that 87 million new cases in individuals who were 15 to 49 years of age occurred in 2016. The growing number of gonorrhoea cases is concerning given the rise in gonococci developing antimicrobial resistance (AMR). Therefore, a global action plan is needed to facilitate surveillance. Indeed, the WHO has made surveillance leading to the elimination of STIs (including gonorrhoea) a global health priority. The availability of whole genome sequence data offers new opportunities to combat gonorrhoea. This can be through (i) enhanced surveillance of the global prevalence of AMR, (ii) improved understanding of the population biology of the gonococcus, and (iii) opportunities to mine sequence data in the search for vaccine candidates. Here, we review the current status in Neisseria gonorrhoeae genomics. In particular, we explore how genomics continues to advance our understanding of this complex pathogen.
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Affiliation(s)
- Odile B Harrison
- Department of Zoology, University of Oxford, The Peter Medawar Building, Oxford, UK
| | - Martin CJ Maiden
- Department of Zoology, University of Oxford, The Peter Medawar Building, Oxford, UK
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Chen M, Harrison OB, Bratcher HB, Bo Z, Jolley KA, Rodrigues CM, Bray JE, Guo Q, Zhang X, Chen M, Maiden MC. Evolution of Sequence Type 4821 Clonal Complex Hyperinvasive and Quinolone-Resistant Meningococci. Emerg Infect Dis 2021; 27:1110-1122. [PMID: 33754991 PMCID: PMC8007298 DOI: 10.3201/eid2704.203612] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Expansion of quinolone-resistant Neisseria meningitidis clone ChinaCC4821-R1-C/B from sequence type (ST) 4821 clonal complex (CC4821) caused a serogroup shift from serogroup A to serogroup C invasive meningococcal disease (IMD) in China. To determine the relationship among globally distributed CC4821 meningococci, we analyzed whole-genome sequence data from 173 CC4821 meningococci isolated from 4 continents during 1972–2019. These meningococci clustered into 4 sublineages (1–4); sublineage 1 primarily comprised of IMD isolates (41/50, 82%). Most isolates from outside China (40/49, 81.6%) formed a distinct sublineage, the Europe–USA cluster, with the typical strain designation B:P1.17-6,23:F3-36:ST-3200(CC4821), harboring mutations in penicillin-binding protein 2. These data show that the quinolone-resistant clone ChinaCC4821-R1-C/B has expanded to other countries. The increasing distribution worldwide of serogroup B CC4821 raises the concern that CC4821 has the potential to cause a pandemic that would be challenging to control, despite indirect evidence that the Trumenba vaccine might afford some protection.
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Meehan M, Eogan M, McCallion N, Cunney R, Bray JE, Jolley KA, Unitt A, Maiden MCJ, Harrison OB, Drew RJ. Genomic epidemiology of group B streptococci spanning 10 years in an Irish maternity hospital, 2008-2017. J Infect 2021; 83:37-45. [PMID: 33862060 DOI: 10.1016/j.jinf.2021.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/30/2021] [Accepted: 04/05/2021] [Indexed: 02/02/2023]
Abstract
OBJECTIVES The genomic epidemiology of group b streptococcal (GBS) isolates from the Rotunda maternity hospital, Dublin, 2008-2017, was investigated. METHODS Whole genome sequences of isolates (invasive, n = 114; non-invasive, n = 76) from infants and women were analysed using the PubMLST database (https://pubmlst.org/sagalactiae/). RESULTS Serotypes III (36%), Ia (18%), V (17%), II (11%) and Ib, (9%) and sequence types (ST) 17 (23%), ST-23 (14%), ST-1 (12%) and ST-19 (7%) were most common. Core genome MLST (cgMLST) differentiated isolates of the same ST, grouped STs into five lineages congruent with known clonal complexes and identified known mother-baby pairs and suspected linked infant cases. Clonal complex (CC) 17 accounted for 40% and 22% of infant and maternal invasive cases, respectively and 21% of non-invasive isolates. CC23 and CC19 were associated with maternal disease (30%) and carriage (24%), respectively. Erythromycin (26%) and clindamycin (18%) resistance increased over the study period and was associated with presence of the erm(B) gene (55%), CC1 (33%) and CC19 (24%). A multi-resistant integrative conjugative element incorporated in the PI-1 locus was detected in CC17, an ST-12 and ST-23 isolate confirming the global dissemination of this element. All isolates possessed one or more pilus islands. Genes encoding other potential protective proteins including Sip, C5a peptidase and Srr1 were present in 100%, 99.5% and 65.8% of isolates, respectively. The srr2 gene was unique to CC17. CONCLUSIONS The PubMLST.org website provides a valuable framework for genomic GBS surveillance to inform on local and global GBS epidemiology, preventive and control measures.
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Affiliation(s)
- Mary Meehan
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland at Temple Street, Dublin, Ireland.
| | - Maeve Eogan
- Department of Obstetrics and Gynaecology, Rotunda Hospital, Dublin, Ireland
| | - Naomi McCallion
- Department of Neonatology, The Rotunda Hospital, Dublin, Ireland; Department of Paediatrics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Robert Cunney
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland at Temple Street, Dublin, Ireland; Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - James E Bray
- Department of Zoology, University of Oxford, Peter Medawar Building, Oxford OX1 3SY, UK
| | - Keith A Jolley
- Department of Zoology, University of Oxford, Peter Medawar Building, Oxford OX1 3SY, UK
| | - Anastasia Unitt
- Department of Zoology, University of Oxford, Peter Medawar Building, Oxford OX1 3SY, UK
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, Peter Medawar Building, Oxford OX1 3SY, UK
| | - Odile B Harrison
- Department of Zoology, University of Oxford, Peter Medawar Building, Oxford OX1 3SY, UK
| | - Richard J Drew
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland at Temple Street, Dublin, Ireland; Clinical Innovation Unit, Rotunda Hospital, Dublin, Ireland; Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
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11
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Yahara K, Ma KC, Mortimer TD, Shimuta K, Nakayama SI, Hirabayashi A, Suzuki M, Jinnai M, Ohya H, Kuroki T, Watanabe Y, Yasuda M, Deguchi T, Eldholm V, Harrison OB, Maiden MCJ, Grad YH, Ohnishi M. Emergence and evolution of antimicrobial resistance genes and mutations in Neisseria gonorrhoeae. Genome Med 2021; 13:51. [PMID: 33785063 PMCID: PMC8008663 DOI: 10.1186/s13073-021-00860-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/24/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Antimicrobial resistance in Neisseria gonorrhoeae is a global health concern. Strains from two internationally circulating sequence types, ST-7363 and ST-1901, have acquired resistance to third-generation cephalosporins, mainly due to mosaic penA alleles. These two STs were first detected in Japan; however, the timeline, mechanism, and process of emergence and spread of these mosaic penA alleles to other countries remain unknown. METHODS We studied the evolution of penA alleles by obtaining the complete genomes from three Japanese ST-1901 clinical isolates harboring mosaic penA allele 34 (penA-34) dating from 2005 and generating a phylogenetic representation of 1075 strains sampled from 35 countries. We also sequenced the genomes of 103 Japanese ST-7363 N. gonorrhoeae isolates from 1996 to 2005 and reconstructed a phylogeny including 88 previously sequenced genomes. RESULTS Based on an estimate of the time-of-emergence of ST-1901 (harboring mosaic penA-34) and ST-7363 (harboring mosaic penA-10), and > 300 additional genome sequences of Japanese strains representing multiple STs isolated in 1996-2015, we suggest that penA-34 in ST-1901 was generated from penA-10 via recombination with another Neisseria species, followed by recombination with a gonococcal strain harboring wildtype penA-1. Following the acquisition of penA-10 in ST-7363, a dominant sub-lineage rapidly acquired fluoroquinolone resistance mutations at GyrA 95 and ParC 87-88, by independent mutations rather than horizontal gene transfer. Data in the literature suggest that the emergence of these resistance determinants may reflect selection from the standard treatment regimens in Japan at that time. CONCLUSIONS Our findings highlight how antibiotic use and recombination across and within Neisseria species intersect in driving the emergence and spread of drug-resistant gonorrhea.
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Affiliation(s)
- Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan.
| | - Kevin C Ma
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ken Shimuta
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shu-Ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Aki Hirabayashi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Michio Jinnai
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
| | - Hitomi Ohya
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
| | - Toshiro Kuroki
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
- Present address: Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoinooka, Imabari, Ehime, 794-8555, Japan
| | - Yuko Watanabe
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
| | - Mitsuru Yasuda
- Center for Nutrition Support and Infection Control, Gifu University Hospital, Gifu, Japan
| | - Takashi Deguchi
- Department of Urology, Kizawa Memorial Hospital, Gifu, Japan
| | - Vegard Eldholm
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | | | | | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan.
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12
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Diallo K, Feteh VF, Ibe L, Antonio M, Caugant DA, du Plessis M, Deghmane AE, Feavers IM, Fernandez K, Fox LM, Rodrigues CMC, Ronveaux O, Taha MK, Wang X, Brueggemann AB, Maiden MCJ, Harrison OB. Molecular diagnostic assays for the detection of common bacterial meningitis pathogens: A narrative review. EBioMedicine 2021; 65:103274. [PMID: 33721818 PMCID: PMC7957090 DOI: 10.1016/j.ebiom.2021.103274] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/29/2022] Open
Abstract
Bacterial meningitis is a major global cause of morbidity and mortality. Rapid identification of the aetiological agent of meningitis is essential for clinical and public health management and disease prevention given the wide range of pathogens that cause the clinical syndrome and the availability of vaccines that protect against some, but not all, of these. Since microbiological culture is complex, slow, and often impacted by prior antimicrobial treatment of the patient, molecular diagnostic assays have been developed for bacterial detection. Distinguishing between meningitis caused by Neisseria meningitidis (meningococcus), Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, and Streptococcus agalactiae and identifying their polysaccharide capsules is especially important. Here, we review methods used in the identification of these bacteria, providing an up-to-date account of available assays, allowing clinicians and diagnostic laboratories to make informed decisions about which assays to use.
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Affiliation(s)
- Kanny Diallo
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Cote d'Ivoire
| | - Vitalis F Feteh
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Lilian Ibe
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, Gambia; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Dominique A Caugant
- WHO Collaborating Center for Reference and Research on Meningococci, Norwegian Institute of Public Health, Oslo N-0213, Norway
| | - Mignon du Plessis
- A division of the National Health Laboratory Service (NHLS), National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | | | - Ian M Feavers
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom
| | | | - LeAnne M Fox
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Division of Bacterial Diseases, Meningitis and Vaccine Preventable Diseases Branch, United States
| | - Charlene M C Rodrigues
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Department of Paediatric Infectious Diseases, St George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | | | | | - Xin Wang
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Division of Bacterial Diseases, Meningitis and Vaccine Preventable Diseases Branch, United States
| | - Angela B Brueggemann
- Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom
| | - Odile B Harrison
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom.
