During a 2015 trip to Egypt, Tom Patterson suffered a gallstone attack and soon fell terribly ill. But that’s not what nearly killed him.
Patterson had been infected by Acinetobacter baumannii, a superbug that grew in a cyst inside his abdomen. The particular superbug — a bacterium resistant to multiple antibiotics — is often found in troops returning from the Middle East. The World Health Organization has named it one of the 12 most deadly superbugs on the planet.
The infection spread throughout Patterson’s body, leaving him fighting for his life. Soon, he was in a coma.
His wife, Steffanie Strathdee, felt chagrined — it was like the universe was playing a cruel joke. She’s an epidemiologist, professor, and associate dean of global health sciences at the University of California San Diego School of Medicine, but the force of the superbug blindsided her. She couldn’t believe it was stealing her husband’s life and didn’t know the superbug crisis was on track to kill one person every three seconds by 2050.
Strathdee watched as her husband went in and out of septic shock. Reality hit her: Tom was going to die unless something drastic happened. “If he’s going to die,” she recalls thinking, “then I want to know that I left no stone unturned.”
Sepsis is an exaggerated immune response to a bacterial infection, often triggered by a superbug infection that remains undeterred by antibiotics. Each year, nearly 300,000 people die from sepsis and 1.2 million die from superbugs. And more are dying each year. The problem has become worse amid the COVID-19 pandemic, and Vatsan Raman is well aware of its tragic consequences.
“Bacterial infections are a slow-burning epidemic that has been happening for the last 20 years,” says Raman, associate professor of biochemistry and bacteriology at CALS. “It’s a compelling societal problem. If you were to list some of the grand challenges that society faces, bacterial resistance to drugs is among the top three.”
Raman wondered if molecular methods and synthetic biology could be applied to the superbug crisis and potentially save lives. When he learned about phage therapy, Raman felt cautiously optimistic — it seemed to hold true promise.
In nature, bacteriophages are the natural predators of bacteria. Phages, as they’re commonly known, are classified as viruses; they infiltrate the walls of bacteria and hack their biological machinery to make a slew of baby phages. Those baby phages fill the bacterium until it explodes; then they seek other bacterial cells to destroy. Bacteria mutate to survive these attacks from phages, Raman says, in an evolutionary arms race that has been raging for billions of years.
As Raman studied phages, he wondered whether their natural powers could be harnessed to fight multidrug-resistant bacteria. If an effective process could be found, thousands — perhaps millions — of lives could be saved. “That’s the idea that got me involved in this space,” he says.
“I have thought of the phage as the ultimate smart drug,” Raman says. “It precisely targets a pathogen, unlike traditional antibiotics , which cause collateral damage. It is evolvable, which means that if bacteria become resistant to a phage, we can evolve the phage using synthetic biology to remain effective against the bacteria. With traditional antibiotics, once bacteria become resistant, it is a dead end. Finally, there is a limitless supply of phages in nature to work with. Some estimates suggest there are more than [one nonillion] phages on Earth.”
The goal of Raman’s lab has always been to repurpose nature’s processes in ways that are beneficial to humans. For the last five years, he and his team have been working on ways to make thousands of mutations to phages. With phage therapy, they want to see what mutations can best kill the deadliest bacteria in the world, hoping to fight back against the superbug crisis.
“You can think of this as supercharging evolution,” Raman says.
As Strathdee scoured medical journals for ideas to save her husband, she read about phage therapy. She knew what phages were but didn’t know much about how they could be used as medicine. Strathdee felt thrilled to find a lead, far-fetched as it may be. But as Patterson was fighting for his life, phage therapy was still on the fringes of U.S. science, where it was never widely studied as a human therapy.
Strathdee read the history of phage therapy, finding that many U.S. scientists had turned their backs on it in the 1930s. Scientists in the Soviet Union were studying phage therapy, and few Americans of that era wanted any associations with communism. Then, after Scottish scientist Alexander Fleming discovered penicillin, the Western world found its own way to treat bacterial infections. The idea of phage therapy remained dormant for decades in U.S. research labs; it was practiced primarily in Eastern European countries, such as Poland, Russia, and Georgia.
But perhaps phage therapy could help Patterson, who lay in a two-month coma. Strathdee’s colleague, Chip Schooley, chief of infectious diseases at the UCSD School of Medicine, thought that phage therapy could be approved for Patterson as a last resort. He contacted the Food and Drug Administration to get approval for compassionate use of phage therapy, which, at the time, was the only way it could be administered to humans stateside.
Schooley and Strathdee recruited colleagues from universities around the world to search their phage libraries and send any phages that had the potential to destroy Patterson’s bacterial infection. They also engaged in phage hunts to source them from sewage, barnyards, and bogs. Within three weeks, Patterson’s doctors had two phage cocktails ready, even receiving reinforcements from the U.S. Navy. Researchers purified the first phage cocktail and started treating Patterson, the first time in U.S. history that doctors delivered phages to a patient intravenously. They did so out of urgency, as Patterson seemed to have little time left.
