Soon after bacteria-killing viruses were independently discovered by English physician Frederick Twort in 1915 and by French microbiologist Felix d’Herelle in 1917, the tiny microbes were seen to have therapeutic potential. Twort suggested that bacteria-depleted zones on his culture plates could have been caused by an “ultra-microscopic virus,” but he cautiously allowed that they might have been due to a strictly bacterial process of some kind. d’Herelle was bolder. He quickly focused on what he called the bacteriophage—the “eater of bacteria”—and whether it could be used to fight infections.

Indeed, in 1919, d’Herelle and his colleagues administered a cocktail of different phages to a 12-year-old boy with dysentery, who reportedly recovered within days. Early successes such as these prompted interest in the development of phage therapy—at least until the advent of broad-spectrum antibiotics. Antibiotics progressed so quickly that interest in using viruses to treat bacterial infections soon waned in the United States and Western Europe.

Today, phages are back in the limelight in Western medicine as the worrying spread of antibiotic resistance among bacteria has underscored the need for new bacteria-killing therapeutics. Drug-resistant diseases cause some 700,000 or more deaths globally every year, a toll that could rise to 10 million deaths annually by 2050, according to one of the figures cited by the United Nations Interagency Coordination Group on Antimicrobial Resistance.1

“The challenges of antimicrobial resistance are complex and multifaceted,” the report stated, “but they are not insurmountable.” Doubtless this assessment is widely held by phage therapy experts. They are well aware that viruses can encounter bacterial resistance, and that viruses are often too specific to be broadly effective. Nonetheless, many phage therapy experts are optimistic about making progress.

At the 4th Annual Bacteriophage Therapy Summit (a digital event that took place February 14–16, 2022), phage therapy experts discussed new insights into phage-bacteria interactions, the capabilities of new development platforms, and novel means of eliminating drug-resistant or otherwise problematic bacteria. On the whole, the event’s participants maintained that phages are poised to become effective therapeutics.

Tackling prosthetic joint infections

Hesham Abdelbary, MD, an orthopedic surgeon-scientist at the Ottawa Hospital in Canada, knows the risks of bacterial infections in patients who undergo joint replacements to treat degenerative joint disease or joint destruction from metastatic bone cancer. Despite physicians’ best efforts to sterilize implants and support patients’ immune systems, over 10% of immunocompromised or cancer patients can develop a prosthetic joint infection. The standard approach of treating such infections—additional surgery and antibiotics—is only 60–80% effective. That’s partly because bacteria cluster into complex, matrix-reinforced biofilms on implant surfaces, shielding themselves from the host immune system and antimicrobial therapy.

At the summit, Abdelbary stressed that biofilm formation is “a devastating complication.” He also suggested that it could be countered by lytic bacteriophages. These microbes produce enzymes that break down biofilm matrices and kill the bacterial cells within.

In one 2018 in vitro study, Abdelbary and his colleagues found that administering the Staphylococcus aureus–targeting phage SATA-8505 prior to certain antibiotics would kill the biofilm-forming bacteria much more effectively than either treatment alone.2 “I see phage therapy as a complement to antibiotics,” Abdelbary remarked. “It’s not a replacement.”

Abdelbary’s collaborators at the Université Laval and the biotechnology company Cytophage Technologies are working to identify an antibiotic-enhancing cocktail of different phages, an approach that decreases the chances of bacteria tolerating the therapy if they develop resistance to individual phages. Meanwhile, Abdelbary and his colleagues have developed a rat model with titanium hip implants that mimics a human prosthetic joint infection.3 The next step is to examine the phages’ efficacy in infected rats—for instance, via local injections or implant coatings—and monitor for any side effects or impacts on bone health.

Phages go personal

The Belgium-based biotechnology company Vésale Bioscience is pursuing a personalized phage therapy approach. To Bob Blasdel, PhD, the company’s research director, the limited efficacy of phage cocktails in some previous clinical trials illustrates the challenges in developing a one-size-fits-all therapeutic that works across a broad range of bacteria in different patients.4 In addition, Blasdel believes that the current approach of testing and approving fixed antimicrobial therapies is unsustainable.

At the summit, Blasdel supported this view by pointing out that bacteria develop resistance faster than new drugs can be developed. He added, “We see the need for a model that can evolve with the bacteria that ail patients.”

The company’s solution is a “phagogram” for physicians to rapidly identify the most effective phages for a given patient. The diagnostic tool consists of a panel that includes up to 15 phages that can be tested against Staphylococcus, Pseudomonas, and Klebsiella isolates from patients; new phages can be added if bacterial resistance ensues.