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13
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MacLennan JM, Rodrigues CMC, Bratcher HB, Lekshmi A, Finn A, Oliver J, Wootton M, Ray S, Cameron C, Smith A, Heath PT, Bartolf A, Nolan T, Hughes S, Varghese A, Snape MD, Sewell R, Cunningham R, Stolton A, Kay C, Palmer K, Baxter D, Suggitt D, Zipitis CS, Pemberton N, Jolley KA, Bray JE, Harrison OB, Ladhani SN, Pollard AJ, Borrow R, Gray SJ, Trotter C, Maiden MCJ. Meningococcal carriage in periods of high and low invasive meningococcal disease incidence in the UK: comparison of UKMenCar1-4 cross-sectional survey results. Lancet Infect Dis 2021; 21:677-687. [PMID: 33482143 PMCID: PMC8064914 DOI: 10.1016/s1473-3099(20)30842-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 06/16/2020] [Accepted: 10/13/2020] [Indexed: 02/02/2023]
Abstract
Background The incidence of invasive meningococcal disease in the UK decreased by approximately four times from 1999 to 2014, with reductions in serogroup C and serogroup B disease. Lower serogroup C invasive meningococcal disease incidence was attributable to implementation of the meningococcal serogroup C conjugate vaccine in 1999, through direct and indirect protection, but no vaccine was implemented against serogroup B disease. UK Meningococcal Carriage surveys 1–3 (UKMenCar1–3), conducted in 1999, 2000, and 2001, were essential for understanding the impact of vaccination. To investigate the decline in invasive meningococcal disease incidence, we did a large oropharyngeal carriage survey in 2014–15, immediately before the changes to meningococcal vaccines in the UK national immunisation schedule. Methods UKMenCar4 was a cross-sectional survey in adolescents aged 15–19 years who were enrolled from schools and colleges geographically local to one of 11 UK sampling centres between Sept 1, 2014, and March 30, 2015. Participants provided an oropharyngeal swab sample and completed a questionnaire on risk factors for carriage, including social behaviours. Samples were cultured for putative Neisseria spp, which were characterised with serogrouping and whole-genome sequencing. Data from this study were compared with the results from the UKMenCar1–3 surveys (1999–2001). Findings From the 19 641 participants (11 332 female, 8242 male, 67 not stated) in UKMenCar4 with culturable swabs and completed risk-factor questionnaires, 1420 meningococci were isolated, with a carriage prevalence of 7·23% (95% CI 6·88–7·60). Carriage prevalence was substantially lower in UKMenCar4 than in the previous surveys: carriage prevalence was 16·6% (95% CI 15·89–17·22; 2306/13 901) in UKMenCar1 (1999), 17·6% (17·05–18·22; 2873/16 295) in UKMenCar2 (2000), and 18·7% (18·12–19·27; 3283/17 569) in UKMenCar3 (2001). Carriage prevalence was lower for all serogroups in UKMenCar4 than in UKMenCar1–3, except for serogroup Y, which was unchanged. The prevalence of carriage-promoting social behaviours decreased from 1999 to 2014–15, with individuals reporting regular cigarette smoking decreasing from 2932 (21·5%) of 13 650 to 2202 (11·2%) of 19 641, kissing in the past week from 6127 (44·8%) of 13 679 to 7320 (37·3%) of 19 641, and attendance at pubs and nightclubs in the past week from 8436 (62·1%) of 13 594 to 7662 (39·0%) of 19 641 (all p<0·0001). Interpretation We show that meningococcal carriage prevalence in adolescents sampled nationally during a low incidence period (2014–15) was less than half of that in an equivalent population during a high incidence period (1999–2001). Disease and carriage caused by serogroup C was well controlled by ongoing vaccination. The prevalence of behaviours associated with carriage declined, suggesting that public health policies aimed at influencing behaviour might have further reduced disease. Funding Wellcome Trust, UK Department of Health, and National Institute for Health Research.
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Affiliation(s)
- Jenny M MacLennan
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Charlene M C Rodrigues
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Holly B Bratcher
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Aiswarya Lekshmi
- Meningococcal Reference Unit, Public Health England, Manchester Public Health Laboratory, Manchester Royal Infirmary, Manchester, UK
| | - Adam Finn
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Jenny Oliver
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Mandy Wootton
- Division of Public Health Wales, Temple of Peace and Health, Cardiff, UK
| | - Samantha Ray
- Division of Public Health Wales, Temple of Peace and Health, Cardiff, UK
| | - Claire Cameron
- NHS National Services Scotland, Health Protection Scotland, Glasgow, UK
| | - Andrew Smith
- Glasgow Dental School, University of Glasgow, UK; Scottish Microbiology Reference Laboratory, NHS Greater Glasgow & Clyde, Glasgow, UK
| | - Paul T Heath
- St George's Vaccine Institute, Institute of Infection & Immunity, St George's University of London, London, UK
| | - Angela Bartolf
- St George's Vaccine Institute, Institute of Infection & Immunity, St George's University of London, London, UK
| | - Tracey Nolan
- Research and Development Department, Maidstone and Tunbridge Wells NHS Trust, Maidstone, Kent, UK
| | - Stephen Hughes
- Central Manchester University Hospitals, NHS Foundation Trust, Manchester, UK
| | - Anu Varghese
- Central Manchester University Hospitals, NHS Foundation Trust, Manchester, UK
| | - Matthew D Snape
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - Richard Sewell
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - Richard Cunningham
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Alison Stolton
- Microbiology Department, University Hospitals Plymouth NHS Trust, UK
| | - Carole Kay
- Lancashire and South Cumbria NHS Foundation Trust, Preston, Lancashire, UK
| | - Karen Palmer
- Lancashire and South Cumbria NHS Foundation Trust, Preston, Lancashire, UK
| | - David Baxter
- Stockport NHS Foundation Trust, Stepping Hill Hospital, Stockport, UK
| | - Debbie Suggitt
- Stockport NHS Foundation Trust, Stepping Hill Hospital, Stockport, UK
| | - Christos S Zipitis
- Manchester Academic Health Science Centre, University of Manchester, Manchester, UK; Department of Paediatrics, Wrightington Wigan and Leigh NHS Foundation Trust, Wigan, UK
| | - Nicola Pemberton
- Clinical Trials Department, Wrightington Wigan and Leigh NHS Foundation Trust, Wigan, UK
| | - Keith A Jolley
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - James E Bray
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Odile B Harrison
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Shamez N Ladhani
- Paediatric Infectious Diseases Research Group, St George's University of London, London, UK; Immunisation and Countermeasures Division, Public Health England, London, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - Raymond Borrow
- Meningococcal Reference Unit, Public Health England, Manchester Public Health Laboratory, Manchester Royal Infirmary, Manchester, UK
| | - Stephen J Gray
- Meningococcal Reference Unit, Public Health England, Manchester Public Health Laboratory, Manchester Royal Infirmary, Manchester, UK
| | - Caroline Trotter
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Martin C J Maiden
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK.
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14
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Harrison OB, Cehovin A, Skett J, Jolley KA, Massari P, Genco CA, Tang CM, Maiden MCJ. Neisseria gonorrhoeae Population Genomics: Use of the Gonococcal Core Genome to Improve Surveillance of Antimicrobial Resistance. J Infect Dis 2020; 222:1816-1825. [PMID: 32163580 PMCID: PMC7653085 DOI: 10.1093/infdis/jiaa002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/07/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Gonorrhea, caused by the bacterium Neisseria gonorrhoeae, is a globally prevalent sexually transmitted infection. The dynamics of gonococcal population biology have been poorly defined due to a lack of resolution in strain typing methods. METHODS In this study, we assess how the core genome can be used to improve our understanding of gonococcal population structure compared with current typing schemes. RESULTS A total of 1668 loci were identified as core to the gonococcal genome. These were organized into a core genome multilocus sequence typing scheme (N gonorrhoeae cgMLST v1.0). A clustering algorithm using a threshold of 400 allelic differences between isolates resolved gonococci into discrete and stable core genome groups, some of which persisted for multiple decades. These groups were associated with antimicrobial genotypes and non-overlapping NG-STAR and NG-MAST sequence types. The MLST-STs were more widely distributed among core genome groups. CONCLUSIONS Clustering with cgMLST identified globally distributed, persistent, gonococcal lineages improving understanding of the population biology of gonococci and revealing its population structure. These findings have implications for the emergence of antimicrobial resistance in gonococci and how this is associated with lineages, some of which are more predisposed to developing antimicrobial resistance than others.
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Affiliation(s)
- Odile B Harrison
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
| | - Ana Cehovin
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Jessica Skett
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
| | - Keith A Jolley
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
| | - Paola Massari
- Department of Immunology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Caroline Attardo Genco
- Department of Immunology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Christoph M Tang
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Martin C J Maiden
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
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15
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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: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Rodgers E, Bentley SD, Borrow R, Bratcher HB, Brisse S, Brueggemann AB, Caugant DA, Findlow J, Fox L, Glennie L, Harrison LH, Harrison OB, Heyderman RS, van Rensburg MJ, Jolley KA, Kwambana-Adams B, Ladhani S, LaForce M, Levin M, Lucidarme J, MacAlasdair N, Maclennan J, Maiden MCJ, Maynard-Smith L, Muzzi A, Oster P, Rodrigues CMC, Ronveaux O, Serino L, Smith V, van der Ende A, Vázquez J, Wang X, Yezli S, Stuart JM. The global meningitis genome partnership. J Infect 2020; 81:510-520. [PMID: 32615197 DOI: 10.1016/j.jinf.2020.06.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 10/24/2022]
Abstract
Genomic surveillance of bacterial meningitis pathogens is essential for effective disease control globally, enabling identification of emerging and expanding strains and consequent public health interventions. While there has been a rise in the use of whole genome sequencing, this has been driven predominately by a subset of countries with adequate capacity and resources. Global capacity to participate in surveillance needs to be expanded, particularly in low and middle-income countries with high disease burdens. In light of this, the WHO-led collaboration, Defeating Meningitis by 2030 Global Roadmap, has called for the establishment of a Global Meningitis Genome Partnership that links resources for: N. meningitidis (Nm), S. pneumoniae (Sp), H. influenzae (Hi) and S. agalactiae (Sa) to improve worldwide co-ordination of strain identification and tracking. Existing platforms containing relevant genomes include: PubMLST: Nm (31,622), Sp (15,132), Hi (1935), Sa (9026); The Wellcome Sanger Institute: Nm (13,711), Sp (> 24,000), Sa (6200), Hi (1738); and BMGAP: Nm (8785), Hi (2030). A steering group is being established to coordinate the initiative and encourage high-quality data curation. Next steps include: developing guidelines on open-access sharing of genomic data; defining a core set of metadata; and facilitating development of user-friendly interfaces that represent publicly available data.
