Genomic islands in Pseudomonas encode modular hotspots of defence and anti-defence systems.

Bacteria use diverse defence systems to resist phage predation, many of which cluster within mobile genetic elements (MGEs) and defence islands. In Pseudomonas aeruginosa, genomic and pathogenicity islands-such as the pathogenicity islands (PAPI), genomic islands (PAGI), and Liverpool epidemic strain islands (LESGI)-have been linked to virulence and adaptation, but their contribution to the organization and spread of defence systems remains unexplored. Here, we show that these islands serve as hubs for the assembly and spread of defence systems, revealing an underappreciated role in shaping the bacterium's antiviral arsenal. We identify 11 conserved hotspots that encode defence and anti-defence genes, but rarely co-occur with virulence factors, resistance genes, or interbacterial competition modules. The frequent co-occurrence of defence and anti-defence genes within these loci points to an ongoing, intense molecular arms race between bacteria, MGEs, and lytic phages. Notably, these hotspots are found beyond their original island contexts, appearing across diverse Pseudomonas species and, in some cases, other genera. Together, our findings expand the known bacterial immunity landscape in P. aeruginosa, redefine the roles of these islands as defence and anti-defence reservoirs, and establish a framework for scalable discovery and annotation of novel defence and anti-defence systems in bacterial genomes.