Evidence map›Paper›PMID 31133745›Full record

ArticleNature genetics2019

Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.

Mark R Davies, Liam McIntyre, Ankur Mutreja, Jake A Lacey, John A Lees, Rebecca J Towers, Sebastián Duchêne, Pierre R Smeesters, Hannah R Frost, David J Price and 28 more

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 133 papers.

0numbers the graph read from it
0cells of the map it votes in
133citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

133 citing papers in PubMed.

  1. Review
  2. Article
  3. Genomic analysis and clinical characteristics of a seasonal upsurge of Streptococcus pyogenes emm12.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026
    Article
  4. Observational
  5. Article
  6. Review
  7. Article
  8. Review
  9. Review
  10. Identification of immunostimulatory antigens in Group AProceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  11. Article
  12. Review
  13. Article
  14. Article
  15. Article
  16. Article
  17. Review
  18. Beyond theMicrobiology spectrum · 2026
    Article
  19. Review
  20. Article

73 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

38 authors.

Mark R DaviesDepartment of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia. mark.davies1@unimelb.edu.au.ORCID http://orcid.org/0000-0001-6141-5179
Liam McIntyreDepartment of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia.
Ankur MutrejaThe Wellcome Trust Sanger Institute, Hinxton, UK.
Jake A LaceyDoherty Department, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia.
John A LeesDepartment of Microbiology, New York University School of Medicine, New York, NY, USA.
Rebecca J TowersMenzies School of Health Research, Darwin, Northern Territory, Australia.
Sebastián DuchêneDepartment of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia.
Pierre R SmeestersMolecular Bacteriology Laboratory, Université Libre de Bruxelles, Brussels, Belgium.
Hannah R FrostMolecular Bacteriology Laboratory, Université Libre de Bruxelles, Brussels, Belgium.ORCID http://orcid.org/0000-0002-1543-2805
David J PriceCentre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia.ORCID http://orcid.org/0000-0003-0076-3123
Matthew T G HoldenThe Wellcome Trust Sanger Institute, Hinxton, UK.ORCID http://orcid.org/0000-0002-4958-2166
Sophia DavidThe Wellcome Trust Sanger Institute, Hinxton, UK.
Philip M GiffardMenzies School of Health Research, Darwin, Northern Territory, Australia.
Kate A WorthingDepartment of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia.
Anna C SealeWellcome Trust Research Centre, Kilifi, Kenya.
James A BerkleyCentre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-1236-849X
Simon R HarrisThe Wellcome Trust Sanger Institute, Hinxton, UK.
Tania Rivera-HernandezSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
Olga BerkingSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
Amanda J CorkSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
Rosângela S L A TorresLaboratory of Bacteriology, Epidemiology Laboratory and Disease Control Division, Laboratório Central do Estado do Paraná, Curitiba, Brazil.
Trevor LithgowInfection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia.
Richard A StrugnellDepartment of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia.ORCID http://orcid.org/0000-0003-0614-5641
Rene BergmannHelmholtz Centre for Infection Research, Braunschweig, Germany.
Patric Nitsche-SchmitzHelmholtz Centre for Infection Research, Braunschweig, Germany.
Gusharan S ChhatwalHelmholtz Centre for Infection Research, Braunschweig, Germany.
Stephen D BentleyThe Wellcome Trust Sanger Institute, Hinxton, UK.
John D FraserFaculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
Nicole J MorelandFaculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
Jonathan R CarapetisTelethon Kids Institute, University of Western Australia and Perth Children's Hospital, Perth, Western Australia, Australia.
Andrew C SteerMurdoch Childrens Research Institute, Melbourne, Victoria, Australia.
Julian ParkhillThe Wellcome Trust Sanger Institute, Hinxton, UK.ORCID http://orcid.org/0000-0002-7069-5958
Allan SaulGSK Vaccines Institute for Global Health, Siena, Italy.
Deborah A WilliamsonMicrobiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia.
Bart J CurrieMenzies School of Health Research, Darwin, Northern Territory, Australia.
Steven Y C TongDoherty Department, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia.
Gordon DouganThe Wellcome Trust Sanger Institute, Hinxton, UK.
Mark J WalkerSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia. mark.walker@uq.edu.au.ORCID http://orcid.org/0000-0001-7423-2769

Funding

Medical Research Council MR/R015600/1Wellcome Trust 098051Wellcome Trust 206194
6 · The paper itself

Abstract

Group A Streptococcus (GAS; Streptococcus pyogenes) is a bacterial pathogen for which a commercial vaccine for humans is not available. Employing the advantages of high-throughput DNA sequencing technology to vaccine design, we have analyzed 2,083 globally sampled GAS genomes. The global GAS population structure reveals extensive genomic heterogeneity driven by homologous recombination and overlaid with high levels of accessory gene plasticity. We identified the existence of more than 290 clinically associated genomic phylogroups across 22 countries, highlighting challenges in designing vaccines of global utility. To determine vaccine candidate coverage, we investigated all of the previously described GAS candidate antigens for gene carriage and gene sequence heterogeneity. Only 15 of 28 vaccine antigen candidates were found to have both low naturally occurring sequence variation and high (>99%) coverage across this diverse GAS population. This technological platform for vaccine coverage determination is equally applicable to prospective GAS vaccine antigens identified in future studies.

Indexed as

GenomicsAntigens, BacterialGenome, BacterialGenome-Wide Association StudyHumansPhylogenyRecombination, GeneticStreptococcal InfectionsStreptococcal VaccinesStreptococcus pyogenesAntigens, BacterialStreptococcal Vaccines

Identifiers

PMID31133745
PMCPMC6650292

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.