One of the challenges of phage therapy is the risk of target bacteria developing resistance to bacteriophages during treatment. Special "training" techniques that encourage phages to coevolve with bacteria and "train" phages to bypass bacterial resistance mechanisms may help overcome this obstacle.

Even before the discovery of bacteriophages, Félix d'Hérelle was involved in combating the locust plague in Argentina. To eradicate the dreaded pests, he used bacterial pathogens of locusts, whose virulence he enhanced through "coevolutionary training"—repeated passages of the bacteria through the insects' bodies.

Today, various groups of scientists are attempting to use "coevolutionary training" to enhance the ability of phages to kill bacteria. This approach is based on the ability of phages, through natural evolutionary mechanisms—variability and natural selection—to overcome bacterial resistance factors.

Phage training involves repeated passage of phages through bacterial cultures, which promotes coevolution between phages and bacteria. A recent paper published in PNAS* found that training the λ phage significantly increased its effectiveness against E. coli . Specifically, trained phages utilized an additional receptor during binding to the target bacterium (untrained phages utilized only the LamB receptor, while trained phages utilized both LamB and OmpF).

When grown in culture flasks, untrained phages inhibited bacterial growth for no more than a few days. Bacterial resistance to untrained phages developed rapidly and irreversibly. Trained phages, on the other hand, were capable of inhibiting bacteria at 1,000 times higher concentrations for at least three weeks. Why is this?

Scientists have found that the number of mutations arising in bacteria in the presence of trained phages is 100 times lower than in the presence of "wild" strains, i.e., those that have not undergone the training procedure. While a single mutation in the bacterial genome is sufficient to develop resistance to untrained phages, trained phages require several. Furthermore, mutant bacteria that have acquired resistance to phages through mutations pay a higher price for this, requiring significantly more resources to grow.

Scientists sequenced the trained phage and discovered recombinations with genes from an ancient prophage that had been dormant in the genome of the bacterium used to train the phage. This recombination significantly improved the growth performance of the λ phage, as the ancient phage (which had lost some genes and transformed into a prophage) transferred new information about the infection pathways of the target bacterium to the λ phage.

A study of trained phages revealed that some of them use one receptor during bacterial infection, while others use two. The former were more effective in inhibiting bacterial growth than untrained phages, but less effective than trained phages, which use two receptors.

The authors note that the advantages of trained phages are due to several complementary mechanisms, in particular the use of several receptors to interact with the bacteria and recombination with the genes of the prophage integrated into the DNA of the target bacterium.

* Borin JM, Avrani S, Barrick JE, Petrie KL, Meyer JR. Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance / Proceedings of the National Academy of Sciences, 2021, 118 (23): e2104592118. DOI: 10.1073/pnas.2104592118