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Affiliation(s)
- Elizabeth Rodgers
- Meningitis Research Foundation, Newminster House, 27-29 Newminster House, Baldwin Street, Bristol BS1 1LT, UK.
| | - Stephen D Bentley
- Wellcome Sanger Institute, Parasites and microbes, Hinxton CB10 1SA, UK
| | - Ray Borrow
- Public Health England, Meningococcal Reference Unit, Manchester Royal Infirmary, Manchester M13 9WZ, UK
| | | | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Angela B Brueggemann
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Dominique A Caugant
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jamie Findlow
- Pfizer Limited, Walton Oaks, Dorking Road, Tadworth, Surrey KT20 7NS, UK
| | - LeAnne Fox
- Meningitis and Vaccine Preventable Disease Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, United States
| | - Linda Glennie
- Meningitis Research Foundation, Newminster House, 27-29 Newminster House, Baldwin Street, Bristol BS1 1LT, UK
| | - Lee H Harrison
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, PA, United States
| | | | - Robert S Heyderman
- NIHR Global Health Mucosal Pathogens Research Unit, Division of Infection & Immunity, University College London, London, UK
| | | | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | - Brenda Kwambana-Adams
- NIHR Global Health Mucosal Pathogens Research Unit, Division of Infection & Immunity, University College London, London, UK
| | - Shamez Ladhani
- Public Health England, Immunisation and Countermeasures Division, 61 Colindale Avenue, London NW9 5EQ, UK; Paediatric Infectious Diseases Research Group (PIDRG), St. George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | | | | | - Jay Lucidarme
- Public Health England, Meningococcal Reference Unit, Manchester Royal Infirmary, Manchester M13 9WZ, UK
| | - Neil MacAlasdair
- Wellcome Sanger Institute, Parasites and microbes, Hinxton CB10 1SA, UK
| | - Jenny Maclennan
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | | | | | | | | | | | | | | | - Vinny Smith
- Meningitis Research Foundation, Newminster House, 27-29 Newminster House, Baldwin Street, Bristol BS1 1LT, UK
| | - Arie van der Ende
- Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam UMC and, the Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam, the Netherlands
| | | | - Xin Wang
- Meningitis and Vaccine Preventable Disease Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, United States
| | - Saber Yezli
- Ministry of Health, The Global Centre for Mass Gatherings Medicine, Riyadh, Saudi Arabia
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17
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Retchless AC, Fox LM, Maiden MCJ, Smith V, Harrison LH, Glennie L, Harrison OB, Wang X. Toward a Global Genomic Epidemiology of Meningococcal Disease. J Infect Dis 2020; 220:S266-S273. [PMID: 31671445 DOI: 10.1093/infdis/jiz279] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Whole-genome sequencing (WGS) is invaluable for studying the epidemiology of meningococcal disease. Here we provide a perspective on the use of WGS for meningococcal molecular surveillance and outbreak investigation, where it helps to characterize pathogens, predict pathogen traits, identify emerging pathogens, and investigate pathogen transmission during outbreaks. Standardization of WGS workflows has facilitated their implementation by clinical and public health laboratories (PHLs), but further development is required for metagenomic shotgun sequencing and targeted sequencing to be widely available for culture-free characterization of bacterial meningitis pathogens. Internet-accessible servers are being established to support bioinformatics analysis, data management, and data sharing among PHLs. However, establishing WGS capacity requires investments in laboratory infrastructure and technical knowledge, which is particularly challenging in resource-limited regions, including the African meningitis belt. Strategic WGS implementation is necessary to monitor the molecular epidemiology of meningococcal disease in these regions and construct a global view of meningococcal disease epidemiology.
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Affiliation(s)
- Adam C Retchless
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - LeAnne M Fox
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Vincent Smith
- Meningitis Research Foundation, Bristol, United Kingdom
| | - Lee H Harrison
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Linda Glennie
- Meningitis Research Foundation, Bristol, United Kingdom
| | - Odile B Harrison
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Xin Wang
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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18
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Zhu T, McClure R, Harrison OB, Genco C, Massari P. Integrated Bioinformatic Analyses and Immune Characterization of New Neisseria gonorrhoeae Vaccine Antigens Expressed during Natural Mucosal Infection. Vaccines (Basel) 2019; 7:E153. [PMID: 31627489 PMCID: PMC6963464 DOI: 10.3390/vaccines7040153] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 02/07/2023] Open
Abstract
There is an increasingly severe trend of antibiotic-resistant Neisseria gonorrhoeae strains worldwide and new therapeutic strategies are needed against this sexually-transmitted pathogen. Despite the urgency, progress towards a gonococcal vaccine has been slowed by a scarcity of suitable antigens, lack of correlates of protection in humans and limited animal models of infection. N. gonorrhoeae gene expression levels in the natural human host does not reflect expression in vitro, further complicating in vitro-basedvaccine analysis platforms. We designed a novel candidate antigen selection strategy (CASS), based on a reverse vaccinology-like approach coupled with bioinformatics. We utilized the CASS to mine gonococcal proteins expressed during human mucosal infection, reported in our previous studies, and focused on a large pool of hypothetical proteins as an untapped source of potential new antigens. Via two discovery and analysis phases (DAP), we identified 36 targets predicted to be immunogenic, membrane-associated proteins conserved in N. gonorrhoeae and suitable for recombinant expression. Six initial candidates were produced and used to immunize mice. Characterization of the immune responses indicated cross-reactive antibodies and serum bactericidal activity against different N. gonorrhoeae strains. These results support the CASS as a tool for the discovery of new vaccine candidates.
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Affiliation(s)
- Tianmou Zhu
- Department of Immunology, Tufts University School of Medicine, Boston, MA 02111, USA.
| | - Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Odile B Harrison
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK.
| | - Caroline Genco
- Department of Immunology, Tufts University School of Medicine, Boston, MA 02111, USA.
| | - Paola Massari
- Department of Immunology, Tufts University School of Medicine, Boston, MA 02111, USA.
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19
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Diallo K, MacLennan J, Harrison OB, Msefula C, Sow SO, Daugla DM, Johnson E, Trotter C, MacLennan CA, Parkhill J, Borrow R, Greenwood BM, Maiden MCJ. Genomic characterization of novel Neisseria species. Sci Rep 2019; 9:13742. [PMID: 31551478 PMCID: PMC6760525 DOI: 10.1038/s41598-019-50203-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 09/04/2019] [Indexed: 12/11/2022] Open
Abstract
Of the ten human-restricted Neisseria species two, Neisseria meningitidis, and Neisseria gonorrhoeae, cause invasive disease: the other eight are carried asymptomatically in the pharynx, possibly modulating meningococcal and gonococcal infections. Consequently, characterizing their diversity is important for understanding the microbiome in health and disease. Whole genome sequences from 181 Neisseria isolates were examined, including those of three well-defined species (N. meningitidis; N. gonorrhoeae; and Neisseria polysaccharea) and genomes of isolates unassigned to any species (Nspp). Sequence analysis of ribosomal genes, and a set of core (cgMLST) genes were used to infer phylogenetic relationships. Average Nucleotide Identity (ANI) and phenotypic data were used to define species clusters, and morphological and metabolic differences among them. Phylogenetic analyses identified two polyphyletic clusters (N. polysaccharea and Nspp.), while, cgMLST data grouped Nspp isolates into nine clusters and identified at least three N. polysaccharea clusters. ANI results classified Nspp into seven putative species, and also indicated at least three putative N. polysaccharea species. Electron microscopy identified morphological differences among these species. This genomic approach provided a consistent methodology for species characterization using distinct phylogenetic clusters. Seven putative novel Neisseria species were identified, confirming the importance of genomic studies in the characterization of the genus Neisseria.
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Affiliation(s)
- Kanny Diallo
- Centre pour les Vaccins en Développement, Bamako, Mali. .,Department of Zoology, University of Oxford, Oxford, UK.
| | | | | | - Chisomo Msefula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Samba O Sow
- Centre pour les Vaccins en Développement, Bamako, Mali
| | | | - Errin Johnson
- Electron Microscopy Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Caroline Trotter
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Calman A MacLennan
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Ray Borrow
- Vaccine Evaluation Unit, Public Health England, Manchester, UK
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20
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Clemence MEA, Harrison OB, Maiden MCJ. Neisseria meningitidis has acquired sequences within the capsule locus by horizontal genetic transfer. Wellcome Open Res 2019; 4:99. [PMID: 31346553 PMCID: PMC6619384 DOI: 10.12688/wellcomeopenres.15333.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2019] [Indexed: 12/24/2022] Open
Abstract
Background: Expression of a capsule from one of serogroups A, B, C, W, X or Y is usually required for
Neisseria meningitidis (
Nme) to cause invasive meningococcal disease. The capsule is encoded by the capsule locus,
cps, which is proposed to have been acquired by a formerly capsule null organism by horizontal genetic transfer (HGT) from another species. Following identification of putative capsule genes in non-pathogenic
Neisseria species, this hypothesis is re-examined. Methods: Whole genome sequence data from
Neisseria species, including
Nme genomes from a diverse range of clonal complexes and capsule genogroups, and non-
Neisseria species, were obtained from PubMLST and GenBank. Sequence alignments of genes from the meningococcal
cps, and predicted orthologues in other species, were analysed using Neighbor-nets, BOOTSCANing and maximum likelihood phylogenies. Results: The meningococcal
cps was highly mosaic within regions B, C and D. A subset of sequences within regions B and C were phylogenetically nested within homologous sequences belonging to
N. subflava, consistent with HGT event in which
N. subflava was the donor. In the
cps of 23/39 isolates, the two copies of region D were highly divergent, with
rfbABC’ sequences being more closely related to predicted orthologues in the proposed species
N. weixii (GenBank accession number
CP023429.1) than the same genes in
Nme isolates lacking a capsule. There was also evidence of mosaicism in the
rfbABC’ sequences of the remaining 16 isolates, as well as
rfbABC from many isolates. Conclusions: Data are consistent with the
en bloc acquisition of
cps in meningococci from
N. subflava, followed by further recombination events with other
Neisseria species. Nevertheless, the data cannot refute an alternative model, in which native meningococcal capsule existed prior to undergoing HGT with
N. subflava and other species. Within-genus recombination events may have given rise to the diversity of meningococcal capsule serogroups.
