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  • Review Article
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CRISPR–Cas therapies targeting bacteria

Nature Reviews Bioengineering volume 3, pages 627–644 (2025)Cite this article

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Abstract

Technologies derived from the CRISPR (clustered regularly interspaced short palindromic repeats)–Cas immune system of prokaryotes have revolutionized our ability to cleave and modify target nucleic acid sequences. In addition to the use of CRISPR–Cas tools for the editing of human genes, they can also be designed to target pathogenic and commensal bacteria that colonize the body, offering new pathways for the treatment of infections and microbiome modulation. In this Review, we explore how the CRISPR–Cas toolbox can be engineered to kill or modify specific bacteria. We discuss DNA-targeting and RNA-targeting strategies, outlining how these can be applied to disarm bacteria by removing, modifying or silencing specific genes. Furthermore, we examine the delivery of CRISPR–Cas tools by bacteriophages and through conjugation and explore intracellular barriers to CRISPR–Cas tool maintenance and expression. Finally, we highlight therapeutic opportunities in the treatment of infectious diseases and for the modification of the microbiome, outlining progress and challenges in translating these approaches into clinical applications.

Key points

  • CRISPR (clustered regularly interspaced short palindromic repeats)–Cas systems can be designed as tools to kill or modify target bacteria, for example, by targeting antibiotic resistance genes, virulence factors or genes involved in microbiome-related diseases.

  • CRISPR–Cas tools can be delivered to target bacteria by phage particles or plasmid conjugation.

  • Delivery of CRISPR–Cas therapeutics requires engineering to enhance efficiency, adapt the host range to the target strains and bypass bacterial defence mechanisms.

  • First clinical trials have demonstrated the safety of Cas-armed phages.

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Fig. 1: CRISPR–Cas therapeutics targeting bacteria.
Fig. 2: Modes of action for various CRISPR–Cas tools.
Fig. 3: CRISPR–Cas tool delivery by phages and plasmids.
Fig. 4: Challenges in CRISPR–Cas tool delivery.

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Acknowledgements

We thank the Synthetic Biology group at Institute Pasteur for discussions. F.B. was supported by the SNSF (P500PB_210944). D.B. and B.B. were supported by the European Research Council (101044479) and Agence Nationale de la Recherche (ANR-10-LABX-62-IBEID). In some instances, we have used ChatGPT to reformulate sentences and improve style. All generated text has been carefully reviewed for accuracy.

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  1. These authors contributed equally: Beatriz Beamud, Raphael Laurenceau.

Authors and Affiliations

  1. Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France

    Fabienne Benz, Beatriz Beamud, Raphael Laurenceau, Amandine Maire & David Bikard

  2. Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France

    Fabienne Benz & Raphael Laurenceau

  3. Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France

    Amandine Maire

  4. Eligo Bioscience, Paris, France

    Xavier Duportet, Antoine Decrulle & David Bikard

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Contributions

F.B. and D.B. conceptualized the project. B.B. and R.L. contributed to structuring the manuscript. F.B., B.B., R.L., A.M., X.D., A.D. and D.B. wrote the manuscript. F.B., B.B. and R.L. prepared figures and tables. D.B. supervised the project. All authors made a substantial contribution to the discussion of content and editing of the manuscript.

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The following authors have links to Eligo Bioscience, of which work is cited and discussed in this article: D.B is a co-founder, shareholder and advisor; X.D. is a co-founder, CEO and shareholder; and A.D. is an employee and shareholder. These authors are also listed as inventors on several patents in the field. This relationship has been disclosed to the journal, and all authors declare that there are no other competing interests.

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Benz, F., Beamud, B., Laurenceau, R. et al. CRISPR–Cas therapies targeting bacteria. Nat Rev Bioeng 3, 627–644 (2025). https://doi.org/10.1038/s44222-025-00311-8

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