The phagogram works by detecting ATP released by dying bacteria and signs that the phages “outreplicate” the bacteria. Pharmacists can then prepare personalized medicines based on the two or three winning phages—an approach that has been employed on more than 100 patients with various infections at Belgium’s Queen Astrid Military Hospital.5

In Europe, this approach could be commercialized through an extrapolation of Belgium’s “magistral preparation” framework, a set of regulations for compounding/pharmacy preparations. It is designed to allow pharmacists to prepare personalized therapeutics in cases where conventional therapies such as antibiotics aren’t sufficiently effective or safe for particular patients, for instance, due to antibiotic resistance or medication allergies. It is a way to bypass the need for clinical trials for each phage formulation.

As Blasdel pointed out, magistral preparations can shift the focus of evaluations from treatments to diagnostics. “It’s the diagnostic that we will be testing for safety and efficacy,” Blasdel said.

Using bacterial machinery against bacteria

Other groups are tinkering with the DNA of bacteriophages to make them more effective killers. For example, Phico Therapeutics, a biotechnology company in the United Kingdom, is genetically engineering phages to rapidly introduce a gene for a small, acid-soluble spore protein, or SASP, into bacterial cells.

pan-spectrum antibacterial phage technology
Phico Therapeutics develops pan-spectrum antibacterial phage technology as the basis of a new generation of antibiotics. The company’s SASPject platform uses engineered phages to inject genes encoding small acid-soluble spore proteins (SASPs) directly into targeted bacteria. The injected genes direct the targeted bacteria to produce SASPs, which can then bind to bacterial DNA and inactivate it.

In bacteria, SASP genes are ordinarily expressed only during sporulation, when SASPs are used to coat and protect the DNA of bacterial spores. The SASPs make the DNA rigid and dormant. However, when SASP genes are delivered to normally growing bacteria, the bacteria express SASPs that bind to and inactivate their own DNA. “This immediately stops gene transcription,” explained Heather Fairhead, PhD, Phico’s CEO. “The replication of bacteria stops, and the bacteria, obviously, then die.”

Because SASPs bind to DNA in a sequence-independent manner, they’ll silence bacterial genomes even if bacteria mutate in ways that confer resistance to phages. “Phico’s SASP technology, which is called SASPject, is used either on individual phages or mixtures of closely related phages whose binding sites are genetically tweaked to broaden the range of bacterial strains they infect—an approach Fairhead said yields a more reproducible and controllable product than comparatively heterogenous cocktails of different wild-type phages.

In recent in vitro studies by Phico scientists, a phage product called SASPject PT1.2 killed 225 diverse isolates of Staphylococcus aureus, including many that were resistant to the antibiotic methicillin or to an ancestral wild-type phage.6 “Even in bacteria which are resistant to the phage internally—so they can degrade the phage DNA—we still get killing by SASPs,” Fairhead asserted.

 SASPject antibacterial technology's unique mode of action
Phico Therapeutics asserts that its SASPject antibacterial technology has a unique mode of action (detailed in this image) that enables pan-species coverage and reduces the chances that targeted bacteria will develop resistance. The engineered bacteriophages that deliver the small acid-soluble spore proteins (SASPs) can be provided with alternative host receptor binding domains, expanding the host range as required. Because SASPs inactivate bacterial DNA in a sequence-independent manner, their activity is unaffected by DNA mutations.

The plan is to develop PT1.2 into a gel for certain surgery patients to decolonize methicillin-resistant bacteria in the nose to prevent subsequent infection of a wound—following promising safety results in a Phase I study, Fairhead said. Phico’s current focus, however, is developing an intravenous phage therapy for ventilator-associated pneumonia caused by drug-resistant Pseudomonas aeruginosa. Phase I studies are planned for 2023.

Phages meet the skin microbiome

Another company that employs genetic engineering is Felix Biotechnology. The California-based firm modifies phages to broaden the range of bacterial strains that can be targeted. The company’s core technology rests on a set of machine learning algorithms that sift through genomic sequences of phages and data on their ability to kill various bacteria. For a given target bacterium, the algorithms identify genetic signatures associated with a phage’s host range, which are then used to guide the engineering of phages. “We primarily use the technology to optimize a phenotype,” explained Robert McBride, PhD, the company’s co-founder and CEO.

Felix’s main focus has been developing treatments for patients with life-threatening infections. “In 2021, the company launched a Phase I/ II study to test the inhalable phage therapy YPT-01—which consists of phage selected for various features, including ones that aim to resensitize bacteria to antibiotics—in 36 cystic fibrosis patients with chronic airway infections of Pseudomonas aeruginosa.7   The trial used wild-type phages, but the commercial version of YPT-01 is engineered,” McBride said.