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Affiliation(s)
| | - Odile B Harrison
- Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK
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21
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Clemence MEA, Harrison OB, Maiden MCJ. Neisseria meningitidis has acquired sequences within the capsule locus by horizontal genetic transfer. Wellcome Open Res 2019; 4:99. [DOI: 10.12688/wellcomeopenres.15333.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2019] [Indexed: 11/20/2022] Open
Abstract
Background:Expression of a capsule from one of serogroups A, B, C, W, X or Y is usually required forNeisseria meningitidis(Nme) to cause invasive meningococcal disease. The capsule is encoded by the capsule locus,cps, which is proposed to have been acquired by a formerly capsule null organism by horizontal genetic transfer (HGT) from another species. Following identification of putative capsule genes in non-pathogenicNeisseriaspecies, this hypothesis is re-examined.Methods:Whole genome sequence data fromNeisseriaspecies, includingNmegenomes from a diverse range of clonal complexes and capsule genogroups, and non-Neisseriaspecies, were obtained from PubMLST and GenBank. Sequence alignments of genes from the meningococcalcps, and predicted orthologues in other species, were analysed using Neighbor-nets, BOOTSCANing and maximum likelihood phylogenies.Results:The meningococcalcpswas highly mosaic within regions B, C and D. A subset of sequences within regions B and C were phylogenetically nested within homologous sequences belonging toN. subflava, consistent with HGT event in whichN. subflavawas the donor. In thecpsof 23/39 isolates, the two copies of region D were highly divergent, withrfbABC’sequences being more closely related to predicted orthologues in the proposed speciesN. weixii (GenBank accession numberCP023429.1) than the same genes inNmeisolates lacking a capsule. There was also evidence of mosaicism in therfbABC’sequences of the remaining 16 isolates, as well asrfbABCfrom many isolates.Conclusions:Data are consistent with theen blocacquisition ofcpsin meningococci fromN. subflava, followed by further recombination events with otherNeisseriaspecies. Nevertheless, the data cannot refute an alternative model, in which native meningococcal capsule existed prior to undergoing HGT withN. subflavaand other species. Within-genus recombination events may have given rise to the diversity of meningococcal capsule serogroups.
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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Diallo K, Coulibaly MD, Rebbetts LS, Harrison OB, Lucidarme J, Gamougam K, Tekletsion YK, Bugri A, Toure A, Issaka B, Dieng M, Trotter C, Collard JM, Sow SO, Wang X, Mayer LW, Borrow R, Greenwood BM, Maiden MCJ, Manigart O. Development of a PCR algorithm to detect and characterize Neisseria meningitidis carriage isolates in the African meningitis belt. PLoS One 2018; 13:e0206453. [PMID: 30517103 PMCID: PMC6281270 DOI: 10.1371/journal.pone.0206453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 10/12/2018] [Indexed: 12/25/2022] Open
Abstract
Improved methods for the detection and characterization of carried Neisseria meningitidis isolates are needed. We evaluated a multiplex PCR algorithm for the detection of a variety of carriage strains in the meningitis belt. To further improve the sensitivity and specificity of the existing PCR assays, primers for gel-based PCR assays (sodC, H, Z) and primers/probe for real-time quantitative PCR (qPCR) assays (porA, cnl, sodC, H, E, Z) were modified or created using Primer Express software. Optimized multiplex PCR assays were tested on 247 well-characterised carriage isolates from six countries of the African meningitis belt. The PCR algorithm developed enabled the detection of N. meningitidis species using gel-based and real-time multiplex PCR targeting porA, sodC, cnl and characterization of capsule genes through sequential multiplex PCR assays for genogroups (A, W, X, then B, C, Y and finally H, E and Z). Targeting both porA and sodC genes together allowed the detection of meningococci with a sensitivity of 96% and 89% and a specificity of 78% and 67%, for qPCR and gel-based PCR respectively. The sensitivity and specificity ranges for capsular genogrouping of N. meningitidis are 67% - 100% and 98%-100% respectively for gel-based PCR and 90%-100% and 99%-100% for qPCR. We developed a PCR algorithm that allows simple, rapid and systematic detection and characterisation of most major and minor N. meningitidis capsular groups, including uncommon capsular groups (H, E, Z).
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Affiliation(s)
- Kanny Diallo
- Centre pour le Développement des Vaccins (CVD), Bamako, Mali
- University of Oxford (Department of Zoology), Oxford, United Kingdom
| | | | - Lisa S. Rebbetts
- University of Oxford (Department of Zoology), Oxford, United Kingdom
| | - Odile B. Harrison
- University of Oxford (Department of Zoology), Oxford, United Kingdom
| | - Jay Lucidarme
- Public Health England, (PHE–Vaccine Evaluation Unit), Manchester, United Kingdom
| | - Kadidja Gamougam
- Centre de Support en Santé Internationale (CSSI), Ndjamena, Chad
| | | | - Akalifa Bugri
- Navrongo Health Research Centre (NHRC), Navrongo, Ghana
| | - Aliou Toure
- Centre pour le Développement des Vaccins (CVD), Bamako, Mali
| | - Bassira Issaka
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Marietou Dieng
- Institut de Recherche pour le Développement (IRD), Dakar, Senegal
| | - Caroline Trotter
- University of Cambridge (Disease Dynamics Unit -Department of Veterinary Medicine), Cambridge, United Kingdom
| | | | - Samba O. Sow
- Centre pour le Développement des Vaccins (CVD), Bamako, Mali
| | - Xin Wang
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Atlanta, United States of America
| | - Leonard W. Mayer
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Atlanta, United States of America
| | - Ray Borrow
- Public Health England, (PHE–Vaccine Evaluation Unit), Manchester, United Kingdom
| | - Brian M. Greenwood
- London School of Hygiene and Tropical Medicine (LSHTM), London, United Kingdom
| | | | - Olivier Manigart
- London School of Hygiene and Tropical Medicine (LSHTM), London, United Kingdom
- * E-mail:
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25
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Chen M, Rodrigues CMC, Harrison OB, Zhang C, Tan T, Chen J, Zhang X, Chen M, Maiden MCJ. Author Correction: Invasive meningococcal disease in Shanghai, China from 1950 to 2016: implications for serogroup B vaccine implementation. Sci Rep 2018; 8:13484. [PMID: 30177791 PMCID: PMC6120928 DOI: 10.1038/s41598-018-31649-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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26
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Alfsnes K, Frye SA, Eriksson J, Eldholm V, Brynildsrud OB, Bohlin J, Harrison OB, Hood DW, Maiden MCJ, Tønjum T, Ambur OH. A genomic view of experimental intraspecies and interspecies transformation of a rifampicin-resistance allele into Neisseria meningitidis. Microb Genom 2018; 4. [PMID: 30251949 PMCID: PMC6321871 DOI: 10.1099/mgen.0.000222] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The spread of antibiotic resistance within and between different bacterial populations is a major health problem on a global scale. The identification of genetic transformation in genomic data from Neisseria meningitidis, the meningococcus (Mc), and other bacteria is problematic, since similar or even identical alleles may be involved. A particular challenge in naturally transformable bacteria generally is to distinguish between common ancestry and true recombined sites in sampled genome sequences. Furthermore, the identification of recombination following experimental transformation of homologous alleles requires identifiable differences between donor and recipient, which in itself influences the propensity for homologous recombination (HR). This study identifies the distribution of HR events following intraspecies and interspecies Mc transformations of rpoB alleles encoding rifampicin resistance by whole-genome DNA sequencing and single nucleotide variant analysis. The HR events analysed were confined to the genomic region surrounding the single nucleotide genetic marker used for selection. An exponential length distribution of these recombined events was found, ranging from a few nucleotides to about 72 kb stretches. The lengths of imported sequences were on average found to be longer following experimental transformation of the recipient with genomic DNA from an intraspecies versus an interspecies donor (P<0.001). The recombination events were generally observed to be mosaic, with donor sequences interspersed with recipient sequence. Here, we present four models to explain these observations, by fragmentation of the transformed DNA, by interruptions of the recombination mechanism, by secondary recombination of endogenous self-DNA, or by repair/replication mechanisms.
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Affiliation(s)
| | - Stephan A Frye
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Jens Eriksson
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Vegard Eldholm
- 3Department of Molecular Biology, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ola Brønstad Brynildsrud
- 4Department of Methodology Research and Analysis, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jon Bohlin
- 4Department of Methodology Research and Analysis, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Odile B Harrison
- 5The Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Derek W Hood
- 6Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
| | - Martin C J Maiden
- 5The Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Tone Tønjum
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,7Department of Microbiology, University of Oslo, Oslo, Norway
| | - Ole Herman Ambur
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,8OsloMet - Oslo Metropolitan University, Oslo, Norway
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27
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Cehovin A, Harrison OB, Lewis SB, Ward PN, Ngetsa C, Graham SM, Sanders EJ, Maiden MCJ, Tang CM. Identification of Novel Neisseria gonorrhoeae Lineages Harboring Resistance Plasmids in Coastal Kenya. J Infect Dis 2018; 218:801-808. [PMID: 29701830 PMCID: PMC6057544 DOI: 10.1093/infdis/jiy240] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/20/2018] [Indexed: 11/13/2022] Open
Abstract
Background Africa has the highest incidence of gonorrhea in the world. However, little is known about gonococcal populations in this continent or mechanisms of antimicrobial resistance (AMR). Methods Whole-genome sequence data were analyzed from 103 Neisseria gonorrhoeae isolates from 73 patients, mainly men who have sex with men, from coastal Kenya. We annotated loci, defined the core genome, defined mechanisms of AMR, and performed phylogenetic analysis. For patients with multiple episodes of gonorrhea, we determined whether infections occurred with related strains. Results We identified 3 clusters of isolates that are phylogenetically distinct from isolates found elsewhere. Plasmids were virtually ubiquitous: pTetM and pblaTEM were found in 97%, and 55% of isolates, respectively. This was associated with high doxycycline use for undiagnosed sexually transmitted infections. Twenty-three percent of multiple episodes of gonorrhea in the same individual were caused by a related strain, suggesting inadequate treatment or reinfection. Conclusions The prevalence of plasmid-mediated AMR in Kenyan gonococci contrasts with that in wealthy countries, where AMR is largely chromosomally mediated. Antimicrobials have a profound effect on the maintenance of lineages harboring plasmids. Doxycycline can select for tetracycline and penicillin resistance, through plasmid cooperation. Understanding the mechanisms of AMR in high-risk groups is required to inform treatment strategies.
