The effect of competitor and phage on the evolution and diversification of Pseudomonas aeruginosa in a synthetic cystic fibrosis nutritional environment

Lung disease, caused primarily by the bacterium Pseudomonas aeruginosa, is the leading cause of death for patients with the genetic disease cystic fibrosis (CF). P. aeruginosa is intrinsically antibiotic resistant and chronic lung infections with this bacterium are notoriously intractable to treat. As such, there is much interest in using bacteriophage (phage), viruses that specifically target bacteria, to treat P. aeruginosa lung infections of cystic fibrosis patients. However, as with antibiotic resistance evolution, bacteria also evolve resistance to phage. Additionally, there is little understanding about how phage resistance evolution is affected by factors in the CF lung, including bacterial competitors and the nutritional environment. As such, this project aimed to understand how selection by the lytic pseudomonal phages 14/1 and PNM drives resistance evolution and diversification in the absence and presence of the bacterial competitor, S. maltophilia. In coculture, phage initially reduced the abundance of P. aeruginosa, which allowed S. maltophilia to increase in density. P. aeruginosa evolved resistance to the phages present and increased in density with time. Phage also increased P. aeruginosa diversification of non-ancestral morphologies, but this effect was abrogated by the presence of the competitor. Phage resistance evolution was associated with trade-offs in growth after 48 hours and increased susceptibility to colistin. Evolution with competitor was associated with increased susceptibility to tobramycin whilst adaptation to the nutritional environment was linked to increased susceptibility to meropenem. These findings have important implications for the future of phage therapy. Herein, it is shown that application of phage not only reduces focal pathogen densities but also increases susceptibility to antibiotics. Therefore, phage applied together with antibiotics may be optimal to eliminate P. aeruginosa from the lungs of cystic fibrosis patients.