Parallel evolution of Pseudomonas aeruginosa phage resistance and virulence loss in response to phage treatment in vivo and in vitro

  1. Meaghan Castledine  Is a corresponding author
  2. Daniel Padfield
  3. Pawel Sierocinski
  4. Jesica Soria Pascual
  5. Adam Hughes
  6. Lotta Mäkinen
  7. Ville-Petri Friman
  8. Jean-Paul Pirnay
  9. Maya Merabishvili
  10. Daniel de Vos
  11. Angus Buckling
  1. University of Exeter, United Kingdom
  2. University of York, United Kingdom
  3. Queen Astrid Military Hospital, Belgium

Abstract

With rising antibiotic resistance, there has been increasing interest in treating pathogenic bacteria with bacteriophages (phage therapy). One limitation of phage therapy is the ease at which bacteria can evolve resistance. Negative effects of resistance may be mitigated when resistance results in reduced bacterial growth and virulence, or when phage coevolve to overcome resistance. Resistance evolution and its consequences are contingent on the bacteria-phage combination and their environmental context, making therapeutic outcomes hard to predict. One solution might be to conduct 'in vitro evolutionary simulations' using bacteria-phage combinations from the therapeutic context. Overall, our aim was to investigate parallels between in vitro experiments and in vivo dynamics in a human participant. Evolutionary dynamics were similar, with high levels of resistance evolving quickly with limited evidence of phage evolution. Resistant bacteria - evolved in vitro and in vivo - had lower virulence. In vivo, this was linked to lower growth rates of resistant isolates, whereas in vitro phage resistant isolates evolved greater biofilm production. Population sequencing suggests resistance resulted from selection on de novo mutations rather than sorting of existing variants. These results highlight the speed at which phage resistance can evolve in vivo, and how in vitro experiments may give useful insights for clinical evolutionary outcomes.

Data availability

All data and R script files can be found at the following GitHub repository. This repository outlines how the files may be used for analysis and Figure production. A full description of data file meanings and annotated R scripts is provided.https://github.com/mcastledine96/Parallel_evolution_phage_resistance_virulence_trade-offs_invivo_invitroRaw sequencing files have been archived on the European Nucleotide Archive with the project accession number PRJEB47945https://www.ebi.ac.uk/ena/browser/view/PRJEB47945?show=reads

The following data sets were generated

Article and author information

Author details

  1. Meaghan Castledine

    College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
    For correspondence
    mcastledine96@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5752-2641
  2. Daniel Padfield

    College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6799-9670
  3. Pawel Sierocinski

    College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Jesica Soria Pascual

    College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Adam Hughes

    College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. Lotta Mäkinen

    College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  7. Ville-Petri Friman

    Department of Biology, University of York, York, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  8. Jean-Paul Pirnay

    Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  9. Maya Merabishvili

    Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  10. Daniel de Vos

    Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  11. Angus Buckling

    College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

Funding

Medical Research Council (MR/N0137941/1)

  • Meaghan Castledine

Royal Society (CH160068)

  • Angus Buckling

Natural Environment Research Council (NE/S000771/1)

  • Angus Buckling

Royal Higher Institute for Defence (HFM 19-12)

  • Maya Merabishvili

Biotechnology and Biological Sciences Research Council (BB/T014342/1)

  • Ville-Petri Friman

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Gisela Storz, National Institute of Child Health and Human Development, United States

Ethics

Human subjects: The decolonisation study protocol was approved by the Leading Ethics Committee of the "Université Catholique de Louvain" (Avis N{degree sign}: B-403201111110). The study was performed in accordance with the ethical standards as laid down in the Declaration of Helsinki and as revised in 2013. The patients gave informed consent and their anonymity was preserved.

Version history

  1. Preprint posted: September 6, 2021 (view preprint)
  2. Received: September 7, 2021
  3. Accepted: February 20, 2022
  4. Accepted Manuscript published: February 21, 2022 (version 1)
  5. Version of Record published: March 10, 2022 (version 2)

Copyright

© 2022, Castledine et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Meaghan Castledine
  2. Daniel Padfield
  3. Pawel Sierocinski
  4. Jesica Soria Pascual
  5. Adam Hughes
  6. Lotta Mäkinen
  7. Ville-Petri Friman
  8. Jean-Paul Pirnay
  9. Maya Merabishvili
  10. Daniel de Vos
  11. Angus Buckling
(2022)
Parallel evolution of Pseudomonas aeruginosa phage resistance and virulence loss in response to phage treatment in vivo and in vitro
eLife 11:e73679.
https://doi.org/10.7554/eLife.73679

Share this article

https://doi.org/10.7554/eLife.73679

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