Fighting Antibiotic Resistance with Biology

Before COVID engulfed the world in crisis, another microbial threat loomed large: antimicrobial resistance. In the U.S. alone, more than 2.8 million people acquire antibiotic-resistant infections each year and 35,000 die as a result. Scientists have been warning about an impending crisis for decades as the pipeline for new antibiotics has dried up. In 2019, the problem had become so dire that Robert Redfield, the director of the U.S. CDC at the time, wrote in a report that we should “Stop referring to a coming post-antibiotic era—it’s already here.”

Phages—or viruses that infect and kill bacteria—are one of the most promising weapons against bacteria that have acquired resistance to antibiotics. Yet, in most of the world they have been relegated to the realm of alternative medicine, only administered as a last resort when all other treatments have failed. As a result, most of the research regarding their use is in small case study reports that aren’t up to the scale and caliber of large clinical trials needed for regulatory approval.

But things might be about to change. In July, the NIH-backed Antibacterial Resistance Leadership Group will enroll the first patients in a phase two clinical trial to assess the safety and microbiological activity of phage therapy in cystic fibrosis patients who are colonized with multi-drug resistant Pseudomonas aeruginosa. The trial will gather rigorous data on a patient population for whom phage therapy is not a last resort but a first pass. The study is the first to be funded by the National Institutes of Health through the Antibacterial Resistance Leadership Group. It aims to collect rigorous data on safety, efficacy and other pharmacologic factors like absorption, metabolism, excretion, dosage, and good manufacturing practices.

“I think we’re in a phase right now where people want to rigorously plan clinical trials,” said Robert Schooley, Infectious Disease Specialist at the University of California San Diego, and co-principal investigator on the trial. “That’s the first step toward bringing this to larger patient populations around the world.”

The trial, which is being conducted in partnership with the Walter Reed Army Institute of Research and Adaptive Phage Therapeutics, aims to enroll between 30 and 40 patients into several groups to establish proper dosing and administration intervals. They also hope to glean information about how to monitor the efficacy of future trials by assessing phage numbers in the sputum and other body tissues and samples. Many hope that it is the first of many to collect information useful for bringing phages into the clinic.

“Trials like this need to get done because there’s multiple bacterial pathogens that are of global significance,” says Steffanie Strathdee, an infectious disease epidemiologist from the University of California at San Diego.

Strathdee had a very personal experience with phage therapy several years ago. While vacationing with her husband in Egypt, he suddenly fell violently ill. What seemed at first like a bad bout of food poisoning worsened over a couple of days into excruciating back pain and they decided to seek medical help. Unbeknownst to him, a superbug infection had taken root in his body after a gallstone became lodged in his bile duct.

The culprit was Acinetobacter baumannii. The bacteria, which is now widespread throughout the globe, has an exceptional knack for picking up resistance to a variety of drugs. It claims the lives of up to 40 percent of the people it infects, and it has become so troublesome in recent years that the World Health Organization listed it as a critical priority for which new antibiotics are urgently needed. The infection left Strathdee’s husband fighting for his life.

“It was horrifying to think that my husband was exploring a pyramid one day and the next day was fighting for his life,” she says.

Doctors tried over 20 different antibiotic treatments with no relief. His immune system just grew weaker as the bacteria gained a stronger foothold. Eventually the infection spread to the blood, leading to bouts of septic shock. Strathdee’s husband fell into a coma and her desperation grew. With very few options left, she found an article on phage therapy and after being encouraged by her colleague, Robert Schooley, she began searching for researchers who would agree to find phages that could be used to treat her husband.

The first known reports of phages came from the Ganges river. In 1892, English doctor Ernest Hankin travelled to India due to strange rumors that the waters of the Ganges had healing properties that counteracted cholera. Despite the river being a place where thousands of people washed themselves and their cattle, the brown and cloudy water that contained half-burnt and decomposing corpses had significantly fewer bacteria than European rivers. Roughly twenty years later, a self-taught microbiologist, Felix d’Herelle, suggested that a virus might be responsible for killing bacteria. And then in 1919, the first therapeutic use of phages occurred when Felix, who was then an intern at the Pasteur Institute in Paris gave a phage cocktail to a 12-year-old boy with severe dysentery. After a single dose, his symptoms subsided.

Strathdee reached out to several researchers who agreed to receive her husband’s bacterial culture and undertake a phage hunt. Within three weeks, two groups each developed cocktails of four phages that were effective in killing the exact strain of A. baumannii that was overtaking her husband. Schooley was granted emergency approval from the FDA to deliver the cocktail intravenously to her dying husband. To their amazement and delight, it worked. He made a full recovery.

