Modular small RNA drives the emergence of virulence traits and environmental trade-offs in Vibrio cholerae

The molecular drivers and fitness trade-offs controlling the transition of environmental bacteria into human pathogens remain enigmatic. Here, we describe a small RNA (sRNA) with a unique modular structure that shapes the evolution of toxigenic Vibrio cholerae, the agent of cholera. The sRNA comprises a variable 5' module located within the ompU ORF and a conserved 3' region downstream. This atypical location confers a distinct bimodular structure to the OmpU-encoded sRNA (OueS), generating allelic variants with unique functions. Unlike environmental counterparts, the OueS allele from toxigenic strains controls phenotypes essential during host colonization in a domain-dependent manner: a) inhibits biofilm formation by suppressing RyhB, b) confers resistance against intestinal bacteriophages by activating the CBASS system, and c) drives mucus penetration. Toxigenic OueS is essential for successful intestinal colonization and acts as a functional surrogate of the master virulence regulator ToxR, controlling over 84% of its regulome. However, this allele leads to reduced competitive fitness during colonization of natural reservoirs when compared to environmental ones. Finally, we determined that the acquisition of the ompU ORF is modular and controlled by exogenous conditions, providing critical insights into the evolution of toxigenic V. cholerae and the emergence of pathogenic traits in bacteria.