Integrons are anti-phage defence libraries in Vibrio parahaemolyticus

Bacterial genomes have regions known as defence islands that encode diverse systems to protect against phage infection. Although genetic elements that capture and store gene cassettes in Vibrio species, called integrons, are known to play an important role in bacterial adaptation, a role in phage defence had not been defined. Here we combine bioinformatic and molecular techniques to show that the chromosomal integron of Vibrio parahaemolyticus is a hotspot for anti-phage defence genes. Using bioinformatics, we discovered that previously characterized defences localize to integrons. Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence. Our work reveals that integrons are an important reservoir of defence systems in V. parahaemolyticus. As integrons are of ancient origin and are widely distributed among Proteobacteria, these results provide an approach for the discovery of anti-phage defence systems across a broad range of bacteria.