Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 27, Number 4—April 2021
Research

Genomic Surveillance of a Globally Circulating Distinct Group W Clonal Complex 11 Meningococcal Variant, New Zealand, 2013–2018

Zuyu Yang1, Xiaoyun Ren1, Heather Davies, Timothy Wood, Liza Lopez, Jill Sherwood, Audrey Tiong, and Philip E. CarterComments to Author 
Author affiliation: Institute of Environmental Science and Research, Porirua, New Zealand

Main Article

Figure 3

Phylogenetic analysis of New Zealand Neisseria meningitidis isolates, 2013–2018. Maximum-likelihood phylogeny was constructed by using a generalized time reversible substitution model and core single-nucleotide polymorphism alignments with RAxML version 8.2.12 (33). Branches with >90% bootstrap consensus (200 bootstrap replications) are highlighted with a red dot. Isolate names and clades are colored according to their clonal complex designation. The inner ring indicates the group and outer ring designates the year of isolation of the isolates. N1 lineage corresponds to sequence type that does not have clonal complex designation. NA corresponds to individual isolates where clonal complex is not assigned. Scale bar indicates average number of substitutions per site.

Figure 3. Phylogenetic analysis of New Zealand Neisseria meningitidis isolates, 2013–2018. Maximum-likelihood phylogeny was constructed by using a generalized time reversible substitution model and core single-nucleotide polymorphism alignments with RAxML version 8.2.12 (33). Branches with >90% bootstrap consensus (200 bootstrap replications) are highlighted with a red dot. Isolate names and clades are colored according to their clonal complex designation. The inner ring indicates the group and outer ring designates the year of isolation of the isolates. N1 lineage corresponds to sequence type that does not have clonal complex designation. NA corresponds to individual isolates where clonal complex is not assigned. Scale bar indicates average number of substitutions per site.

