Scientists from the Massachusetts Institute of Technology (MIT) have proposed a new strategy for rapidly producing phage preparations to combat various strains of pathogenic bacteria.

Bacteriophages (phages) have recently attracted increasing attention due to their ability to kill pathogenic bacteria against which antimicrobials are ineffective—those with multiple antibiotic resistance. The mechanisms of action of antibiotics and bacteriophages differ fundamentally, and in many cases, their combined use is advisable.

Bacteriophages act very specifically: one strain of bacteriophages can destroy members of a single species, several strains, or even a single strain of bacteria. On the one hand, this narrow focus of action is an advantage of phages over antibiotics, which destroy both harmful and beneficial bacteria in the body. However, on the other hand, in cases of severe infections caused by resistant microorganisms, finding a specific phage and quickly producing a phage preparation can be problematic. Scientists at MIT have made an important step toward solving this issue. They have learned to quickly produce bacteriophages capable of killing different strains of Escherichia coli . To do this, they induce a mutation in the phage gene encoding a protein that binds to the target bacterium. As a result, the phage changes its specificity and begins to recognize other strains of E. coli. Furthermore, thanks to these mutations, bacteria are less likely to develop resistance to phages.

The U.S. Food and Drug Administration (FDA) has approved a number of bacteriophage preparations for use in the food industry (for food processing). However, phage preparations are used sparingly in medical practice in the United States and Europe, in part because the registration procedure for such biophages, which must be specifically developed for specific patients, is not fully developed.

A technique developed by MIT scientists led by Kevin Yehl and Sebastien Lemire may help solve this problem. They created a universal viral scaffold that can be easily customized to recognize and attack a specific target bacterial strain or to overcome the phage resistance mechanisms that bacteria develop.

In 2015, researchers used a T7 phage with a natural ability to kill E. coli and demonstrated that they could program it to destroy various strains of E. coli through specific rearrangements in the genes encoding the tail fibers—the proteins responsible for recognizing and interacting with the surface of bacterial cells. Now, the scientists propose* a strategy that allows for the rapid creation and testing of a significantly larger number of modified bacteriophage variants.

The secondary structure of the protein filaments on the phage tail was previously determined. They were found to be fragments of beta-sheets connected by loops. Scientists hypothesized that the amino acid residues located in the loops (which are known to often protrude from the surface of the protein molecule) are important for recognizing target bacteria but have minimal impact on the spatial structure of the bacteriophage filament. These loop residues were systematically mutated.

Researchers created phages with approximately 10 million different strands and tested them on E. coli, which was resistant to the natural bacteriophage. Some modified phages successfully destroyed E. coli strains resistant to the natural bacteriophage.

Understanding the molecular mechanisms of interaction between bacteriophages and bacteria using modern bioengineering approaches has helped create a vast library of different bacteriophage variants, each of which can potentially recognize different receptors on the surface of E. coli . Also important is that, unlike phage therapy with a single bacteriophage strain, the simultaneous use of different phages from the library dramatically reduces the likelihood of bacteria developing resistance to treatment.

The authors of the work, which will be published in the journal Cell* in October 2019, plan to create phage “blanks” for other pathogenic bacteria.

* Yehl K, Lemire S, Yang AC et al. Engineering Phage Host-Range and Suppressing Bacterial Resistance through Phage Tail Fiber Mutagenesis // Cell, 2019, 179 (2): 459-469.E9. DOI: https://doi.org/10.1016/j.cell.2019.09.015