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Affiliation(s)
- Ana Cehovin
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
| | | | - Steven B Lewis
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
| | - Philip N Ward
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
| | - Caroline Ngetsa
- Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi, Kenya
| | - Susan M Graham
- Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi, Kenya
- University of Washington, Seattle
| | - Eduard J Sanders
- Nuffield Department of Medicine, University of Oxford, United Kingdom
- Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Global Health, University of Amsterdam, The Netherlands
| | | | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Versteeg B, Bruisten SM, Pannekoek Y, Jolley KA, Maiden MCJ, van der Ende A, Harrison OB. Genomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease. BMC Genomics 2018; 19:130. [PMID: 29426279 PMCID: PMC5810182 DOI: 10.1186/s12864-018-4522-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/31/2018] [Indexed: 12/02/2022] Open
Abstract
Background Chlamydia trachomatis (Ct) plasmid has been shown to encode genes essential for infection. We evaluated the population structure of Ct using whole-genome sequence data (WGS). In particular, the relationship between the Ct genome, plasmid and disease was investigated. Results WGS data from 157 Ct isolates deposited in the Chlamydiales pubMLST database (http://pubMLST.org/chlamydiales/) were annotated with 902 genes including the core and accessory genome. Plasmid associated genes were annotated and a plasmid MLST scheme was defined allowing plasmid sequence types to be determined. Plasmid allelic variation was investigated. Phylogenetic relationships were examined using the Genome Comparator tool available in pubMLST. Phylogenetic analyses identified four distinct Ct core genome clusters and six plasmid clusters, with a strong association between the chromosomal genotype and plasmid. This in turn was linked to ompA genovars and disease phenotype. Horizontal genetic transfer of plasmids was observed for three urogenital-associated isolates, which possessed plasmids more commonly found in isolates resulting from ocular infections. The pgp3 gene was identified as the most polymorphic plasmid gene and pgp4 was the most conserved. Conclusion A strong association between chromosomal genome, plasmid type and disease was observed, consistent with previous studies. This suggests co-evolution of the Ct chromosome and their plasmids, but we confirmed that plasmid transfer can occur between isolates. These data provide a better understanding of the genetic diversity occurring across the Ct genome in association with the plasmid content. Electronic supplementary material The online version of this article (10.1186/s12864-018-4522-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bart Versteeg
- Public Health Laboratory, Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands.
| | - Sylvia M Bruisten
- Public Health Laboratory, Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands.,Amsterdam Infection & Immunity Institute, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Yvonne Pannekoek
- Amsterdam Infection & Immunity Institute, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.,Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Keith A Jolley
- Peter Medawar building, Department of Zoology, University of Oxford, Oxford, UK
| | - Martin C J Maiden
- Peter Medawar building, Department of Zoology, University of Oxford, Oxford, UK
| | - Arie van der Ende
- Amsterdam Infection & Immunity Institute, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.,Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Odile B Harrison
- Peter Medawar building, Department of Zoology, University of Oxford, Oxford, UK
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Diallo K, Gamougam K, Daugla DM, Harrison OB, Bray JE, Caugant DA, Lucidarme J, Trotter CL, Hassan-King M, Stuart JM, Manigart O, Greenwood BM, Maiden MCJ. Hierarchical genomic analysis of carried and invasive serogroup A Neisseria meningitidis during the 2011 epidemic in Chad. BMC Genomics 2017; 18:398. [PMID: 28532434 PMCID: PMC5441073 DOI: 10.1186/s12864-017-3789-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/12/2017] [Indexed: 12/12/2022] Open
Abstract
Background Serogroup A Neisseria meningitidis (NmA) was the cause of the 2011 meningitis epidemics in Chad. This bacterium, often carried asymptomatically, is considered to be an “accidental pathogen”; however, the transition from carriage to disease phenotype remains poorly understood. This study examined the role genetic diversity might play in this transition by comparing genomes from geographically and temporally matched invasive and carried NmA isolates. Results All 23 NmA isolates belonged to the ST-5 clonal complex (cc5). Ribosomal MLST comparison with other publically available NmA:cc5 showed that isolates were closely related, although those from Chad formed two distinct branches and did not cluster with other NmA, based on their MLST profile, geographical and temporal location. Whole genome MLST (wgMLST) comparison identified 242 variable genes among all Chadian isolates and clustered them into three distinct phylogenetic groups (Clusters 1, 2, and 3): no systematic clustering by disease or carriage source was observed. There was a significant difference (p = 0.0070) between the mean age of the individuals from which isolates from Cluster 1 and Cluster 2 were obtained, irrespective of whether the person was a case or a carrier. Conclusions Whole genome sequencing provided high-resolution characterization of the genetic diversity of these closely related NmA isolates. The invasive meningococcal isolates obtained during the epidemic were not homogeneous; rather, a variety of closely related but distinct clones were circulating in the human population with some clones preferentially colonizing specific age groups, reflecting a potential age-related niche adaptation. Systematic genetic differences were not identified between carriage and disease isolates consistent with invasive meningococcal disease being a multi-factorial event resulting from changes in host-pathogen interactions along with the bacterium. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3789-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kanny Diallo
- Centre pour les Vaccins en Développement, Bamako, Mali. .,Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, OX1 3SY, Oxford, UK.
| | | | | | - Odile B Harrison
- Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, OX1 3SY, Oxford, UK
| | - James E Bray
- Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, OX1 3SY, Oxford, UK
| | | | - Jay Lucidarme
- Vaccine Evaluation Unit, Public Health England, Manchester, UK
| | - Caroline L Trotter
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - James M Stuart
- London School of Hygiene & Tropical Medicine, London, UK
| | | | | | - Martin C J Maiden
- Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, OX1 3SY, Oxford, UK
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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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Ganesh K, Allam M, Wolter N, Bratcher HB, Harrison OB, Lucidarme J, Borrow R, de Gouveia L, Meiring S, Birkhead M, Maiden MCJ, von Gottberg A, du Plessis M. Molecular characterization of invasive capsule null Neisseria meningitidis in South Africa. BMC Microbiol 2017; 17:40. [PMID: 28222677 PMCID: PMC5320719 DOI: 10.1186/s12866-017-0942-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 01/31/2017] [Indexed: 12/15/2022] Open
Abstract
Background The meningococcal capsule is an important virulence determinant. Unencapsulated meningococci lacking capsule biosynthesis genes and containing the capsule null locus (cnl) are predominantly non-pathogenic. Rare cases of invasive meningococcal disease caused by cnl isolates belonging to sequence types (ST) and clonal complexes (cc) ST-845 (cc845), ST-198 (cc198), ST-192 (cc192) and ST-53 (cc53) have been documented. The clinical significance of these isolates however remains unclear. We identified four invasive cnl meningococci through laboratory-based surveillance in South Africa from 2003 through 2013, which we aimed to characterize using whole genome data. Results One isolate [NG: P1.7-2,30: F1-2: ST-53 (cc53)] contained cnl allele 12, and caused empyema in an adult male with bronchiectasis from tuberculosis, diabetes mellitus and a smoking history. Three isolates were NG: P1.18-11,42-2: FΔ: ST-192 (cc192) and contained cnl allele 2. One patient was an adolescent male with meningitis. The remaining two isolates were from recurrent disease episodes (8 months apart) in a male child with deficiency of the sixth complement component, and with the exception of two single nucleotide polymorphisms, contained identical core genomes. The ST-53 (cc53) isolate possessed alleles for NHBA peptide 191 and fHbp variant 2; whilst the ST-192 (cc192) isolates contained NHBA peptide 704 and fHbp variant 3. All four isolates lacked nadA. Comparison of the South African genomes to 61 additional cnl genomes on the PubMLST Neisseria database (http://pubmlst.org/neisseria/), determined that most putative virulence genes could be found in both invasive and carriage phenotypes. Conclusions Although rare, invasive disease by cnl meningococci may be associated with host immunodeficiency and such patients may benefit from protein-based meningococcal vaccines. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0942-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karistha Ganesh
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa. .,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Mushal Allam
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Jay Lucidarme
- Meningococcal Reference Unit, Public Health England, Manchester Medical Microbiology Partnership, Manchester Royal Infirmary, Manchester, UK
| | - Ray Borrow
- Meningococcal Reference Unit, Public Health England, Manchester Medical Microbiology Partnership, Manchester Royal Infirmary, Manchester, UK
| | - Linda de Gouveia
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Susan Meiring
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Monica Birkhead
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Harrison OB, Cole K, Peters J, Cresswell F, Dean G, Eyre DW, Paul J, Maiden MC. Genomic analysis of urogenital and rectal Neisseria meningitidis isolates reveals encapsulated hyperinvasive meningococci and coincident multidrug-resistant gonococci. Sex Transm Infect 2017; 93:445-451. [PMID: 28137933 PMCID: PMC5574384 DOI: 10.1136/sextrans-2016-052781] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 11/11/2016] [Accepted: 12/10/2016] [Indexed: 01/30/2023] Open
Abstract
Objective Invasive meningococcal disease (IMD) outbreaks in men who have sex with men (MSM) have been associated with meningococcal colonisation of the urethra and rectum, but little is known about this colonisation or co-colonisation with the closely related gonococcus. Whole genome sequencing (WGS) was employed to explore these phenomena. Methods Meningococci isolated from the urogenital tract and rectum (n=23) and coincident gonococci (n=14) were analysed by WGS along with contemporary meningococci from IMD (n=11). All isolates were obtained from hospital admissions in Brighton, UK, 2011–2013. Assembled WGS were deposited in the PubMLST/neisseria database (http://pubmlst.org/neisseria) and compared at genomic loci common to gonococci or meningococci. Results As expected, most meningococci from IMD were encapsulated and belonged to hyperinvasive lineages. So too were meningococci found in the urogenital tract and rectum, contrasting to those asymptomatically carried in the nasopharynx where such meningococci are rare. Five hyperinvasive meningococcal lineages and four distinct gonococcal genotypes were recovered, including multiresistant ST-1901 (NG MAST-1407) gonococci. Conclusions These data were consistent with a predisposition for potentially virulent encapsulated hyperinvasive meningococci to colonise the urethra and rectum, which suggests their involvement in MSM IMD outbreaks. The coincidence of multiresistant gonococci raises wider public health concerns.
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Affiliation(s)
| | - Kevin Cole
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | - Joanna Peters
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | - Fiona Cresswell
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | - Gillian Dean
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | - David W Eyre
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - John Paul
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
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Weyand NJ, Ma M, Phifer-Rixey M, Taku NA, Rendón MA, Hockenberry AM, Kim WJ, Agellon AB, Biais N, Suzuki TA, Goodyer-Sait L, Harrison OB, Bratcher HB, Nachman MW, Maiden MCJ, So M. Isolation and characterization of Neisseria musculi sp. nov., from the wild house mouse. Int J Syst Evol Microbiol 2016; 66:3585-3593. [PMID: 27298306 PMCID: PMC5880574 DOI: 10.1099/ijsem.0.001237] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 06/10/2016] [Indexed: 12/16/2022] Open
Abstract
Members of the genus Neisseria have been isolated from or detected in a wide range of animals, from non-human primates and felids to a rodent, the guinea pig. By means of selective culture, biochemical testing, Gram staining and PCR screening for the Neisseria-specific internal transcribed spacer region of the rRNA operon, we isolated four strains of the genus Neisseria from the oral cavity of the wild house mouse, Mus musculus subsp. domesticus. The isolates are highly related and form a separate clade in the genus, as judged by tree analyses using either multi-locus sequence typing of ribosomal genes or core genes. One isolate, provisionally named Neisseria musculi sp. nov. (type strain AP2031T=DSM 101846T=CCUG 68283T=LMG 29261T), was studied further. Strain AP2031T/N. musculi grew well in vitro. It was naturally competent, taking up DNA in a DNA uptake sequence and pilT-dependent manner, and was amenable to genetic manipulation. These and other genomic attributes of N. musculi sp. nov. make it an ideal candidate for use in developing a mouse model for studying Neisseria-host interactions.
