Are cures for some of the world’s deadliest diseases hiding in our sewers?

Scientists are turning to a surprising ally in the battle against drug-resistant bacteria: A special type of virus found in our most polluted places.

By Jess Craig
Published 19 Dec 2022, 12:37 GMT
Martin Georges, a technician in Dr. Lillian Musila’s laboratory at the Kenya Medical Research Institute, pipettes ...
Martin Georges, a technician in Dr. Lillian Musila’s laboratory at the Kenya Medical Research Institute, pipettes bacteriophages onto a petri dish containing bacteria.
Photograph by Jess Craig

Early one morning in October, Lillian Musila, Martin Georges, and Moses Gachoya packed lab coats, medical gloves, and plastic coolers into a white Toyota 4X4, departed the manicured grounds of the Kenya Medical Research Institute campus, and set off for the outskirts of town. Their destinations are the dirtiest, germ-teeming places that come to mind: sewage treatment plants, polluted rivers, the wastewater that runs between the densely packed, tin-roofed shops and homes in Kibera, one of Africa’s largest slums.

For most people, just the thought of the disease-causing bacteria and viruses in these places would spark a shudder. But for Musila, an infectious diseases researcher, these places are, paradoxically, brimming with urgently needed weapons to treat some of the deadliest superbug infections in the world. Musila and her team are searching for bacteriophages, or phages—viruses that infect and kill bacteria, generally without harming the human host.

“The concept is that the enemy of my enemy is my friend,” Musila, a principal research scientist in the Department of Emerging Infectious Diseases explained.

Antibiotics have been a cornerstone of modern medicine since the 1940s, helping to increase the human lifespan by 23 years. But today, many types of disease-causing bacteria have developed ways of evading antibiotics, a phenomenon called antimicrobial resistance, or AMR. The World Health Organisation cites AMR as one of the most urgent public health threats to humanity. Researchers estimated that drug-resistant bacteria caused more than a million deaths in 2019, making AMR a leading cause of death globally.

New antibiotics are urgently needed, but a new antibiotic class has not been discovered since the 1980s. Today with few pharmaceutical companies actively developing antibiotics, phage therapy is one of the few possible solutions to AMR.

Although phage therapies are still an emerging area of research, they have been safely and effectively used in the former Soviet Union and post-Soviet states since their discovery in 1917. Emerging evidence from clinical trials and emergency use cases in Europe and the U.S. indicates that phages are safe and effective in treating even those infections all known antibiotics cannot cure.

Eight years ago, Musila learned that AMR was already a major challenge in the country and began working on a nationwide surveillance project examining AMR in bacteria from patients hospitalised across Kenya. Although there are challenges with unbiased data collection, Musila and her colleagues found that around 60 percent of documented infections were resistant to multiple types of antibiotics, including the cheapest, most readily available ones, she recalled. Her team started sounding the alarm. But Musila, whose background is in developing new clinical diagnostics and therapies, wanted to do more than describe the problem.

“It felt like we were just going around declaring doom and the impending end of the world,” Musila said. “I thought, you know, we can't just sit here and document that things are bad. We wanted to look at solutions.” She attended a conference where she heard about ongoing phage research, and when she returned to her laboratory, she wrote up a protocol and, in 2016, launched her first phage hunt.

The hunt

At the Nairobi City Water and Sewerage Company, Georges, a technician in Musila’s lab, and Gachoya, an intern, buttoned their blue lab coats, snapped on disposable gloves, and cautiously approached the edge of a deep cement pond containing brown, bubbling sewage. In the foul water, bacteria are hard at work breaking down solid waste, and phages, found naturally in the environment, are busy infecting those bacteria, replicating, and then bursting out of them to find their next host.

As Musila watched, Georges plunged a yellow plastic container into the sludge and retrieved it with a thin rope. Carefully, he poured the specimen into a plastic container; Gachoya labelled it “sewage” and dropped it into an empty cooler. They collected more samples at the front of the plant where raw sewage rushes into the facility. Then they drove into Kibera; Georges waded into a shallow stream where wastewater rushed over layers of trash and repeated the collection process.