In a frustrating turn, Patterson’s infection became resistant to all phages except for one the Navy had sent. The Navy had found that this new phage matched mutated bacteria discovered in a Maryland sewage treatment plant. Once again, doctors purified a phage cocktail, injected it into Patterson, and hoped for the best.
In 2021, Raman was one of 12 investigators across the U.S. to receive a grant from the National Institute of Allergy and Infectious Diseases (NIAID), which is a branch of the National Institutes of Health, to study phage therapy. These were the first series of phage therapy grants NIAID had ever given.
“It was an exciting grant to get,” Raman says. “Now we’re at the point where we’ve developed some of these tools.”
Raman and his team published a paper in the journal eLife in March 2021 highlighting a method they created, one that would systematically map how altering a phage’s DNA sequence changes how it interacts with bacterial hosts. The process is about removing roadblocks that impede the phage’s ability to attack bacteria, Raman says.
The method, dubbed ORACLE — optimized recombination, accumulation, and library expression — makes tens of thousands of changes to the phage’s DNA. While evolution makes one change at a time to see if a version of a phage can kill the current version of its host, ORACLE makes thousands of changes at once, searching for the phage mutations that will kill drug-resistant bacteria.
“We’ve accumulated mutations of phages that are highly effective at killing each host, much more so than in nature,” Raman says.
Each phage genome generally has dozens of genes, Raman says, some of which are good candidates for laboratory-guided evolution to improve a phage’s ability to kill bacteria. In his lab, they identify the most effective genes and then acquire synthetic DNA from a commercial manufacturer to introduce mutations into the phage’s gene pool. ORACLE searches for the most effective phage genes, introducing mutations that will make the phages even more effective at fighting bacteria.
“We have the spool of DNA — it could be 10 or 1,000 changes you want — and we replace the native DNA of the phage with all the synthetic changes that we designed,” Raman says. “Now that we have a million different baby phages, and each baby phage has a new sequence, we put them through a giant competition. We give these phages bacteria to attack — the phage that is the most effective at killing the bacteria will make more of itself. The phage that has an ineffective mutation will just drop out simply because it can’t make more baby phages. After a few cycles, we can select the fittest phage. It’s just like how nature does reproduction, except we’re doing it much faster. It’s highly effective.”
Raman credits Phil Huss PhD’22, who recently graduated from UW’s Microbiology Doctoral Training Program and now works as a researcher in Raman’s lab, as the creator of ORACLE. Huss said that he was inspired to create ORACLE when he wanted to do deep mutational scanning on phages, but no way to do so existed. “I had to make a way,” Huss says.
Over the course of about 18 months, Huss created a process that combines cutting-edge synthetic DNA and genome editing technologies to create a tool to precisely modify the phage genome. Recombining synthetic DNA into the phage genome was the hardest piece of the process to integrate, Huss says. In recombination, pieces of DNA are broken and reassembled to create new combinations of alleles (the different versions of DNA sequences). For ORACLE, Huss says that recombination had to take place as the phage was already attempting to destroy the host. “That was the one process when, once it worked, I knew that the whole thing could work,” he says.
The promise of ORACLE, according to Huss, is that it will help researchers know more about different parts of the phage that can be effective killers of bacteria. If a phage is good at killing E. coli or salmonella, researchers can use that knowledge to design phages that will target these bacteria, thus fighting back against the problem of drug-resistant bacteria.
And ORACLE is a much speedier process than traditional methods of phage-finding. Searching through phage libraries to find a phage that could kill a multidrug-resistant bacteria could take weeks, even months. ORACLE moves faster, finding and creating effective bacteria killers within two to three days, according to Raman.
“Biologists have accumulated that information [in phage libraries] over decades of work,” he says. “We’re standing on their shoulders. We know what phages can infect what bacteria. Now, the question is, can we supercharge evolution and make them really good at infecting that bacteria?”
Three days after Patterson began receiving intravenous phage therapy, he woke up from his coma. The phage cocktail seemed to work in concert with one of the antibiotics he had been receiving. Within three months, he was free of infection. Soon, Patterson was back to work as a psychology researcher at UCSD. Something drastic had truly happened.
Strathdee was amazed and grateful. After deep reflection, she decided to become an advocate for phage therapy and an activist for solutions to antimicrobial resistance.
“My husband and I were very privileged,” Strathdee says. “Initially, we thought it was the worst thing that could ever happen. But if we lived anywhere else, or if I didn’t have resources and connections, then he would have died. And that’s what happens to the majority of people in middle-income countries. We’re trying to pay it forward by helping other people get this treatment more easily than we did.”
Patterson’s story went viral, receiving news coverage and case-study write-ups in top medical journals. Together, Patterson and Strathdee wrote the book The Perfect Predator: A Scientist’s Race to Save Her Husband from a Deadly Superbug. Strathdee, alongside Schooley, also became codirector at UCSD’s Center for Innovative Phage Applications and Therapeutics (IPATH). Strathdee has had more than 1,500 people around the world contact her to ask for help in accessing phage therapy, and IPATH has been able to help many of them.