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Affiliation(s)
- Nathan J. Weyand
- Department of Immunobiology and BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA
| | - Mancheong Ma
- Department of Immunobiology and BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA
| | - Megan Phifer-Rixey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Nyiawung A. Taku
- Department of Immunobiology and BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA
| | - María A. Rendón
- Department of Immunobiology and BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA
| | - Alyson M. Hockenberry
- Department of Immunobiology and BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA
| | - Won J. Kim
- Department of Immunobiology and BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA
| | - Al B. Agellon
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Nicolas Biais
- Department of Biology, Brooklyn College of the City University of New York, Brooklyn, NY 11210, USA
| | - Taichi A. Suzuki
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | | | | | | | - Michael W. Nachman
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | | | - Magdalene So
- Department of Immunobiology and BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA
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Harrison OB, Clemence M, Dillard JP, Tang CM, Trees D, Grad YH, Maiden MCJ. Genomic analyses of Neisseria gonorrhoeae reveal an association of the gonococcal genetic island with antimicrobial resistance. J Infect 2016; 73:578-587. [PMID: 27575582 PMCID: PMC5127880 DOI: 10.1016/j.jinf.2016.08.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 08/18/2016] [Accepted: 08/20/2016] [Indexed: 02/03/2023]
Abstract
OBJECTIVES Antimicrobial resistance (AMR) threatens our ability to treat the sexually transmitted bacterial infection gonorrhoea. The increasing availability of whole genome sequence (WGS) data from Neisseria gonorrhoeae isolates, however, provides us with an opportunity in which WGS can be mined for AMR determinants. METHODS Chromosomal and plasmid genes implicated in AMR were catalogued on the PubMLST Neisseria database (http://pubmlst.org/neisseria). AMR genotypes were identified in WGS from 289 gonococci for which MICs against several antimicrobial compounds had been determined. Whole genome comparisons were undertaken using whole genome MLST (wgMLST). RESULTS Clusters of isolates with distinct AMR genotypes were apparent following wgMLST analysis consistent with the occurrence of genome wide genetic variation. This included the presence of the gonococcal genetic island (GGI), a type 4 secretion system shown to increase recombination and for which possession was significantly associated with AMR to multiple antimicrobials. CONCLUSIONS Evolution of the gonococcal genome occurs in response to antimicrobial selective pressure resulting in the formation of distinct N. gonorrhoeae populations evidenced by the wgMLST clusters seen here. Genomic islands offer selective advantages to host bacteria and possession of the GGI may, not only facilitate the spread of AMR in gonococcal populations, but may also confer fitness advantages.
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Affiliation(s)
| | | | - Joseph P Dillard
- Department of Medical Microbiology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - David Trees
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yonatan H Grad
- Harvard TH Chan School of Public Health, Boston, MA, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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Ghoul M, West SA, Johansen HK, Molin S, Harrison OB, Maiden MCJ, Jelsbak L, Bruce JB, Griffin AS. Bacteriocin-mediated competition in cystic fibrosis lung infections. Proc Biol Sci 2016; 282:rspb.2015.0972. [PMID: 26311664 DOI: 10.1098/rspb.2015.0972] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Bacteriocins are toxins produced by bacteria to kill competitors of the same species. Theory and laboratory experiments suggest that bacteriocin production and immunity play a key role in the competitive dynamics of bacterial strains. The extent to which this is the case in natural populations,especially human pathogens, remains to be tested. We examined the role of bacteriocins in competition using Pseudomonas aeruginosa strains infecting lungs of humans with cystic fibrosis (CF). We assessed the ability of different strains to kill each other using phenotypic assays, and sequenced their genomes to determine what bacteriocins (pyocins) they carry. We found that(i) isolates from later infection stages inhibited earlier infecting strains less,but were more inhibited by pyocins produced by earlier infecting strains and carried fewer pyocin types; (ii) this difference between early and late infections appears to be caused by a difference in pyocin diversity between competing genotypes and not by loss of pyocin genes within a lineage overtime; (iii) pyocin inhibition does not explain why certain strains outcompete others within lung infections; (iv) strains frequently carry the pyocin-killing gene, but not the immunity gene, suggesting resistance occurs via other unknown mechanisms. Our results show that, in contrast to patterns observed in experimental studies, pyocin production does not appear to have a major influence on strain competition during CF lung infections.
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37
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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] [What about the content of this article? (0)] [Affiliation(s)] [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. Lancet Infect Dis 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Bennett JS, Watkins ER, Jolley KA, Harrison OB, Maiden MCJ. Identifying Neisseria species by use of the 50S ribosomal protein L6 (rplF) gene. J Clin Microbiol 2014; 52:1375-81. [PMID: 24523465 PMCID: PMC3993661 DOI: 10.1128/jcm.03529-13] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/03/2014] [Indexed: 02/05/2023] Open
Abstract
The comparison of 16S rRNA gene sequences is widely used to differentiate bacteria; however, this gene can lack resolution among closely related but distinct members of the same genus. This is a problem in clinical situations in those genera, such as Neisseria, where some species are associated with disease while others are not. Here, we identified and validated an alternative genetic target common to all Neisseria species which can be readily sequenced to provide an assay that rapidly and accurately discriminates among members of the genus. Ribosomal multilocus sequence typing (rMLST) using ribosomal protein genes has been shown to unambiguously identify these bacteria. The PubMLST Neisseria database (http://pubmlst.org/neisseria/) was queried to extract the 53 ribosomal protein gene sequences from 44 genomes from diverse species. Phylogenies reconstructed from these genes were examined, and a single 413-bp fragment of the 50S ribosomal protein L6 (rplF) gene was identified which produced a phylogeny that was congruent with the phylogeny reconstructed from concatenated ribosomal protein genes. Primers that enabled the amplification and direct sequencing of the rplF gene fragment were designed to validate the assay in vitro and in silico. Allele sequences were defined for the gene fragment, associated with particular species names, and stored on the PubMLST Neisseria database, providing a curated electronic resource. This approach provides an alternative to 16S rRNA gene sequencing, which can be readily replicated for other organisms for which more resolution is required, and it has potential applications in high-resolution metagenomic studies.
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Affiliation(s)
- Julia S Bennett
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Daugla DM, Gami JP, Gamougam K, Naibei N, Mbainadji L, Narbé M, Toralta J, Kodbesse B, Ngadoua C, Coldiron ME, Fermon F, Page AL, Djingarey MH, Hugonnet S, Harrison OB, Rebbetts LS, Tekletsion Y, Watkins ER, Hill D, Caugant DA, Chandramohan D, Hassan-King M, Manigart O, Nascimento M, Woukeu A, Trotter C, Stuart JM, Maiden M, Greenwood BM. Effect of a serogroup A meningococcal conjugate vaccine (PsA-TT) on serogroup A meningococcal meningitis and carriage in Chad: a community study [corrected]. Lancet 2014; 383:40-47. [PMID: 24035220 PMCID: PMC3898950 DOI: 10.1016/s0140-6736(13)61612-8] [Citation(s) in RCA: 217] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
BACKGROUND A serogroup A meningococcal polysaccharide-tetanus toxoid conjugate vaccine (PsA-TT, MenAfriVac) was licensed in India in 2009, and pre-qualified by WHO in 2010, on the basis of its safety and immunogenicity. This vaccine is now being deployed across the African meningitis belt. We studied the effect of PsA-TT on meningococcal meningitis and carriage in Chad during a serogroup A meningococcal meningitis epidemic. METHODS We obtained data for the incidence of meningitis before and after vaccination from national records between January, 2009, and June, 2012. In 2012, surveillance was enhanced in regions where vaccination with PsA-TT had been undertaken in 2011, and in one district where a reactive vaccination campaign in response to an outbreak of meningitis was undertaken. Meningococcal carriage was studied in an age-stratified sample of residents aged 1-29 years of a rural area roughly 13-15 and 2-4 months before and 4-6 months after vaccination. Meningococci obtained from cerebrospinal fluid or oropharyngeal swabs were characterised by conventional microbiological and molecular methods. FINDINGS Roughly 1·8 million individuals aged 1-29 years received one dose of PsA-TT during a vaccination campaign in three regions of Chad in and around the capital N'Djamena during 10 days in December, 2011. The incidence of meningitis during the 2012 meningitis season in these three regions was 2·48 per 100,000 (57 cases in the 2·3 million population), whereas in regions without mass vaccination, incidence was 43·8 per 100,000 (3809 cases per 8·7 million population), a 94% difference in crude incidence (p<0·0001), and an incidence rate ratio of 0·096 (95% CI 0·046-0·198). Despite enhanced surveillance, no case of serogroup A meningococcal meningitis was reported in the three vaccinated regions. 32 serogroup A carriers were identified in 4278 age-stratified individuals (0·75%) living in a rural area near the capital 2-4 months before vaccination, whereas only one serogroup A meningococcus was isolated in 5001 people living in the same community 4-6 months after vaccination (adjusted odds ratio 0·019, 95% CI 0·002-0·138; p<0·0001). INTERPRETATION PSA-TT was highly effective at prevention of serogroup A invasive meningococcal disease and carriage in Chad. How long this protection will persist needs to be established. FUNDING The Bill & Melinda Gates Foundation, the Wellcome Trust, and Médecins Sans Frontères.