Back at the lab, Georges and Gachoya combined all the samples and ran the sewage and wastewater through a tiny filter, sifting out everything but the microscopic phages, which are smaller than even the tiniest viruses and bacteria. They cultivated and multiplied the phages by feeding them bacteria—in this case, drug-resistant Klebsiella pneumonia and Pseudomonas aeruginosa, two common global pathogens and a focus of Musila’s ongoing work—and set the mixture aside.

The next day, the pair placed small drops of liquid containing the phages on bacteria growing in Petri dishes. Phages that kill the bacteria leave a small, circular clearing in on the surface of the dish, a sign that the bacteria that were growing there are dead. The team then work to isolate and purify these killer phages. In just a few days, after sequencing the phage genomes the team will know how many new phages they have discovered and will freeze the novel viruses at -80 degrees Celsius for future research.

Phage discovery is relatively quick and inexpensive, and unlike traditional pharmaceutical research, requires only basic laboratory equipment and skill. By contrast it takes between 10 and 15 years and at least a billion dollars to identify a new antibiotic.

“Undergraduate students, high school students, essentially anyone with a scintilla of curiosity to learn about these things can do this,” said Graham Hatfull, a professor at the University of Pittsburgh, where he runs the SEA-PHAGES program which has taught more than 40,000 first-year students to find phages.

This has critical implications for reducing global inequities in health, research, and access to medicines. Available, albeit limited evidence, suggests that the AMR burden is highest in Africa and Asia. Yet, many developing countries, including 37 in sub-Saharan Africa, do not have a domestic pharmaceutical industry and must import medical supplies, medicines, and vaccines from Europe and the U.S.

“I often point to the inequitable distribution of COVID vaccines during the pandemic and how they were so slow and still are slow to get to developing countries,” said Tobi Nagel who runs the nonprofit organisation Phages for Global Health, which helps to build phage research capacity in developing countries.

The same is true for antibiotics. Many developing countries lack consistent access to even basic antibiotics let alone more advanced drugs or combination antibiotics that are effective against some resistant microbes. In 2019, researchers in Malawi, for instance, reported that only 48.5 percent of basic, essential medicines were stocked at public health facilities while the cost of one course of more than half of those medicines exceeded the average daily wage of Malawians and were unaffordable. Phage therapies can be developed in countries most impacted by AMR while avoiding the cost and technical barriers of traditional pharmaceutical research and development.

“It's an accessible solution for the developing world. I think that's the beauty of it,” Musila said.

In addition, anecdotal evidence suggests that phages found in the same area as the bacteria they infect are more potent than phages found in other parts of the world. When Musila and her team tested phages from researchers in Russia against a panel of bacteria found in Kenya, the Russian viruses were not effective. Ivy Mutai, a phage researcher at the Institute of Primate Research in Nairobi, had a similar experience when she and her colleagues tested phages from Georgia against Kenyan bacteria strains and found them less effective than phages isolated locally.

Phages infect bacteria by binding to one, or at most a few, receptors on the surface of the cell. This specificity is described as a lock-and-key design. In the environment such as sewage or rivers, bacteria evolve to evade the phages and phages in turn adapt to regain the ability to infect bacteria. Over time, this arms race seems to create phages that are highly effective at killing only specific, local bacteria strains.

“You see that geographical variation is quite big,” Mutai explained. “This calls for Kenyans to look for phages specifically for infections in Kenya,” she said.

Phage research and clinical trials

In the six years since Musila launched her first phage hunt, her team has identified more than 150 phages that can target and kill what are called the “ESKAPE” pathogens, an acronym for Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, and other bacteria that most commonly cause drug-resistant infections and deaths in humans.

In addition to her work hunting for phages to fight common human infections, Mutai, under the guidance of Atunga Nyachieo, who heads the phage research program at the Institute of Primate Research, is also interested in identifying phages that could prevent common bacterial diseases in crops or could sanitise medical equipment and surfaces in hospitals which are often a source of drug-resistant pathogens.