Main Article

References
  1. Halperin  SA, Bettinger  JA, Greenwood  B, Harrison  LH, Jelfs  J, Ladhani  SN, et al. The changing and dynamic epidemiology of meningococcal disease. Vaccine. 2012;30(Suppl 2):B26–36. DOIPubMedGoogle Scholar
  2. Harrison  LH, Trotter  CL, Ramsay  ME. Global epidemiology of meningococcal disease. Vaccine. 2009;27(Suppl 2):B51–63. DOIPubMedGoogle Scholar
  3. Maiden  MCJ, Bygraves  JA, Feil  E, Morelli  G, Russell  JE, Urwin  R, et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A. 1998;95:3140–5. DOIPubMedGoogle Scholar
  4. Waśko  I, Hryniewicz  W, Skoczyńska  A. Significance of meningococcal hyperinvasive clonal complexes and their influence on vaccines development. Pol J Microbiol. 2015;64:313–21. DOIPubMedGoogle Scholar
  5. Mustapha  MM, Marsh  JW, Krauland  MG, Fernandez  JO, de Lemos  APS, Dunning Hotopp  JC, et al. Genomic epidemiology of hypervirulent serogroup W, ST-11 Neisseria meningitidis. EBioMedicine. 2015;2:1447–55. DOIPubMedGoogle Scholar
  6. Ladhani  SN, Beebeejaun  K, Lucidarme  J, Campbell  H, Gray  S, Kaczmarski  E, et al. Increase in endemic Neisseria meningitidis capsular group W sequence type 11 complex associated with severe invasive disease in England and Wales. Clin Infect Dis. 2015;60:578–85. DOIPubMedGoogle Scholar
  7. Eriksson  L, Hedberg  ST, Jacobsson  S, Fredlund  H, Mölling  P, Stenmark  B. Whole-genome sequencing of emerging invasive Neisseria meningitidis serogroup W in Sweden. J Clin Microbiol. 2018;56:e01409–17. DOIPubMedGoogle Scholar
  8. Martin  NV, Ong  KS, Howden  BP, Lahra  MM, Lambert  SB, Beard  FH, et al.; Communicable Diseases Network Australia MenW Working Group. Rise in invasive serogroup W meningococcal disease in Australia 2013-2015. Commun Dis Intell Q Rep. 2016;40:E454–9.PubMedGoogle Scholar
  9. Tsang  RSW, Ahmad  T, Tyler  S, Lefebvre  B, Deeks  SL, Gilca  R, et al. Whole genome typing of the recently emerged Canadian serogroup W Neisseria meningitidis sequence type 11 clonal complex isolates associated with invasive meningococcal disease. Int J Infect Dis. 2018;69:55–62. DOIPubMedGoogle Scholar
  10. Potts  CC, Joseph  SJ, Chang  HY, Chen  A, Vuong  J, Hu  F, et al. Population structure of invasive Neisseria meningitidis in the United States, 2011-15. J Infect. 2018;77:427–34. DOIPubMedGoogle Scholar
  11. Lucidarme  J, Hill  DMC, Bratcher  HB, Gray  SJ, du Plessis  M, Tsang  RSW, et al. Genomic resolution of an aggressive, widespread, diverse and expanding meningococcal serogroup B, C and W lineage. J Infect. 2015;71:544–52. DOIPubMedGoogle Scholar
  12. Taha  MK, Achtman  M, Alonso  JM, Greenwood  B, Ramsay  M, Fox  A, et al. Serogroup W135 meningococcal disease in Hajj pilgrims. Lancet. 2000;356:2159. DOIPubMedGoogle Scholar
  13. Weidlich  L, Baethgen  LF, Mayer  LW, Moraes  C, Klein  CC, Nunes  LS, et al. High prevalence of Neisseria meningitidis hypervirulent lineages and emergence of W135:P1.5,2:ST-11 clone in Southern Brazil. J Infect. 2008;57:324–31. DOIPubMedGoogle Scholar
  14. Lucidarme  J, Scott  KJ, Ure  R, Smith  A, Lindsay  D, Stenmark  B, et al. An international invasive meningococcal disease outbreak due to a novel and rapidly expanding serogroup W strain, Scotland and Sweden, July to August 2015. Euro Surveill. 2016;21:15–23. DOIPubMedGoogle Scholar
  15. Krone  M, Gray  S, Abad  R, Skoczyńska  A, Stefanelli  P, van der Ende  A, et al. Increase of invasive meningococcal serogroup W disease in Europe, 2013 to 2017. Euro Surveill. 2019;24:24. DOIPubMedGoogle Scholar
  16. Devoy  AF, Dyet  KH, Martin  DR. Stability of PorA during a meningococcal disease epidemic. J Clin Microbiol. 2005;43:832–7. DOIPubMedGoogle Scholar
  17. Dyet  KH, Martin  DR. Clonal analysis of the serogroup B meningococci causing New Zealand’s epidemic. Epidemiol Infect. 2006;134:377–83. DOIPubMedGoogle Scholar
  18. Sexton  K, Lennon  D, Oster  P, Crengle  S, Martin  D, Mulholland  K, et al. The New Zealand Meningococcal Vaccine Strategy: a tailor-made vaccine to combat a devastating epidemic. N Z Med J. 2004;117:U1015.PubMedGoogle Scholar
  19. Loring  BJ, Turner  N, Petousis-Harris  H. MeNZB vaccine and epidemic control: when do you stop vaccinating? Vaccine. 2008;26:5899–904. DOIPubMedGoogle Scholar
  20. Institute of Environmental Science and Research Limited. Notifiable Diseases in New Zealand: Annual Report 2016. Porirua, New Zealand [cited 2020 Nov 3]. https://surv.esr.cri.nz/surveillance/annual_surveillance.php?we_objectID=4656
  21. Bennett  DE, Cafferkey  MT. Consecutive use of two multiplex PCR-based assays for simultaneous identification and determination of capsular status of nine common Neisseria meningitidis serogroups associated with invasive disease. J Clin Microbiol. 2006;44:1127–31. DOIPubMedGoogle Scholar
