Natural Bred ε-Phages Have an Improved Host Range and Virulence against Uropathogenic over Their Ancestor Phages.

Alternative treatments for infections are urgently needed, and phage therapy is a promising option where antibiotics fail, especially for urinary tract infections (UTI). We used wastewater-isolated phages to test their lytic activity against a panel of 47 strains reflecting the diversity of strains found in UTI, including sequence type 131, 73 and 69. The plaquing host range (PHR) was between 13 and 63%. In contrast, the kinetic host range (KHR), describing the percentage of strains for which growth in suspension was suppressed for 24 h, was between 0% and 19%, substantially lower than the PHR. To improve the phage host range and their efficacy, we bred the phages by mixing and propagating cocktails on a subset of strains. The bred phages, which we termed evolution-squared ε-phages, of a mixture of have KHRs up to 23% broader compared to their ancestors. Furthermore, using constant phage concentrations, ε-phages suppressed the growth of higher bacterial inocula than their ancestors did. Thus, the ε-phages were more virulent compared to their ancestors. Analysis of the genetic sequences of the ε-phages with the broadest host range reveals that they are mosaic intercrossings of 2-3 ancestor phages. The recombination sites are distributed over the whole length of the genome. All ε-phages are devoid of genes conferring lysogeny, antibiotic resistance, or virulence. Overall, this study shows that ε-phages are remarkably more suitable than the wild-type phages for phage therapy.