Prophage taming by the adherent-invasiveEscherichia coliLF82 upon macrophage infection

Adherent-invasiveEscherichia coli(AIEC) strains are frequently recovered from stools of patients with dysbiotic microbiota. They have remarkable properties of adherence to the intestinal epithelium, and survive better than otherE. coliin macrophages. The best studied of these AIEC is probably strain LF82, which was isolated from a Crohn’s disease patient. This strain contains five complete prophages, which have not been studied until now. We undertook their analysis, bothin vitroand inside macrophages, and show that all of them form virions. The Gally prophage is by far the most active, generating spontaneously over 108viral particles per mL of culture supernatantsin vitro, more than 100-fold higher than the other phages. Gally is over-induced after a genotoxic stress generated by ciprofloxacin and trimethoprim. However, upon macrophage infection, Gally virion production is decreased by more than 20-fold, and the transcription profile of the prophage indicates that part of the structural module is specifically repressed while the replication module is overexpressed compared to unstressed culture conditions. We conclude that strain LF82 has evolved an efficient way to “tame” its most active prophage upon macrophage infection, which may participate to its good survival in macrophages. The results are discussed in light of the active lysogeny process.AUTHOR SUMMARYProphages are bacterial viruses stably integrated into their host, to which they can provide new functions, thus increasing their fitness in the environment. Thereby, they can participate to the virulence of bacterial pathogens. However, prophages are double-edged swords that can be awakened in response to genotoxic stresses, resulting in the death of their bacterial host. This raises the question of the effect of this type of stress in the natural environments where their bacterial hosts exert their virulence. In this study, we characterized the five active prophages present inEscherichia coliLF82, a strain belonging to the intestinal microbiota and suspected to be involved in Crohn’s disease via its ability to invade macrophages, a highly genotoxic environment. We show that LF82 inhibits the awakening of its prophages in macrophages, allowing it to survive there. Moreover, deletion of its most active prophage does not affect the viability of LF82 in this environment. These results show that LF82 has tamed its prophages in macrophages and also suggest that if they convey fitness advantages, they probably do so in environments differing from macrophages, and which remain to be discovered.