PARADE

Objectives. This project aims to investigate the influence of bacterial viruses (phages) on the selection, maintenance and global spread of epidemic clones belonging to the opportunistic pathogenic bacterium Pseudomonas aeruginosa. Phages, by causing bacterial lysis, play a crucial role in regulating bacterial populations in ecosystems. This regulation can lead to shifts in bacterial composition, influencing which clones persist, particularly in the face of environmental stresses like antibiotic use. Preliminary studies in our group have shown that nearly all genomes of isolates of the clone ST235 of P. aeruginosa (a high-risk, multidrug-resistant epidemic clone) contain a specific cluster of genes that enables the bacterium to resist phages. This project will focus on the 10 genes of this cluster to understand their roles in phage defence (in particular the PsyrTA and Gabija systems); this should allow us to test the hypothesis that phage resistance

can facilitate the spread of epidemic clones.

Achievement. To achieve these goals, we will use both molecular biology and bioinformatics approaches. The 10 ST235-specific genes will be individually inactivated and subsequently complemented through chromosomal insertion to assess their role in conferring bacterial resistance to phage-mediated lysis. To achieve this, we will use (i) phages collected and purified from effluents of wastewater treatment plant, and (ii) characterised phages purchased from national collections. With the support of the Microbiological Resource Center (MRC, CHU Besançon) and the Bioinformatics platform 2B2S (CHU/UFR Santé, Besançon), we will investigate the distribution of the major PsyrTA and Gabija defence systems in clinical and environmental strains across the species. Additionally, we will assess whether major high-risk clones (ST235, but also ST111, ST175, ST244, ST395) accumulate anti-phage defence systems in comparison with sporadic clones.

Relevance to HARMI. The HARMI starter AAP will allow the laboratory to open a new research axis focused on the impact of bacterial phages on the maintenance and dissemination of high-risk epidemic clones. This structuring project will enable the development of a new partnership based on (i) the molecular biology and fundamental microbiology expertise of the Chrono-environnement laboratory (EPE), (ii) the epidemiological expertise of the MRC (CHU Besançon), (iii) the bioinformatics skills of the 2B2S platform (CHU/UFR Santé, Besançon), and (iii) an international collaboration with the Laboratory of bacteriophages and phagotherapy (CHUV, University of Lausanne).