Amoxicillin-resistant Streptococcus pneumoniae can be resensitized by targeting the mevalonate pathway as indicated by sCRilecs-seq

  1. Liselot Dewachter
  2. Julien Dénéréaz
  3. Xue Liu
  4. Vincent de Bakker
  5. Charlotte Costa
  6. Mara Baldry
  7. Jean-Claude Sirard
  8. Jan-Willem Veening  Is a corresponding author
  1. University of Lausanne, Switzerland
  2. Shenzhen University Health Science Center, China
  3. University of Lille, France

Abstract

Antibiotic resistance in the important opportunistic human pathogen Streptococcus pneumoniae is on the rise. This is particularly problematic in the case of the β-lactam antibiotic amoxicillin, which is the first-line therapy. It is therefore crucial to uncover targets that would kill or resensitize amoxicillin-resistant pneumococci. To do so, we developed a genome-wide, single-cell based, gene silencing screen using CRISPR interference called sCRilecs-seq (subsets of CRISPR interference libraries extracted by fluorescence activated cell sorting coupled to next generation sequencing). Since amoxicillin affects growth and division, sCRilecs-seq was used to identify targets that are responsible for maintaining proper cell size. Our screen revealed that downregulation of the mevalonate pathway leads to extensive cell elongation. Further investigation into this phenotype indicates that it is caused by a reduced availability of cell wall precursors at the site of cell wall synthesis due to a limitation in the production of undecaprenyl phosphate (Und-P), the lipid carrier that is responsible for transporting these precursors across the cell membrane. The data suggest that, whereas peptidoglycan synthesis continues even with reduced Und-P levels, cell constriction is specifically halted. We successfully exploited this knowledge to create a combination treatment strategy where the FDA-approved drug clomiphene, an inhibitor of Und-P synthesis, is paired up with amoxicillin. Our results show that clomiphene potentiates the antimicrobial activity of amoxicillin and that combination therapy resensitizes amoxicillin-resistant S. pneumoniae. These findings could provide a starting point to develop a solution for the increasing amount of hard-to-treat amoxicillin-resistant pneumococcal infections.

Data availability

Sequencing data is available at SRA under accession number PRJNA763896. Much of this work is based upon microscopy and snap shots and movies of most experiments are included in the manuscript and supporting files. Raw microscopy images are available at the BioImage Archive (accession number S-BIAD477).

The following data sets were generated

Article and author information

Author details

  1. Liselot Dewachter

    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1080-1656
  2. Julien Dénéréaz

    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  3. Xue Liu

    Department of Pharmacology, Shenzhen University Health Science Center, Shenzhen, China
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6485-1865
  4. Vincent de Bakker

    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1019-3558
  5. Charlotte Costa

    University of Lille, Lille, France
    Competing interests
    The authors declare that no competing interests exist.
  6. Mara Baldry

    University of Lille, Lille, France
    Competing interests
    The authors declare that no competing interests exist.
  7. Jean-Claude Sirard

    University of Lille, Lille, France
    Competing interests
    The authors declare that no competing interests exist.
  8. Jan-Willem Veening

    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    For correspondence
    Jan-Willem.Veening@unil.ch
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3162-6634

Funding

European Commission (Marie Skłodowska Curie 837923)

  • Liselot Dewachter

European Research Council (771534-PneumoCaTChER)

  • Jan-Willem Veening

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (310030_200792,310030_192517,40AR40_185533,51NF40_180541)

  • Jan-Willem Veening

HORIZON EUROPE Framework Programme (847786)

  • Jean-Claude Sirard

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

Ethics

Animal experimentation: All experiments complied with national, institutional and European regulations and ethical guidelines, were approved by our Institutional Animal Care and Use guidelines (D59-350009, Institut Pasteur de Lille; Protocol APAFIS#16966 201805311410769_v3) and were conducted by qualified, accredited personnel.

Reviewing Editor

  1. Malcolm Winkler

Publication history

  1. Received: November 16, 2021
  2. Accepted: June 23, 2022
  3. Accepted Manuscript published: June 24, 2022 (version 1)

Copyright

© 2022, Dewachter 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. Liselot Dewachter
  2. Julien Dénéréaz
  3. Xue Liu
  4. Vincent de Bakker
  5. Charlotte Costa
  6. Mara Baldry
  7. Jean-Claude Sirard
  8. Jan-Willem Veening
(2022)
Amoxicillin-resistant Streptococcus pneumoniae can be resensitized by targeting the mevalonate pathway as indicated by sCRilecs-seq
eLife 11:e75607.
https://doi.org/10.7554/eLife.75607

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