IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-43160-y.html
   My bibliography  Save this article

The metabolic, virulence and antimicrobial resistance profiles of colonising Streptococcus pneumoniae shift after PCV13 introduction in urban Malawi

Author

Listed:
  • Uri Obolski

    (Tel Aviv University
    Tel Aviv University)

  • Todd D. Swarthout

    (Malawi Liverpool Wellcome Programme
    University College London
    University Medical Center Utrecht)

  • Akuzike Kalizang’oma

    (Malawi Liverpool Wellcome Programme
    University College London)

  • Thandie S. Mwalukomo

    (Kamuzu University of Health Sciences)

  • Jia Mun Chan

    (University College London)

  • Caroline M. Weight

    (University College London
    Lancaster University
    Lancaster University)

  • Comfort Brown

    (Malawi Liverpool Wellcome Programme)

  • Rory Cave

    (University College London)

  • Jen Cornick

    (Malawi Liverpool Wellcome Programme
    University of Liverpool)

  • Arox Wadson Kamng’ona

    (Kamuzu University of Health Sciences)

  • Jacquline Msefula

    (Kamuzu University of Health Sciences)

  • Giuseppe Ercoli

    (University College London)

  • Jeremy S. Brown

    (University College London)

  • José Lourenço

    (University of Oxford
    Biomedical Research Centre)

  • Martin C. Maiden

    (University of Oxford)

  • Neil French

    (University of Liverpool)

  • Sunetra Gupta

    (University of Oxford)

  • Robert S. Heyderman

    (Malawi Liverpool Wellcome Programme
    University College London)

Abstract

Streptococcus pneumoniae causes substantial mortality among children under 5-years-old worldwide. Polysaccharide conjugate vaccines (PCVs) are highly effective at reducing vaccine serotype disease, but emergence of non-vaccine serotypes and persistent nasopharyngeal carriage threaten this success. We investigated the hypothesis that following vaccine, adapted pneumococcal genotypes emerge with the potential for vaccine escape. We genome sequenced 2804 penumococcal isolates, collected 4-8 years after introduction of PCV13 in Blantyre, Malawi. We developed a pipeline to cluster the pneumococcal population based on metabolic core genes into “Metabolic genotypes” (MTs). We show that S. pneumoniae population genetics are characterised by emergence of MTs with distinct virulence and antimicrobial resistance (AMR) profiles. Preliminary in vitro and murine experiments revealed that representative isolates from emerging MTs differed in growth, haemolytic, epithelial infection, and murine colonisation characteristics. Our results suggest that in the context of PCV13 introduction, pneumococcal population dynamics had shifted, a phenomenon that could further undermine vaccine control and promote spread of AMR.

Suggested Citation

  • Uri Obolski & Todd D. Swarthout & Akuzike Kalizang’oma & Thandie S. Mwalukomo & Jia Mun Chan & Caroline M. Weight & Comfort Brown & Rory Cave & Jen Cornick & Arox Wadson Kamng’ona & Jacquline Msefula , 2023. "The metabolic, virulence and antimicrobial resistance profiles of colonising Streptococcus pneumoniae shift after PCV13 introduction in urban Malawi," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43160-y
    DOI: 10.1038/s41467-023-43160-y
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-43160-y
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-43160-y?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Nicholas J. Croucher & Paul G. Coupland & Abbie E. Stevenson & Alanna Callendrello & Stephen D. Bentley & William P. Hanage, 2014. "Diversification of bacterial genome content through distinct mechanisms over different timescales," Nature Communications, Nature, vol. 5(1), pages 1-12, December.
    2. Todd D. Swarthout & Claudio Fronterre & José Lourenço & Uri Obolski & Andrea Gori & Naor Bar-Zeev & Dean Everett & Arox W. Kamng’ona & Thandie S. Mwalukomo & Andrew A. Mataya & Charles Mwansambo & Mar, 2020. "High residual carriage of vaccine-serotype Streptococcus pneumoniae after introduction of pneumococcal conjugate vaccine in Malawi," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    3. Caroline M. Weight & Cristina Venturini & Sherin Pojar & Simon P. Jochems & Jesús Reiné & Elissavet Nikolaou & Carla Solórzano & Mahdad Noursadeghi & Jeremy S. Brown & Daniela M. Ferreira & Robert S. , 2019. "Microinvasion by Streptococcus pneumoniae induces epithelial innate immunity during colonisation at the human mucosal surface," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
    4. Nicholas J Croucher & Lisa Kagedan & Claudette M Thompson & Julian Parkhill & Stephen D Bentley & Jonathan A Finkelstein & Marc Lipsitch & William P Hanage, 2015. "Selective and Genetic Constraints on Pneumococcal Serotype Switching," PLOS Genetics, Public Library of Science, vol. 11(3), pages 1-21, March.
    5. Evelyn Balsells & Laurence Guillot & Harish Nair & Moe H Kyaw, 2017. "Serotype distribution of Streptococcus pneumoniae causing invasive disease in children in the post-PCV era: A systematic review and meta-analysis," PLOS ONE, Public Library of Science, vol. 12(5), pages 1-20, May.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Deus Thindwa & Samuel Clifford & Jackie Kleynhans & Anne Gottberg & Sibongile Walaza & Susan Meiring & Todd D. Swarthout & Elizabeth Miller & Peter McIntyre & Nick Andrews & Zahin Amin-Chowdhury & Nor, 2023. "Optimal age targeting for pneumococcal vaccination in older adults; a modelling study," Nature Communications, Nature, vol. 14(1), pages 1-8, December.
    2. Pekka Marttinen & William P Hanage, 2017. "Speciation trajectories in recombining bacterial species," PLOS Computational Biology, Public Library of Science, vol. 13(7), pages 1-15, July.
    3. Peter Francis Raguindin, 0. "The changing epidemiology of pneumococcal diseases: new challenges after widespread routine immunization," International Journal of Public Health, Springer;Swiss School of Public Health (SSPH+), vol. 0, pages 1-2.
    4. Peter Francis Raguindin, 2020. "The changing epidemiology of pneumococcal diseases: new challenges after widespread routine immunization," International Journal of Public Health, Springer;Swiss School of Public Health (SSPH+), vol. 65(6), pages 709-710, July.
    5. Claire Mollendorf & Tuya Mungun & Munkhchuluun Ulziibayar & Paige Skoko & Laura Boelsen & Cattram Nguyen & Purevsuren Batsaikhan & Bujinlkham Suuri & Dashtseren Luvsantseren & Dorj Narangerel & Bilegt, 2024. "Effect of pneumococcal conjugate vaccine six years post-introduction on pneumococcal carriage in Ulaanbaatar, Mongolia," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    6. Kadi J. Horn & Melissa A. Schopper & Zoe G. Drigot & Sarah E. Clark, 2022. "Airway Prevotella promote TLR2-dependent neutrophil activation and rapid clearance of Streptococcus pneumoniae from the lung," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    7. Nicholas J Croucher & Lisa Kagedan & Claudette M Thompson & Julian Parkhill & Stephen D Bentley & Jonathan A Finkelstein & Marc Lipsitch & William P Hanage, 2015. "Selective and Genetic Constraints on Pneumococcal Serotype Switching," PLOS Genetics, Public Library of Science, vol. 11(3), pages 1-21, March.
    8. Matthieu Haudiquet & Julie Bris & Amandine Nucci & Rémy A. Bonnin & Pilar Domingo-Calap & Eduardo P. C. Rocha & Olaya Rendueles, 2024. "Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43160-y. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.