Directed evolution of phages in biofilms enhances Pseudomonas aeruginosa control through improved lipopolysaccharide recognition

Luciana Meneses, Lucie Valentová, Sílvio B. Santos, Jelena Erdmann, Aurélie Crabbé, Pavel Plevka, Susanne Häussler, Diana P. Pires (), Tom Coenye and Joana Azeredo ()
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Luciana Meneses: University of Minho, CEB - Centre of Biological Engineering
Lucie Valentová: Masaryk University, Central European Institute of Technology
Sílvio B. Santos: University of Minho, CEB - Centre of Biological Engineering
Jelena Erdmann: Centre for Experimental and Clinical Infection Research, Institute for Molecular Bacteriology, TWINCORE
Aurélie Crabbé: Ghent University, Laboratory of Pharmaceutical Microbiology
Pavel Plevka: Masaryk University, Central European Institute of Technology
Susanne Häussler: Centre for Experimental and Clinical Infection Research, Institute for Molecular Bacteriology, TWINCORE
Diana P. Pires: University of Minho, CEB - Centre of Biological Engineering
Tom Coenye: Ghent University, Laboratory of Pharmaceutical Microbiology
Joana Azeredo: University of Minho, CEB - Centre of Biological Engineering

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract 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.

Date: 2025
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DOI: 10.1038/s41467-025-65014-5

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