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The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies

Author

Listed:
  • Samuel Lipworth

    (University of Oxford
    Oxford University Hospitals NHS Foundation Trust)

  • William Matlock

    (University of Oxford)

  • Liam Shaw

    (University of Oxford)

  • Karina-Doris Vihta

    (University of Oxford)

  • Gillian Rodger

    (University of Oxford)

  • Kevin Chau

    (University of Oxford)

  • Leanne Barker

    (University of Oxford)

  • Sophie George

    (University of Oxford)

  • James Kavanagh

    (University of Oxford)

  • Timothy Davies

    (University of Oxford
    University of Oxford)

  • Alison Vaughan

    (University of Oxford)

  • Monique Andersson

    (Oxford University Hospitals NHS Foundation Trust)

  • Katie Jeffery

    (Oxford University Hospitals NHS Foundation Trust)

  • Sarah Oakley

    (Oxford University Hospitals NHS Foundation Trust)

  • Marcus Morgan

    (Oxford University Hospitals NHS Foundation Trust)

  • Susan Hopkins

    (United Kingdom Health Security Agency)

  • Timothy Peto

    (University of Oxford
    Oxford University Hospitals NHS Foundation Trust
    John Radcliffe Hospital)

  • Derrick Crook

    (University of Oxford
    Oxford University Hospitals NHS Foundation Trust
    John Radcliffe Hospital)

  • A. Sarah Walker

    (University of Oxford
    John Radcliffe Hospital)

  • Nicole Stoesser

    (University of Oxford
    Oxford University Hospitals NHS Foundation Trust
    John Radcliffe Hospital)

Abstract

Plasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to plasmids carrying antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections in Oxfordshire, UK. The bacteria had been originally isolated in 2009 (194 isolates) and 2018 (368 isolates), plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to a single host species, although there is substantial overlap between species of plasmid gene-repertoire. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative ‘backbone’ of core genes with those carrying no such genes. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes.

Suggested Citation

  • Samuel Lipworth & William Matlock & Liam Shaw & Karina-Doris Vihta & Gillian Rodger & Kevin Chau & Leanne Barker & Sophie George & James Kavanagh & Timothy Davies & Alison Vaughan & Monique Andersson , 2024. "The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-45761-7
    DOI: 10.1038/s41467-024-45761-7
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    References listed on IDEAS

    as
    1. Santiago Redondo-Salvo & Raúl Fernández-López & Raúl Ruiz & Luis Vielva & María de Toro & Eduardo P. C. Rocha & M. Pilar Garcillán-Barcia & Fernando de la Cruz, 2020. "Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    2. Ryan R Wick & Louise M Judd & Kathryn E Holt, 2018. "Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks," PLOS Computational Biology, Public Library of Science, vol. 14(11), pages 1-11, November.
    3. Mislav Acman & Lucy van Dorp & Joanne M. Santini & Francois Balloux, 2020. "Large-scale network analysis captures biological features of bacterial plasmids," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
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