Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance

The evolution of antibiotic-resistant bacteria threatens to become the leading cause of worldwide mortality. This crisis has renewed interest in the practice of phage therapy. Yet, bacteria's capacity to evolve resistance may debilitate this therapy as well. To combat the evolution of phage resistance and improve treatment outcomes, many suggest leveraging phages' ability to counter resistance by evolving phages on target hosts before using them in therapy (phage training). We found that in vitro, lambda trn, a phage trained for 28 d, suppressed bacteria similar to 1,000-fold for three to eight times longer than its untrained ancestor. Prolonged suppression was due to a delay in the evolution of resistance caused by several factors. Mutations that confer resistance to lambda trn are similar to 100x less common, and while the target bacterium can evolve complete resistance to the untrained phage in a single step, multiple mutations are required to evolve complete resistance to lambda trn. Mutations that confer resistance to lambda trn are more costly than mutations for untrained phage resistance. Furthermore, when resistance does evolve, lambda trn is better able to suppress these forms of resistance. One way that lambda trn improved was through recombination with a gene in a defunct prophage in the host genome, which doubled phage fitness. This transfer of information from the host genome is an unexpected but highly efficient mode of training phage. Lastly, we found that many other independently trained lambda phages were able to suppress bacterial populations, supporting the important role training could play during phage therapeutic development.

Automated summary

Training bacteriophages on target hosts before therapy can prolong suppression of antibiotic-resistant bacteria by delaying the evolution of resistance. Evolution of resistance to trained phages is more costly and requires multiple mutations, making them more effective in combating resistance. Transfer of genetic information from host genomes through recombination can enhance phage fitness and improve treatment outcomes, highlighting the potential of training in phage therapy development.