As Patterson’s story became widely known, the U.S. science community rediscovered phage therapy. The Food and Drug Administration began making it easier for people to get access to phage therapy earlier, while the NIH and NIAID began giving grants so researchers could study phage therapy, which includes the funding Raman’s lab received. The FDA also launched the first series of clinical trials for phage therapy.
“We’re entering a new era now,” Strathdee says. “Hopefully, these trials will show that phage therapy works on a broader scale so that the FDA can approve it. Until then, they have to be approved on a case-by-case basis, and it’s generally only for life-threatening cases.”
Raman has seen interest in phage therapy explode since it brought Patterson back from the brink of death.
“There’s a line of companies that are now developing phages and testing them to see how effective they are against different kinds of bacteria,” Raman says. “We’re not at the point where we can administer phages in the clinic, but we’re getting closer and closer.”
In his lab, Raman has seen just how effective phages can be against multidrug-resistant bacteria. His lab picked a drug-resistant bacteria from the CDC’s urgent threat list — one that is completely resistant to more than 35 antibiotics and is partially susceptible to only two last-resort antibiotics. Using ORACLE, they created phages that killed these bacteria in the lab. Raman believes that, once approved clinically, phage therapy will offer medicine a new opportunity to treat stubborn infections.
“The mechanism that the antibiotics use is different from how phages do business,” Raman says. “Bacteria may have picked up all these mutations over time to defend itself against every antibiotic, but the phages get through using a different cell surface protein — it’s essentially like they use a different door to enter the bacteria. That’s what makes the phages attractive, and that’s why we were able to design phages that could kill bacteria that are resistant to 35 different variants.”
Watching a phage kill a multidrug-resistant bacteria in the lab truly sold Huss on the promise of phage therapy. “That was one experiment where we were looking at one region on the phage,” Huss says. “I can only imagine how effective it would be if you look at all the different areas across the phage genome. To me, that made phage therapy seem more real.”
Huss sees ORACLE as a process that will be useful for finding hotspots across phages, information that can be used to better treat multidrug-resistant bacteria. He hopes this method can give other researchers a broader view of the phage structure. “If you’re just trying to look at individual phage variants, you’re only getting this really small piece of the picture,” Huss says. “Our goal was to create tens of thousands of variants to get the entire picture.”
Now Raman’s lab is researching ways that phages and ORACLE can be used to precisely edit the microbiome, for both humans and livestock. And the lab will likely keep taking on new projects. “We like to foster innovation,” Huss says. “Vatsan encourages fresh ideas from everyone in his lab and enjoys exploring the feasibility of those ideas with us.”
Strathdee felt hopeful when hearing about the work from Raman’s lab. She believes that one of the biggest bottlenecks in phage therapy research has been hunting for phages and modifying them genetically — the more solutions look to address this problem, the better. The first genetically modified phage cocktail was used successfully on a human in 2019, she says; and she, like Raman, has noticed that many biotech companies are entering this space. She hopes that research can make up for the lost years when phage therapy went unstudied.
“New antibiotics take 10 to 15 years to develop, and my husband’s phage cocktail was developed within three weeks,” Strathdee says. “Imagine having a phage library, where somebody could just take an already characterized phage and then see if it matches the bacterial isolate. That can be done in 24 hours. There’s an initial start-up cost, but the more it gets done, the cheaper it will get.”
This leads to what Raman considers to be the biggest question for phage therapy: Is it commercially viable? Phage therapy may be a tough sell for large pharmaceutical companies, Raman says, because it’s a treatment that quickly and inexpensively solves a problem. There will be few repeat customers for successful phage therapy treatments, which means it may be hard to profit from phages.
“It’s not obvious to me that there’s a strong business model,” Raman says. The thought of solving this problem himself and entering the commercial side of phages has crossed Raman’s mind. “But,” he says, “we’re not there yet.”
For Strathdee, who has seen the impact of phage therapy firsthand, the biggest question is how to push past the business challenges and bring phage therapy to more patients. Superbugs are a global issue, she says, that will take a collective political will to solve.
“This is a global health problem,” Strathdee says. “We need to have a global health solution.”
Raman believes phage therapy offers a solution to this global health problem, which has caused grief for millions while promising grief for millions more. But while the crisis is tragic, Raman feels a sense of hope. At first cautiously optimistic about phage therapy, now he’s certain that it will save lives.
“I’m more convinced now than ever,” Raman says, “that the phage revolution will have a large impact.”This article was posted in Basic Science, Fall 2022, Features, Health and Wellness and tagged antibiotic resistance, Bacteriology, bacteriophages, Biochemistry, National Institute for Allergies and Infectious Diseases, National Institutes of Health, ORACLE, phage therapy, Phil Huss, sepsis, superbugs, Vatsan Raman.