Temperate bacteriophage induced in Pseudomonas aeruginosa biofilms can modulate bacteriophage and antibiotic resistance

Abstract

Given the high levels of resistance in Gram-negative bacteria, phage therapy is garnering increasing attention. In Germany, a clinical study is already underway investigating a phage cocktail for the treatment of Pseudomonas aeruginosa in cystic fibrosis (CF) patients. In our study, we examined susceptibility to virulent phages and the PF1-like prophage and antimicrobial profiles and of P. aeruginosa isolates from a local cystic fibrosis cohort to identify correlations and lysogenic conversion of the prophegs. Consistent with other studies, prophage Pf4 is the most prevalent in this cohort and is activated in the absence of other influences during biofilm formation. These phages can be transferred to other strains that do not contain Pf1-like prophages, thereby influencing the dynamics of bacterial populations in the CF lung. This also rapidly leads to the emergence of a subpopulation resistant to the virulent phages, potentially complicating phage therapy. However, this subset also becomes more susceptible to most antibiotics commonly used in CF, which could be a useful treatment strategy. Interestingly, this bacterial subset lost its susceptibility to colistin, an important inhaled antibiotic in CF, which could lead to treatment failure. Our research highlights both the difficulties and potential strategies to improve treatment options for CF patients. Author summaryWe investigated 51 P. aeruginosa isolates obtained from CF patients for the presence of PF1-like prophages and characterized their susceptibility prior and after lysogenig conversion of the prophages to three virulent phages. Our study revealed that the temperate phage Pf4 is the most prominent PF1-like prophage in this cohort, undergoing lysogenic conversion during biofilm formation. The virions identified in the biofilm supernatants are superinfective and transferable to other prophage-free P. aeruginosa isolates, shaping population dynamics in the CF lung. Prophage reactivation results in the survival of a sub-population with reduced susceptibility to virulent phages, posing a potential challenge for phage therapy. However, this sub-population exhibited restored susceptibility to most CF-relevant antibiotics, presenting an intriguing therapeutic opportunity. Targeted prophage reactivation could sensitize multidrug-resistant P. aeruginosa in CF patients, enhancing or even restoring antimicrobial efficacy. Notably, this sub-population also showed a loss of colistin susceptibility, which may lead to treatment failure when colistin is used as an inhaled antipseudomonal antibiotic. Our findings highlight both significant challenges and potential therapeutic opportunities for optimizing the treatment of CF patients. However, these findings are preliminary and require further investigation, particularly regarding the possibility of lysogenic conversion in other prophages (such as Siphoviridae) and how these interplays with resistance to virulent phages. Further studies are ongoing and will enhance our understanding of the role of prophages in the pathophysiology of CF.