Mobile Integrons Encode Phage Defense Systems

Abstract

ABSTRACTIntegrons are bacterial genetic elements that capture, stockpile and modulate the expression of genes encoded in integron cassettes. Mobile Integrons (MI) are borne on plasmids, acting as a vehicle for hundreds of antimicrobial resistance genes among key pathogens. These elements also carrygenecassettes ofunknown function (gcus) whose role and adaptive value remains unexplored. Recent years have witnessed the discovery of a myriad defense systems against bacteriophages, highlighting that viral infection is a major selective pressure for bacteria. We hence sought to explore ifgcus could encode phage defense systems. Using the INTEGRALL database, we established a collection of 129gcus in pMBA, a vector where cassettes are established as part of a class 1 integron. PADLOC and DefenseFinder predicted four phage defense systems in this collection, comprising Lamassu, CBASS and two ABI (abortive infection) systems. We experimentally challenged all cassettes with phages and found eleven additional candidates that were not detectedin silico. We have characterized in depth the 15gcus against a panel of phages inEscherichia coliconfirming their role asphage defense integroncassettes (PICs). We used recombination assays to verify that these arebona fideintegron cassettes and are therefore mobile. We show that PICs confer resistance in other clinically relevant species, such asKlebsiella pneumoniaeandPseudomonas aeruginosa.Several PICs also limit prophage activation, providing protection at the population-level. Given the stockpiling capacity of integrons, we explored the additivity of phenotypes and found that integrons with two PICs confer multiphage-resistance. Additionally, when combined with antimicrobial resistance genes, integrons confer simultaneously drug and phage resistance. Crucially, we also show that the position of apicin the array can strongly decrease its cost. Our results prove a role of integrons in phage defense, acting as highly mobile, low-cost defense islands.