A qPCR-Based Screening Platform for Exploratory Assessment of Phage Training Outcomes in

Bacteriophages (phages) represent promising therapeutic agents. Their clinical use is challenged by the rapid rise of resistant bacterial clones. To overcome this problem, phages can be trained in vitro to improve their ability to cope with the possible resistance that may arise. Here, we co-evolved phages with their hosts under different conditions and assessed their ability to infect an adapted bacterial panel using qPCR. The co-evolution experiment yielded a panel of bacterial clones adapted either to a phage, a competing phage, or a cocktail of both. Phages were adapted either in the continuous presence of an evolutionarily naïve host, in a cocktail with a competing phage, under both conditions, or under neither condition. We assessed each resulting phage for its ability to infect evolved bacterial clones in the panel we created, using qPCR for preliminary high-throughput assessment. This allowed us to evaluate 500 phages-bacteria interactions. Overall, qPCR-detected phage production following infection of different bacterial clones improved to varying degrees when evolutionary naïve hosts were added during the training. However, the screening suggests that optimal training conditions are phage-specific. For