  22. Oksanen  G, Blanchet  FG, Friendly  M, Kindt  R, Legendre  P, McGlinn  D, et al. Vegan: community ecology package [cited 2020 Nov 3]. https://CRAN.R-project.org/package=vegan
  23. Bolger  AM, Lohse  M, Usadel  B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20. DOIPubMedGoogle Scholar
  24. Bankevich  A, Nurk  S, Antipov  D, Gurevich  AA, Dvorkin  M, Kulikov  AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77. DOIPubMedGoogle Scholar
  25. Kwong  JC, Gonçalves da Silva  A, Stinear  TP, Howden  BP, Seemann  T. Meningotype: [cited 2020 Nov 3]. https://github.com/MDU-PHL/meningotype
  26. Langmead  B, Trapnell  C, Pop  M, Salzberg  SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25. DOIPubMedGoogle Scholar
  27. Picard toolkit. 2019 [cited 2020 Nov 3]. http://broadinstitute.github.io/picard
  28. Okonechnikov  K, Conesa  A, García-Alcalde  F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. 2016;32:292–4.PubMedGoogle Scholar
  29. Garrison  E. Vcflib [cited 2020 Nov 3]. https://github.com/vcflib/vcflib
  30. Danecek  P, Auton  A, Abecasis  G, Albers  CA, Banks  E, DePristo  MA, et al.; 1000 Genomes Project Analysis Group. The variant call format and VCFtools. Bioinformatics. 2011;27:2156–8. DOIPubMedGoogle Scholar
  31. Quinlan  AR, Hall  IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–2. DOIPubMedGoogle Scholar
  32. Treangen  TJ, Ondov  BD, Koren  S, Phillippy  AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol. 2014;15:524. DOIPubMedGoogle Scholar
  33. Stamatakis  A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3. DOIPubMedGoogle Scholar
  34. Felsenstein  J. Confidence-limits on phylogenies—an approach using the bootstrap. Evolution. 1985;39:783–91. DOIPubMedGoogle Scholar
  35. Didelot  X, Wilson  DJ. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLOS Comput Biol. 2015;11:e1004041. DOIPubMedGoogle Scholar
  36. Letunic  I, Bork  P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44(W1):W242-5. DOIPubMedGoogle Scholar
  37. Jolley  KA, Bray  JE, Maiden  MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 2018;3:124. DOIPubMedGoogle Scholar
  38. Bratcher  HB, Corton  C, Jolley  KA, Parkhill  J, Maiden  MC. A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. BMC Genomics. 2014;15:1138. DOIPubMedGoogle Scholar
  39. Clinical and Laboratory Standards Institute. Performance standards for antimicrobial susceptibility testing: 28th edition (informational supplement M100). Wayne (PA): The Institute; 2018.
  40. Zeileis  A, Leisch  F, Hornik  K, Kleiber  C, Hansen  B, Zeileis  MA. Package ‘strucchange’ [cited 2020 Nov 3]. https://CRAN.R-project.org/package=strucchange
  41. Mowlaboccus  S, Jolley  KA, Bray  JE, Pang  S, Lee  YT, Bew  JD, et al. Clonal expansion of new penicillin-resistant clade of Neisseria meningitidis serogroup W clonal complex 11, Australia. Emerg Infect Dis. 2017;23:1364–7. DOIPubMedGoogle Scholar
  42. Whaley  MJ, Joseph  SJ, Retchless  AC, Kretz  CB, Blain  A, Hu  F, et al. Whole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis. Sci Rep. 2018;8:15803. DOIPubMedGoogle Scholar
  43. Public Health England. Invasive meningococcal disease in England: annual laboratory confirmed reports for epidemiological year 2017 to 2018. London: Public Health England; 2018 [cited 2020 Nov 3]. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/751821/hpr3818_IMD.pdf
  44. Knol  MJ, de Melker  HE, Berbers  GAM, van Ravenhorst  MB, Ruijs  WLM, van Vliet  JA. Meningococcal disease in the Netherlands: background information for the Health Council. RIVM Report 2017–0031. 2017 [cited 2020 Nov 03]. https://www.rivm.nl/bibliotheek/rapporten/2017-0031.pdf
  45. Knol  MJ, Hahné  SJM, Lucidarme  J, Campbell  H, de Melker  HE, Gray  SJ, et al. Temporal associations between national outbreaks of meningococcal serogroup W and C disease in the Netherlands and England: an observational cohort study. Lancet Public Health. 2017;2:e473–82. DOIPubMedGoogle Scholar
  46. Leimkugel  J, Racloz  V, Jacintho da Silva  L, Pluschke  G. Global review of meningococcal disease. A shifting etiology. J Bacterial Res. 2009;1:6–18.
  47. Bröker  M, Jacobsson  S, Kuusi  M, Pace  D, Simões  MJ, Skoczynska  A, et al. Meningococcal serogroup Y emergence in Europe: update 2011. Hum Vaccin Immunother. 2012;8:1907–11. DOIPubMedGoogle Scholar
  48. Ministry of Health Manatū Hauora. Change to treatment recommendations for meningococcal disease. 2018 Nov 30 [cited 2020 Nov 3]. https://www.health.govt.nz/news-media/news-items/change-treatment-recommendations-meningococcal-disease

Main Article

1These authors contributed equally to this article.

Page created: February 17, 2021
Page updated: March 18, 2021
Page reviewed: March 18, 2021
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external