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Affiliation(s)
- D M Daugla
- Centre de Support en Santé International (CSSI), N'Djamena, Chad
| | - J P Gami
- Centre de Support en Santé International (CSSI), N'Djamena, Chad
| | - K Gamougam
- Centre de Support en Santé International (CSSI), N'Djamena, Chad
| | - N Naibei
- Centre de Support en Santé International (CSSI), N'Djamena, Chad
| | - L Mbainadji
- Centre de Support en Santé International (CSSI), N'Djamena, Chad
| | - M Narbé
- Centre de Support en Santé International (CSSI), N'Djamena, Chad
| | - J Toralta
- Centre de Support en Santé International (CSSI), N'Djamena, Chad
| | - B Kodbesse
- Centre de Support en Santé International (CSSI), N'Djamena, Chad
| | - C Ngadoua
- Ministry of Public Health, N'Djamena, Chad
| | - M E Coldiron
- Epicentre, Médecins sans Frontères, Paris, France
| | - F Fermon
- Epicentre, Médecins sans Frontères, Paris, France
| | - A-L Page
- Epicentre, Médecins sans Frontères, Paris, France
| | - M H Djingarey
- WHO Intercountry Support Team, Ougadougou, Burkina Faso
| | - S Hugonnet
- Department of Pandemic and Epidemic Diseases, WHO, Geneva, Switzerland
| | - O B Harrison
- Department of Zoology, University of Oxford, Oxford, UK
| | - L S Rebbetts
- Department of Zoology, University of Oxford, Oxford, UK
| | - Y Tekletsion
- Department of Zoology, University of Oxford, Oxford, UK
| | - E R Watkins
- Department of Zoology, University of Oxford, Oxford, UK
| | - D Hill
- Department of Zoology, University of Oxford, Oxford, UK
| | - D A Caugant
- Norwegian Institute for Public Health, Oslo, Norway
| | - D Chandramohan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - M Hassan-King
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - O Manigart
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - M Nascimento
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - A Woukeu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - C Trotter
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - J M Stuart
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - McJ Maiden
- Department of Zoology, University of Oxford, Oxford, UK
| | - B M Greenwood
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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Harrison OB, Claus H, Jiang Y, Bennett JS, Bratcher HB, Jolley KA, Corton C, Care R, Poolman JT, Zollinger WD, Frasch CE, Stephens DS, Feavers I, Frosch M, Parkhill J, Vogel U, Quail MA, Bentley SD, Maiden MCJ. Description and nomenclature of Neisseria meningitidis capsule locus. Emerg Infect Dis 2013; 19:566-73. [PMID: 23628376 PMCID: PMC3647402 DOI: 10.3201/eid1904.111799] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Pathogenic Neisseria meningitidis isolates contain a polysaccharide capsule that is the main virulence determinant for this bacterium. Thirteen capsular polysaccharides have been described, and nuclear magnetic resonance spectroscopy has enabled determination of the structure of capsular polysaccharides responsible for serogroup specificity. Molecular mechanisms involved in N. meningitidis capsule biosynthesis have also been identified, and genes involved in this process and in cell surface translocation are clustered at a single chromosomal locus termed cps. The use of multiple names for some of the genes involved in capsule synthesis, combined with the need for rapid diagnosis of serogroups commonly associated with invasive meningococcal disease, prompted a requirement for a consistent approach to the nomenclature of capsule genes. In this report, a comprehensive description of all N. meningitidis serogroups is provided, along with a proposed nomenclature, which was presented at the 2012 XVIIIth International Pathogenic Neisseria Conference.
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Harrison OB, Bennett JS, Derrick JP, Maiden MCJ, Bayliss CD. Distribution and diversity of the haemoglobin-haptoglobin iron-acquisition systems in pathogenic and non-pathogenic Neisseria. Microbiology (Reading) 2013; 159:1920-1930. [PMID: 23813677 PMCID: PMC3783016 DOI: 10.1099/mic.0.068874-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A new generation of vaccines containing multiple protein components that aim to provide broad protection against serogroup B meningococci has been developed. One candidate, 4CMenB (4 Component MenB), has been approved by the European Medicines Agency, but is predicted to provide at most 70–80 % strain coverage; hence there is a need for second-generation vaccines that achieve higher levels of coverage. Prior knowledge of the diversity of potential protein vaccine components is a key step in vaccine design. A number of iron import systems have been targeted in meningococcal vaccine development, including the HmbR and HpuAB outer-membrane proteins, which mediate the utilization of haemoglobin or haemoglobin–haptoglobin complexes as iron sources. While the genetic diversity of HmbR has been described, little is known of the diversity of HpuAB. Using whole genome sequences deposited in a Bacterial Isolate Genome Sequence Database (BIGSDB), the prevalence and diversity of HpuAB among Neisseria were investigated. HpuAB was widely present in a range of Neisseria species whereas HmbR was mainly limited to the pathogenic species Neisseria meningitidis and Neisseria gonorrhoeae. Patterns of sequence variation in sequences from HpuAB proteins were suggestive of recombination and diversifying selection consistent with strong immune selection. HpuAB was subject to repeat-mediated phase variation in pathogenic Neisseria and the closely related non-pathogenic Neisseria species Neisseria lactamica and Neisseria polysaccharea but not in the majority of other commensal Neisseria species. These findings are consistent with HpuAB being subject to frequent genetic transfer potentially limiting the efficacy of this receptor as a vaccine candidate.
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Affiliation(s)
- Odile B Harrison
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Julia S Bennett
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Jeremy P Derrick
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
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Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM, Wimalarathna H, Harrison OB, Sheppard SK, Cody AJ, Maiden MCJ. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology (Reading) 2012; 158:1005-1015. [PMID: 22282518 PMCID: PMC3492749 DOI: 10.1099/mic.0.055459-0] [Citation(s) in RCA: 376] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
No single genealogical reconstruction or typing method currently encompasses all levels of bacterial diversity, from domain to strain. We propose ribosomal multilocus sequence typing (rMLST), an approach which indexes variation of the 53 genes encoding the bacterial ribosome protein subunits (rps genes), as a means of integrating microbial genealogy and typing. As with multilocus sequence typing (MLST), rMLST employs curated reference sequences to identify gene variants efficiently and rapidly. The rps loci are ideal targets for a universal characterization scheme as they are: (i) present in all bacteria; (ii) distributed around the chromosome; and (iii) encode proteins which are under stabilizing selection for functional conservation. Collectively, the rps loci exhibit variation that resolves bacteria into groups at all taxonomic and most typing levels, providing significantly more resolution than 16S small subunit rRNA gene phylogenies. A web-accessible expandable database, comprising whole-genome data from more than 1900 bacterial isolates, including 28 draft genomes assembled de novo from the European Bioinformatics Institute (EBI) sequence read archive, has been assembled. The rps gene variation catalogued in this database permits rapid and computationally non-intensive identification of the phylogenetic position of any bacterial sequence at the domain, phylum, class, order, family, genus, species and strain levels. The groupings generated with rMLST data are consistent with current nomenclature schemes and independent of the clustering algorithm used. This approach is applicable to the other domains of life, potentially providing a rational and universal approach to the classification of life that is based on one of its fundamental features, the translation mechanism.
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Affiliation(s)
| | - Carly M Bliss
- Department of Zoology, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | - Alison J Cody
- Department of Zoology, University of Oxford, Oxford, UK
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Harrison OB, Brueggemann AB, Caugant DA, van der Ende A, Frosch M, Gray S, Heuberger S, Krizova P, Olcen P, Slack M, Taha MK, Maiden MCJ. Molecular typing methods for outbreak detection and surveillance of invasive disease caused by Neisseria meningitidis, Haemophilus influenzae and Streptococcus pneumoniae, a review. Microbiology (Reading) 2011; 157:2181-2195. [PMID: 21622526 PMCID: PMC3980633 DOI: 10.1099/mic.0.050518-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Invasive disease caused by the encapsulated bacteria Neisseria meningitidis, Haemophilus influenzae and Streptococcus pneumoniae remains an important cause of morbidity and mortality worldwide, despite the introduction of successful conjugate polysaccharide vaccines that target disease-associated strains. In addition, resistance, or more accurately reduced susceptibility, to therapeutic antibiotics is spreading in populations of these organisms. There is therefore a continuing requirement for the surveillance of vaccine and non-vaccine antigens and antibiotic susceptibilities among isolates from invasive disease, which is only partially met by conventional methods. This need can be met with molecular and especially nucleotide sequence-based typing methods, which are fully developed in the case of N. meningitidis and which could be more widely deployed in clinical laboratories for S. pneumoniae and H. influenzae.
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Affiliation(s)
- Odile B. Harrison
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | | | - Dominique A. Caugant
- Department of Bacteriology and Immunology, Norwegian Institute of Public Health, PO Box 4404 Nydalen, NO-0403 Oslo, Norway
| | - Arie van der Ende
- Academic Medical Center, Department of Medical Microbiology, Reference Laboratory for Bacterial Meningitis, PO Box 22660, 1100 DD Amsterdam, The Netherlands
| | - Matthias Frosch
- Institut für Hygiene und Mikrobiologie, Universität Würzburg, Josef-Schneider Strasse 2, 97080 Würzburg, Germany
| | - Stephen Gray
- Meningococcal Reference Unit, Health Protection Agency, PO Box 209, Clinical Sciences Building 2, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WZ, UK
| | - Sigrid Heuberger
- Österreichische Agentur für Gesundheit und Ernährungssicherheit GmbH, Bereich Humanmedizin, Institut für medizinische Mikrobiologie und Hygiene, Beethovenstraße 6, A-8010 Graz, Austria
| | - Paula Krizova
- National Reference Laboratory for Meningococcal Infections, National Institute of Public Health, Srobarova 48, Prague, Czech Republic
| | - Per Olcen
- Department of Laboratory Medicine, Clinical Microbiology and Immunology, Orebro University Hospital, SE-701 85 Orebro, Sweden
| | - Mary Slack
- Respiratory and Systemic Infection Laboratory, Health Protection Agency Centre for Infections, 61 Colindale Avenue, London NW9 5EQ, UK
| | | | - Martin C. J Maiden
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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Tauseef I, Harrison OB, Wooldridge KG, Feavers IM, Neal KR, Gray SJ, Kriz P, Turner DPJ, Ala'Aldeen DAA, Maiden MCJ, Bayliss CD, Shaw JG. Influence of the combination and phase variation status of the haemoglobin receptors HmbR and HpuAB on meningococcal virulence. Microbiology (Reading) 2011; 157:1446-1456. [PMID: 21310784 PMCID: PMC3352162 DOI: 10.1099/mic.0.046946-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Neisseria meningitidis can utilize haem, haemoglobin and haemoglobin–haptoglobin complexes as sources of iron via two TonB-dependent phase variable haemoglobin receptors, HmbR and HpuAB. HmbR is over-represented in disease isolates, suggesting a link between haemoglobin acquisition and meningococcal disease. This study compared the distribution of HpuAB and phase variation (PV) status of both receptors in disease and carriage isolates. Meningococcal disease (n = 214) and carriage (n = 305) isolates representative of multiple clonal complexes (CCs) were investigated for the distribution, polyG tract lengths and ON/OFF status of both haemoglobin receptors, and for the deletion mechanism for HpuAB. Strains with both receptors or only hmbR were present at similar frequencies among meningococcal disease isolates as compared with carriage isolates. However, >90 % of isolates from the three CCs CC5, CC8 and CC11 with the highest disease to carriage ratios contained both receptors. Strains with an hpuAB-only phenotype were under-represented among disease isolates, suggesting selection against this receptor during systemic disease, possibly due to the receptor having a high level of immunogenicity or being inefficient in acquisition of iron during systemic spread. Absence of hpuAB resulted from either complete deletion or replacement by an insertion element. In an examination of PV status, one or both receptors were found in an ON state in 91 % of disease and 71 % of carriage isolates. We suggest that expression of a haemoglobin receptor, either HmbR or HpuAB, is of major importance for systemic spread of meningococci, and that the presence of both receptors contributes to virulence in some strains.