Thanks to Strathdee and Schooley’s determination, scientific know-how, and large scientific network they were able to help her critically-ill husband get a tailored phage cocktail for his superbug infection. Together, they founded IPATH, the first dedicated phage therapy center in North America that helps other people with life-threatening superbug infections like her husband. IPATH is one of the sites for the new NIH-funded trial. They hope that more clinical trials will usher in an era when phages can be an accessible treatment for all.

A last resort no more

In order for phage therapy to move into the mainstream, scientists are going to have to collect more data regarding its efficacy, safety and pharmacology. According to Steve Abedon, Professor of Microbiology from Ohio State University, the long tradition of using phages in compassionate use cases has hindered the collection of good data on things like efficacy and even dosage. Compassionate use of a drug doesn’t require having controls, for example, or doing studies in large enough numbers to establish statistical significance. In addition, they are often administered after a long course of antibiotics. Many times, the patient remains on the antibiotics when they are given the phage treatment. This type of study design, which is necessitated by ethical requirements of the study, can cloud the results. If a patient recovers it becomes impossible to tell if it is due to the long-term use of antibiotics or the phage cocktail they received.

“There’s this whole tradition of applying phages preclinically and also clinically without really thinking about what the dosage needs to be,” he says.

In a recent paper, Abedon analyzes the results of 70 clinical trials since 2000 that showed low efficacy with phage therapy and he finds discrepancies in dosing. In one study, the phages were used to treat skin infections, but they are administered at much lower titers than intended.

He says the results were “less than satisfactory,” phages showed some efficacy but not better than antibiotics.

“Although phages are older than antibiotics, there just hasn’t been a lot of money invested in phage therapy and it’s a whole new way of looking at things,” he says.

Most drugs today consist of small molecules that can be chemically manufactured, purified, and pressed into a pill. Phages, in contrast, are biological entities that replicate and evolve.

Manufacturing phages requires they be introduced to host bacteria. They grow and divide inside the cell until it bursts, which releases more phages. The process sounds pretty straightforward, but according to Martha Clokie, professor of microbiology at the University of Leicester, it’s harder than it looks.

When phages burst their bacterial host cells, they expel bits of toxic agents like pieces of the bacterial cell membrane that trigger an immune response and endotoxins that can cause fever and inflammation. These need to be removed. Clokie says the process “isn’t trivial.” “I’ve seen trials fail because they can’t get phages made at the appropriate scale and purity,” she says.inexpensively implemented. Clokie says that today it can cost up to one million pounds to produce high- quality phages for a single clinical trial. But she hopes that growing demand for phage therapy will get regulators and scientists interested in streamlining the process. Her lab is working closely with regulators to develop rigorous preclinical assays to determine good manufacturing practices for the field. “In general, there have been very few clinical trials of phages and until you get that clinical trial data, there’s no way it will become mainstream,” she says.

Leveraging biodiversity

Another major hurdle of working with phages is wading through their enormous biodiversity in order to find ones that work. There are an estimated 10 to the 31 phages in the world. This is an impossibly large number that roughly translates to one trillion phages for every grain of sand in the world. While this infinitely large pool of diversity can be a boon to therapeutic discovery, providing the substrate with which to tackle all various strains of drug-resistant bacteria, finding the right phage for the job remains a challenge. “It’s a needle and haystack thing,” says Schooley.

Companies and researchers are experimenting with a variety of ways to better match phages through bioinformatics techniques. Maryland-based biotech company Adaptive Phage Therapeutics, for example, is amassing libraries of phages that have been matched to their bacterial hosts. The company, which is providing phages for the cystic fibrosis trial, keeps the phages in a biobank-type library and can match them to individual infections. According to Greg Merril, chief executive officer and co-founder, they have phages matched to every strain of drug resistant bacteria that has been characterized to date.

“There is no antibiotic that can make a claim like that,” says Merril. He says they are actively updating the library by asking the scientific community to find resistant bacteria they haven’t yet matched. “If we don’t have a phage for it, our experience is that we can find one within weeks,”  he says.  The diversity of phages is what makes them such a good therapy for bacteria that are constantly evolving and outwitting their enemies. “Every antibiotic that has been introduced is now either obsolete or has some level of resistance associated with it. And phage holds the promise of breaking that paradigm, but only if you’re able to leverage the diversity,” he says.

Merril is optimistic that in the future phages will be a continuous supply of drugs that can evolve to meet the constantly evolving landscape of resistance genes.

And as the trial begins enrolling patients in July, Schooley is also optimistic that they will glean good data using the gold standard approaches used in other clinical trials. “That’s the first step toward bringing this to larger patient populations around the world,” he says. “That’s a good step forward.”

Monique Brouillette is a freelance journalist who covers science and health.