At the International Livestock Research Institute, also in Kenya, Angela Makumi and her team have developed a phage treatment that prevents salmonella infections in poultry. Makumi is currently overseeing animal studies to test a phage-containing powder that can be delivered orally to the birds and expects to start field trails in February. Remarkably, it took only two years from the initial phage hunt to develop a viable treatment, she says.

Across the border, Jesca Nakavuma, an associate professor at Makerere University and the chair of PhageTeam Uganda, and her colleagues are working to find phages that kill deadly strains of E. coli found on raw vegetables and destroy a deadly bacteria called Aeromonas hydrophilia that contaminates tanks used in commercial fish farming. In the DRC and Haiti, researchers are working to find phages that kill the bacteria that cause cholera in waterways, wells, and other sources of drinking water to prevent outbreaks.

In the U.S., Australia, and some European countries, phage therapy has been used to treat patients in emergency or compassionate use situations where patients are certain to die from their drug-resistant infections. (Despite growing need, Kenya has no such emergency use mechanism in place.) This occurs, typically, after physicians have exhausted all antibiotic options and they, or patients’ family members, send a sample of bacteria from the patient to phage researchers to test against their collections.

Since 2017, Pittsburgh’s Hatfull and his team have helped treat about 40 patients through compassionate use, he says. His team has amassed a bank of over 10,000 phages isolated from the environment. Today, Hatfull’s lab receives a request from a physician or patient searching for a phage treatment about once every two days, he said.

Only a handful of clinical trials have tested phage therapy in controlled environments, but there are more than 60 trials currently registered in the U.S. alone. Kenya, and many developing countries, do not have the regulatory infrastructure available to use phage therapy in emergency or compassionate use cases. Instead, Musila shares promising phage candidates with the U.S. Walter Reed Army Research Institute, which funds her current work and takes phages on through more advanced testing before they are considered for human use.

Challenges and the future of phages

While there are successful examples of phage eradicating multi-drug resistant microbes in sick patients, there are still many unknowns with phage therapy. By nature, phages replicate inside bacterial cells as they kill them—but it’s not known how quickly this happens once administered to patients. Therefore, it is difficult to calculate and track the dosage of phages at any time. With antibiotics, physicians know the precise dose and how long it takes the drug to break down inside the body. Thus far, evidence indicates that even high phage doses are safe.

One advantage of phages’ lock-and-key specificity means that they kill only specific bacteria, and not the healthy bacteria naturally found in humans. Antibiotics, on the other hand, indiscriminately kill many types of bacteria which can cause severe, long-term side effects.

“The flip side,” said Hatfull, “is that the specificity can be so tight that it only gets certain clinical isolates as opposed to a broad set.” This means that researchers around the world need to develop huge collections of phages against each type of bacteria that cause disease in humans. Hatfull and his research team are working to tease apart phage genomes to understand how they might engineer more potent phages that can target a wider range of bacteria.

Thus far, identifying phages for clinical use in humans is done on a case-to-case basis. This will likely not be sustainable when physicians and patients start relying on phage therapy more routinely. “When we talk about extensively drug-resistant bacteria, we see them often. It's not a rarity. We might be overwhelmed by the need,” Musila said.

Researchers are developing national and global phage banks that physicians and scientists looking for phages can readily access; however, a clear pathway to identify, procure, and mass produce phages for therapy is still needed. It is also unclear if current drug safety and quality regulations are adequate to address phage therapy, especially in developing countries that have never undertaken drug development.

Finally, it is uncertain how long phages would be effective given that bacteria can develop resistance to phages. In Musila’s lab, Georges and Gachoya sometimes see bacteria develop resistance to phages overnight.

Currently, a cocktail of four or five different phages are administered to patients to prevent resistance. Hatfull says his team rarely sees phage-resistant bacteria emerge.

Given the low expense and technical expertise needed for this research, it might be feasible for researchers to continually hunt for new phages as bacteria develop resistance. Sewage, polluted waterways, and other germ-teeming environments are an endless source of new phages, which unlike antibiotics, will continually evolve to kill bacteria.

“It’s a more equal race,” Musila said.


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