Phase variation-based biosensors for bacteriophage detection and phage receptor discrimination

Environmental monitoring of bacteria using phage-based biosensors has been widely developed for many different species. However, there are only a few available methods to detect specific bacteriophages in raw environmental samples. In this work, we developed a simple and efficient assay to rapidly monitor the phage content of a given sample. The assay is based on the bistable expression of the Salmonella enterica opvAB operon. Under regular growth conditions, opvAB is only expressed by a small fraction of the bacterial subpopulation. In the OpvABON subpopulation, synthesis of the OpvA and OpvB products shortens the O-antigen in the lipopolysaccharide and confers resistance to phages that use LPS as a receptor. As a consequence, the OpvABON subpopulation is selected in the presence of such phages. Using an opvAB::gfp fusion, we could monitor LPS-binding phages in various media, including raw water samples. To enlarge our phage-biosensor panoply, we also developed several coliphage biosensors that proved efficient to detect LPS- as well as protein-binding coliphages. Moreover, the combination of these tools allows to identify what is the bacterial receptor triggering phage infection. The opvAB::gfp biosensor thus comes in different flavours to efficiently detect a wide range of bacteriophages and identify the type of receptor they recognize. ImportanceDetection and accurate counting of bacteriophages, the viruses that specifically infect bacteria, from environmental samples still constitutes a challenge for those interested in isolating and characterizing bacteriophages for ecological or biotechnological purposes. This work provides a simple and accurate method based on the bi-stable expression of genes that confer resistance to certain classes of bacteriophages in different bacterial models. It paves the way for future development of highly efficient phage biosensors that can discriminate among several receptor-binding phages and that could be declined in many more versions. In a context where phage ecology, research, and therapy are flourishing again, it becomes essential to possess simple and efficient tools for phage detection.