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Affiliation(s)
- Isfahan Tauseef
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Odile B Harrison
- The Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Karl G Wooldridge
- Molecular Bacteriology and Immunology Group, University of Nottingham, Nottingham, UK
| | - Ian M Feavers
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Hertfordshire EN6 3QG, UK
| | - Keith R Neal
- School of Community Health Sciences, University of Nottingham, Nottingham, UK
| | - Stephen J Gray
- Health Protection Agency, Meningococcal Reference Unit, Manchester Royal Infirmary, Manchester M13 9WL, UK
| | - Paula Kriz
- National Reference Laboratory for Meningococcal Infections, National Institute of Public Health, Prague, Czech Republic
| | - David P J Turner
- Molecular Bacteriology and Immunology Group, University of Nottingham, Nottingham, UK
| | - Dlawer A A Ala'Aldeen
- Molecular Bacteriology and Immunology Group, University of Nottingham, Nottingham, UK
| | - Martin C J Maiden
- The Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
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Aspholm M, Aas FE, Harrison OB, Quinn D, Vik Å, Viburiene R, Tønjum T, Moir J, Maiden MCJ, Koomey M. Structural alterations in a component of cytochrome c oxidase and molecular evolution of pathogenic Neisseria in humans. PLoS Pathog 2010; 6:e1001055. [PMID: 20808844 PMCID: PMC2924362 DOI: 10.1371/journal.ppat.1001055] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 07/21/2010] [Indexed: 12/26/2022] Open
Abstract
Three closely related bacterial species within the genus Neisseria are of importance to human disease and health. Neisseria meningitidis is a major cause of meningitis, while Neisseria gonorrhoeae is the agent of the sexually transmitted disease gonorrhea and Neisseria lactamica is a common, harmless commensal of children. Comparative genomics have yet to yield clear insights into which factors dictate the unique host-parasite relationships exhibited by each since, as a group, they display remarkable conservation at the levels of nucleotide sequence, gene content and synteny. Here, we discovered two rare alterations in the gene encoding the CcoP protein component of cytochrome cbb3 oxidase that are phylogenetically informative. One is a single nucleotide polymorphism resulting in CcoP truncation that acts as a molecular signature for the species N. meningitidis. We go on to show that the ancestral ccoP gene arose by a unique gene duplication and fusion event and is specifically and completely distributed within species of the genus Neisseria. Surprisingly, we found that strains engineered to express either of the two CcoP forms conditionally differed in their capacity to support nitrite-dependent, microaerobic growth mediated by NirK, a nitrite reductase. Thus, we propose that changes in CcoP domain architecture and ensuing alterations in function are key traits in successive, adaptive radiations within these metapopulations. These findings provide a dramatic example of how rare changes in core metabolic proteins can be connected to significant macroevolutionary shifts. They also show how evolutionary change at the molecular level can be linked to metabolic innovation and its reversal as well as demonstrating how genotype can be used to infer alterations of the fitness landscape within a single host. The closely related bacterial species N. meningitidis, N. gonorrhoeae and N. lactamica exclusively colonise mucosal surfaces in humans. While N. gonorrhoeae leads to gonorrhea, the other two species persist mainly in their host in the absence of disease. N. meningitidis does occasionally cause severe, life threatening illness, however. Little is known about the factors and elements that dictate the unique human interactions exhibited by each species. Moreover, the evolutionary relationships between these species are poorly characterized. Here, we describe two successive alterations in a single gene that can be linked first to all species within the genus Neisseria and then the species N. meningitidis. We also show these signature alterations have phenotypic consequences by affecting core respiratory metabolic processes. These findings have significant implications for the evolution of related bacterial species within a single host and provide a novel perspective on the episodic and reversible nature of innovative adaptation.
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Affiliation(s)
- Marina Aspholm
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
| | - Finn Erik Aas
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
| | | | - Diana Quinn
- Department of Biology (Area 10), University of York, Heslington, York, United Kingdom
| | - Åshild Vik
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
| | - Raimonda Viburiene
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
- Institute of Microbiology, University of Oslo, Oslo, Norway
| | - James Moir
- Department of Biology (Area 10), University of York, Heslington, York, United Kingdom
| | | | - Michael Koomey
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
- * E-mail:
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Evans NJ, Harrison OB, Clow K, Derrick JP, Feavers IM, Maiden MCJ. Variation and molecular evolution of HmbR, the Neisseria meningitidis haemoglobin receptor. Microbiology (Reading) 2010; 156:1384-1393. [PMID: 20150237 PMCID: PMC3068627 DOI: 10.1099/mic.0.036475-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Meningococcal disease caused by serogroup B Neisseria meningitidis remains an important health problem in many parts of the world, and there are currently no comprehensive vaccines. Poor immunogenicity, combined with immunological identity to human sialic acids, have hindered the development of a serogroup B conjugate vaccine, resulting in the development of alternative vaccine candidates, including many outer-membrane protein (OMP)-based formulations. However, the design of protein-based meningococcal vaccines is complicated by the high level of genetic and antigenic diversity of the meningococcus. Knowledge of the extent and structuring of this diversity can have implications for the use of particular proteins as potential vaccine candidates. With this in mind, the diversity of the meningococcal OMP HmbR was investigated among N. meningitidis isolates representative of major hyper-invasive lineages. In common with other meningococcal antigens, the genetic diversity of hmbR resulted from a combination of intraspecies horizontal genetic exchange and de novo mutation. Furthermore, genealogical analysis showed an association of hmbR genes with clonal complexes and the occurrence of two hmbR families, A and B. Three variable regions (VR1–VR3), located in loops 2, 3 and 4, were observed with clonal complex structuring of VR types. A minority of codons (3.9 %), located within putative surface-exposed loop regions of a 2D model, were under diversifying selection, indicating regions of the protein likely to be subject to immune attack.
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Affiliation(s)
- Nicholas J. Evans
- Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Odile B. Harrison
- The Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Kirsten Clow
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Jeremy P. Derrick
- Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Ian M. Feavers
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Martin C. J. Maiden
- The Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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Harrison OB, Evans NJ, Blair JM, Grimes HS, Tinsley CR, Nassif X, Kriz P, Ure R, Gray SJ, Derrick JP, Maiden MCJ, Feavers IM. Epidemiological evidence for the role of the hemoglobin receptor, hmbR, in meningococcal virulence. J Infect Dis 2009; 200:94-8. [PMID: 19476432 DOI: 10.1086/599377] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The distribution of the hemoglobin receptor gene (hmbR) was investigated among disease and carriage Neisseria meningitidis isolates, revealing that the gene was detected at a significantly higher frequency among disease isolates than among carriage isolates. In isolates without hmbR, the locus was occupied by the cassettes exl2 or exl3 or by a "pseudo hmbR" gene, designated exl4. The hmbR locus exhibited characteristics of a pathogenicity island in published genomes of N. meningitidis, Neisseria gonorrhoeae, and Neisseria lactamica sequence type-640. These data are consistent with a role for the hmbR gene in meningococcal disease.
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Affiliation(s)
- Odile B Harrison
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Harrison OB, Maiden MCJ, Rokbi B. Distribution of transferrin binding protein B gene (tbpB) variants among Neisseria species. BMC Microbiol 2008; 8:66. [PMID: 18430216 PMCID: PMC2386816 DOI: 10.1186/1471-2180-8-66] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Accepted: 04/22/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transferrin binding protein B (tbpB), an outer membrane lipoprotein, is required for the acquisition of iron from human transferrin. Two tbpB families have been documented in Neisseria meningitidis: an isotype I tbpB gene of 1.8 kb and an isotype II tbpB gene of 2.1 kb, the former expressed by meningococci in the disease-associated ST-11 clonal complex and the latter found among meningococci belonging to the hyper-invasive clonal complexes including ST-8, ST-18, ST-32, ST-41/44 as well as N. gonorrhoeae isolates. The origin of the isotype I tbpB gene is unknown, however several features in common with non-pathogenic Neisseria and the ST-11 clonal complex N. meningitidis isolate FAM18 have been documented leading to the hypothesis that the isotype I tbpB gene may also be shared between non-pathogenic Neisseria and ST-11 meningococci. As a result, the diversity of the tbpB gene was investigated in a defined collection of Neisseria species. RESULTS Two families of isotype I tbpB were identified: family A containing conserved genes belonging to ST-11 meningococci, N. polysaccharea and N. lactamica isolates and family B including more diverse isotype I tbpB genes from N. sicca, N. mucosa, N. flava, N. subflava as well as N. cinerea, N. flavescens and N. polysaccharea isolates. Three isotype II tbpB families were identified with: family C containing diverse tbpB genes belonging to N. polysaccharea, N. lactamica, N. gonorrhoeae and N. meningitidis isolates, family D including another subset of isotype II tbpB genes from N. lactamica isolates and family E solely composed of N. gonorrhoeae tbpB genes. CONCLUSION This study reveals another instance of similarity between meningococci of the ST-11 clonal complex and non-pathogenic Neisseria with the origin of the isotype I tbpB gene resulting from a horizontal genetic transfer event occurring between these two populations.
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Affiliation(s)
- Odile B Harrison
- The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK.
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Harrison OB, Robertson BD, Faust SN, Jepson MA, Goldin RD, Levin M, Heyderman RS. Analysis of pathogen-host cell interactions in purpura fulminans: expression of capsule, type IV pili, and PorA by Neisseria meningitidis in vivo. Infect Immun 2002; 70:5193-201. [PMID: 12183570 PMCID: PMC128269 DOI: 10.1128/iai.70.9.5193-5201.2002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pattern of meningococcal surface structure expression in different microenvironments following bloodstream invasion in vivo is not known. We used immunohistochemistry to determine the expression of capsule, type IV pili, and PorA by meningococci residing in the skin lesions of children with purpura fulminans. All the skin biopsy samples showed evidence of thrombosis and, frequently, a perivascular inflammatory cell infiltrate consisting of neutrophils (elastase positive) and monocytes/macrophages (CD68 positive). Modified Gram staining revealed 20 to over 100 gram-negative diplococci in each 4-microm-thick section, usually grouped into microcolonies. Immunoperoxidase staining demonstrated that the invading meningococci expressed PorA, capsule, and type IV pilin. Expression of these antigens was not restricted to any particular environment and was found in association with meningococci located in leukocytes, small blood vessels, and the dermal interstitium. Confocal laser scanning microscopy demonstrated coexpression of pilin and capsule by numerous microcolonies. However, there was some discordance in capsule and pilin expression within the microcolonies, suggesting phase variation. The strategy employed in this study will be helpful in investigating invasive bacterial diseases where antigenic and phase variation has a significant impact on virulence and on vaccine design.
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Affiliation(s)
- O B Harrison
- Infectious Diseases & Microbiology, Faculty of Medicine, Imperial College, London, United Kingdom
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