Directed evolution of phages in biofilms enhances Pseudomonas aeruginosa control through improved lipopolysaccharide recognition
Pseudomonas aeruginosa is a leading cause of chronic lung infections in cystic fibrosis (CF) patients. While bacteriophages hold potential as a treatment for antibiotic-resistant infections, the complex structure and heterogeneity of P. aeruginosa biofilms pose significant challenges to phage therapy. In this study, we investigate the adaptive evolution of the Pbunavirus phage PE1 to biofilms formed by a CF-derived P. aeruginosa isolate. Our findings reveal that biofilm-adapted PE1 mutants exhibit enhanced efficacy in controlling biofilms in vitro under conditions mimicking the CF lung environment. This improvement is attributed to the mutants' increased ability to recognize the diverse populations within the biofilm. Using a combination of cryo-EM, lipopolysaccharide (LPS) profiling, and adsorption assays, we demonstrate that mutations in tail fiber and baseplate genes of the phage improve adsorption and enable recognition of truncated LPS variants. This study highlights the critical role of biofilm heterogeneity in limiting phage effectiveness, identifies mechanisms to overcome this barrier, and pinpoints specific genomic targets for engineering phages tailored for therapeutic applications in CF patients.
Authors
- Sílvio Roberto Branco Santos (ORCID: https://orcid.org/0000-0003-0801-8080)
- Jelena Erdmann (ORCID: https://orcid.org/0000-0001-6928-3326)
- Susanne Häußler (ORCID: https://orcid.org/0000-0001-6141-9102)
- Lucie Valentová (ORCID: https://orcid.org/0000-0003-0160-2014)
- Joana Azeredo (ORCID: https://orcid.org/0000-0002-5180-7133)
- Luciana Meneses (ORCID: https://orcid.org/0000-0001-9497-1200)
- Pavel Plevka (ORCID: https://orcid.org/0000-0003-4215-3315)
- Aurélie Crabbé (ORCID: https://orcid.org/0000-0003-3084-4418)
- Diana P. Pires (ORCID: https://orcid.org/0000-0003-2055-5743)
- Tom Coenye (ORCID: https://orcid.org/0000-0002-6407-0601)
Institutions
- Central European Institute of Technology (CZ)
- Rigshospitalet (DK)
- Ghent University (BE)
- Central European Institute of Technology – Masaryk University (CZ)
- Helmholtz Centre for Infection Research (DE)
- Center for Experimental and Clinical Infection Research (DE)
- University of Minho (PT)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-11-20
- DOI
- https://doi.org/10.1038/s41467-025-65014-5
- Citations
- 1
- Primary Topic
- Bacteriophages and microbial interactions
- Type
- article
- Field-Weighted Citation Impact
- 1.72
Funders
- European Commission
- Ministerstvo Školství, Mládeže a Tělovýchovy
- Central European Institute of Technology
- Fundación Bancaria Caixa d'Estalvis i Pensions de Barcelona
- HORIZON EUROPE Framework Programme
- Fundação para a Ciência e a Tecnologia
- European Regional Development Fund