In 2019, a paper in Nature Medicine described a British teenager whom doctors pulled back from the brink of death. The young woman had developed a deadly, antibiotic-resistant infection following lung surgery. The treatment? Phage therapy, in which viruses are used to kill dangerous bacteria. This novel approach made headlines around the world. The phage therapy field is witnessing a resurgence. The market for phage therapies is projected to grow 17% by 2030, reaching an annual worth of roughly $84 million. Let’s look at the science behind phage therapy for antibiotic-resistant bacteria.
IMPORTANT TERM: BACTERIOPHAGE
A bacteriophage—also referred to as a phage—is a virus that infects bacteria. By attaching to the microbe’s surface, a phage punches holes in the membrane and injects its own genetic material. The intruding phage replicates, creating so many new viruses that the bacterium explodes. A slew of new viruses infects other bacteria, wiping out the population.
The word “bacteriophage” comes from the Greek word phagein—“to devour.” These ravenous microbes often have a taste for the bacteria that can kill us.
Typically a phage ”partners” with only one type of bacteria. They’ve coevolved for millennia, each adapting and changing in response to the other. That’s key. It means that we’re much less likely to develop “phage resistance”—as we have too many antibiotics.
So when researchers tweak a bacteriophage for therapeutic use, they select one that will attack only nasty bacteria. This remarkable precision leaves many strains of “friendly” bacteria that comprise our gut microbiome alone. Humans have safely coexisted with bacteriophage literally for ages, which suggests the viruses pose only a minimal safety risk.
We’ve known about the bacteria-devouring ability of phage for about a century. However, the seemingly miraculous advent of antibiotics in the late 1920s shifted medicine’s focus to the new wonder drugs. Antibiotics were much easier to manufacture and test in controlled settings.
The alarming emergence of antibiotic resistance has renewed interest in these killer viruses, which are, for the first time starting to be manufactured and tested in a standardized way. Here are some biotech companies delving into the promising world of bacteriophage-based therapeutics.
THE VIROLOGISTMIXOLOGISTS GET BUSY
The first multicenter clinical trial examining bacteriophage as an antibacterial treatment was initiated in 2015 by French biotech Pherecydes (Paris, France). Since bacteriophages are an entirely new type of biologic drug, the researchers had to establish production protocols to meet good manufacturing practice guidelines.
The scientists are studying two viral “cocktails”— mixtures of different bacteriophages that have shown activity against different substrains of a particular bacteria. The first contains 13 phages targeting P. aeruginosa; the second 12 phages that target E. coli. The company is evaluating them against burning wound-associated infections. The company is also on the cusp of clinical trials of phage therapy to treat diabetic foot ulcers infected by S. aureus.
Other companies testing phage cocktails include:
- Armata Pharmaceuticals: (Marina del Rey, California): Phage cocktail AP-SA01 is now in Phase 1b/2a clinical testing for antibiotic-resistant S. aureus against chronic rhinosinusitis and acute, chronic wound, and skin infections. Additional targets include bacteremia, endocarditis, prosthetic joint infections, osteomyelitis, and diabetic foot ulcers.
- TechnoPhage (Lisbon, Portugal): Phage cocktail TP102 has successfully completed Phase II clinical trials for bacteria associated with chronic ulcers in December 2022.
- Intralytix (Baltimore, MD): Completed Phase I studies of a bacteriophage to treat infected wounds. The company is also developing phage-based biologics to fight food-borne pathogens. Its EcoShield targets coli, and SalmoFresh, salmonella.
- EpiBiome (South San Francisco, CA): Phage cocktails targeting E. coli and S. dysenteriae diarrheal infections were in preclinical development by EpiBiome. However, the company was closed in July 2018 and acquired by Locus Biosciences (Morrisville, North Carolina). Locus Biosciences, leveraging its CRISPR-Cas3-engineered phage (“crPhage”) platform, aimed to revolutionize antibiotic product development by combining the safety profile of phages with the efficacy advantage of CRISPR. Locus Biosciences has continued to advance its research and development in precision antimicrobials, with a particular focus on combating antibiotic-resistant “superbug” bacteria such as Clostridium difficile, Pseudomonas aeruginosa, and Enterobacteriaceae.
THE BIOENGINEERS TAKE A WHACK
Creating a phage cocktail is challenging. Happily, it’s also possible to genetically engineer a synthetic virus that combines the desired properties of multiple phages into a single genome.
For example, scientists can insert genes into a phage genome that increases the range of bacteria subtypes an individual phage can attack while maintaining the specificity that prevents it from turning on benign bacteria. Researchers could also add genes to amplify the bacteriophage’s antibacterial response further. Companies that worked with engineered bacteriophage in preclinical development include Viridos (La Jolla, CA, formerly Synthetic Genomics, and EnBiotix (Cambridge, MA), now closed and acquired by Spexis (Allschwil, Switzerland).
LYSINS IN WAIT
A third approach to harnessing the therapeutic power of bacteriophage lies in isolating what makes them toxic. For example, a phage must essentially bash holes in its membranes to inject its genome into bacteria. This blow is itself very damaging to bacteria. The viral protein that creates these tears is lysins—enzymes that chew holes in the bacterial cell wall. In 2019, ContraFect (Yonkers, NY) completed Phase II clinical studies of its drug Exebacase (CF-301)—a lysin—to treat S. aureus bloodstream infections and had demonstrated positive outcomes. Exebacase, when used in combination with standard-of-care (SOC) antibiotics, showcased better clinical response rates in comparison to just the SOC antibiotics alone. Currently, Exebacase is conducting Phase III clinical study known as the “DISRUPT” trial (Direct Lysis of Staph aureus Resistant Pathogen Trial).
Locus Biosciences (Morrisville, NC) identifies bacteriophage that targets specific strains of bacteria and engineers them to deliver CRISPR components to those bacteria, including guide RNA and the Cas3 protein. The guide RNA directs the Cas3 protein to cut up the bacterial DNA.
For CRISPR genome editing, the Cas9 protein is used. Cas9 cuts target DNA in a single, precise location. Cas3 chews up target DNA much more thoroughly than Cas9, making it a better choice for destroying a bacterium. Locus has conducted phase 2/3 of CRISPR-enhanced bacteriophage precision medicine (LBP-EC01) to treat urinary tract infections (UTI) caused by E. coli and announced in September 2022 that they had treated the first patient of UTI in these clinical trials.
Although still in its early days, bacteriophage therapy offers the possibility of a safe, effective, and intriguing solution to one of the significant public health crises of our time.