Felix’s scientists are also working with skin care companies to develop chemical-free ways to selectively eliminate undesirable bacteria to treat ailments such as bed sores and diaper rashes. Unlike many existing personal care products that disturb the native skin microbiome, phages “are really well positioned to be like precision bombs,” McBride noted. “[They can] go in there and take [out] the bad bacteria and preserve the good bacteria.

“The engineered phages deployed by Felix promise to outperform traditional phage cocktails that may work well in situations where only one dose is needed, such as in pneumonia, but could falter in situations where repeated doses are needed. However, Felix’s precision snipers may be a more effective approach in situations where successive exposures to a treatment occur. Such a situation is the treatment of repeated bacterial outbreaks on skin.”

Phages as therapeutic delivery vehicles

Meanwhile, North Carolina–based Locus Biosciences specializes in engineering phages to carry a CRISPR genetic modification system. But rather than the popular DNA-snipping Cas9 enzyme, the phage DNA encodes a Cas3 system, which effectively shreds and destroys bacterial DNA, explained Paul Garofolo, the company’s co-founder and CEO.

“When you add in CRISPR-Cas3, the idea is to make every infection event a kill event,” Garofolo said. The company’s most advanced therapeutic is LBP-EC01, a cocktail of six CRISPR-Cas3-harboring phages designed to tackle multidrug-resistant Escherichia coli strains in urinary tract infections.8 According to Garafolo, LBP-EC01 will soon enter a Phase II/III trial.

The company is also exploring other uses for phages, such as inducing resident gut bacteria to express therapeutic molecules. If phages could be employed this way, they could avoid one of the limitations of conventional therapeutics for conditions such as ulcerative colitis or Crohn’s disease. Because conventional therapeutics are systemically delivered through the bloodstream, they tend to build up in the liver and kidneys without reaching high enough concentrations in the gut itself.

To develop better treatments for conditions such as ulcerative colitis or Crohn’s disease, Locus scientists are tinkering with phages engineered to carry DNA that encodes molecules such as interleukin-10 or tumor necrosis factor-alpha inhibitors. Those phages could be ingested orally and thus delivered to the gut, where they infect certain bacteria and induce local production of the molecules. “The hope would be that you’re having a much better therapeutic effect for that particular target,” Garofolo explained.

Uses for phage technology range from the killing of bacteria to the modulation of the human microbiome. “The applications are limitless,” Garofolo declared.

“I think we’ll see a brand-new field of medicine in the next 20 years as we learn to optimize a patient’s microbiome to treat disease.”

 

References
1. Interagency Coordination Group on Antimicrobial Resistance. No time to wait: Securing the future from drug-resistant infections—Report to the secretary-general of the United Nations. World Organization for Animal Health.
2. Kumuran D, Taha M, Yi Q, et al. Does treatment order matter? Investigating the ability of bacteriophage to augment antibiotic activity against Staphylococcus aureus biofilms. Front. Microbiol. 2018; 9: 127. DOI: 10.3389/fmicb.2018.00127
3. Hadden WJ, Ibrahim M, Taha M, et al. 2021 Frank Stinchfield Award: A novel cemented hip hemiarthroplasty infection model with real-time in vivo imaging in rats. Bone Joint J. 2021; 103-B (7 Suppl. B): 9–16. DOI: 10.1302/0301-620X.103B7.BJJ-2020-2435.R1.
4. Jault P, Leclerc T, Jennes S, et al. Efficacy and tolerability of a cocktail of bacteriophages to treat burn wounds infected by Pseudomonas aeruginosa (PhagoBurn): A randomised, controlled, double-blind phase 1/2 trial. Lancet Infect. Dis. 2019; 19: 35–45. DOI: 10.1016/S1473-3099(18)30482-1.
5. Djebara S, Maussen C, De Vos D, et al. Processing phage therapy requests in a Brussels military hospital: Lessons identified. Viruses 2019; 11: 3. DOI: 10.3390/v11030265.
6. Cass J, Barnard A, Fairhead H. Engineered bacteriophage as a delivery vehicle for antibacterial protein, SASP. Pharmaceuticals (Basel) 2021; 14: 10. DOI: 10.3390/ph14101038.
7. CYstic Fibrosis BacterioPHage Study at Yale (CYPHY). ClinicalTrials.gov Identifier: NCT04684641.
8. Locus Biosciences. Locus Biosciences signs contract with BARDA to advance $144 million precision medicine program to develop LBP-EC01, a crPhageTM product. Published September 30, 2020. Accessed June 22, 2022.

 

Katarina Zimmer is a self-employed science & environmental journalist, writing for GEN.