Determinants of phage resistance in clinical Pseudomonas aeruginosa strains

The global rise of antibiotic resistance has renewed interest in phage therapy as a promising alternative. Yet, bacterial resistance to phages remains a major challenge, long attributed mainly to receptor modifications that block adsorption. Recent discoveries in bacterial immune systems suggest a broader picture : phages may adsorb efficiently but fail at later infection stages, with intracellular defenses, transcriptional regulators, or other factors acting as key determinants of susceptibility. To investigate this, we examined 125 clinical isolates of Pseudomonas aeruginosa from antibiotic treatment failure cases against 8 phages spanning multiple genera. Using highthroughput resistance assays, adsorption tests, genomic analyses, and genome-wide association studies (GWAS), we dissected the mechanisms underlying phage resistance. In the majority of cases, resistance was explained by a lack of adsorption. Nevertheless, we also found a significant negative correlation between the number of defense systems and phage infectivity, although considerable variation remains unexplained. These findings highlight both adsorption failure and intrinsic defenses as major determinants of phage resistance in clinically relevant isolates. Understanding how defense load and composition shape phage susceptibility is crucial for optimizing therapeutic applications and may help predict and circumvent bacterial resistance more effectively.