IIn 2010, a graduate student in Durban, South Africa, found herself scraping the underside of a partially decomposed eggplant. It was, in a sense, homework. She was taking a course at the University of KwaZulu-Natal about viruses that attack bacteria, and a rotten vegetable looked like a good place to find them. The "enriched soil sample," she wrote, was dark and damp, writhing with worms and other cowardly lovers of decay.
The mud proved to be alive also on a microscopic level, and the student soon discovered exactly what he was looking for: a bacteriophage virus never described before that would kill certain mycobacteria. She called him Muddy and went on with his life, earning more degrees, getting a job at a communications agency. Meanwhile, Muddy landed in a lab freezer in Pittsburgh – a filigree tube of ice out of thousands.
But then, on Wednesday, an article published in Nature Medicine took Muddy and two other viruses out of their frozen obscurity. These bacteriophages, the authors report, repress a suppurative antibiotic-resistant infection within a 15-year-old child in London. The patient was not completely cured, but after more than six months of injections and topical treatments, she went from bed to school and was fed with sushi – a remarkable result, since some elements of her "phage therapy" had not been previously tested in humans.
Of the three viruses that have helped, the story of Muddy's origin is by far the most conventional. After all, scientists took phage out of the dirtiest places imaginable and used them as cutting-edge therapies before, harnessing the natural powers of bacteria to blow patients' lives. The two other viruses, meanwhile, had to undergo a kind of reverse tame – genetically engineered, from relatively docile microbial parasites into efficient infection killers.
"It's exciting. … This study is the first we are aware of using a modified phage, "said Dave Ousterout, chief scientific officer of Locus Biosciences, a non-study company that is also working on enhancing the antibacterial capabilities of phage.
For months, enthusiastic rumors about this news have spread, with puzzling hints at lectures, past rumors from biologist to biologist, from academic to entrepreneur. "I kept listening to snacks," said Jessica Sacher, who runs a directory that connects physicians and patients seeking to try phage therapy as a last resort with microbiologists who maintain collections of the virus. "Some other researchers were saying," Just wait, there will be the first report of a modified phage in therapy soon. "
But as in all case reports, the stunning details of how this work was done – in addition to scraping the eggplant, involved a casual encounter in the Republic of Georgia, a close examination of some bird guanos and a breach in British regulation. of genetically modified organisms – have doctors wonder how much development can be expanded to help fight the global antibiotic resistance crisis.
"I still have real reservations about whether this kind of approach could be developed into something that could be used on a large scale," said Marcia Goldberg, infectious disease specialist at Massachusetts General Hospital. "The amount of science you need to develop a therapeutic treatment against a single strain is enormous."
For the teenager in question, it all started with a double lung transplant. She was born with cystic fibrosis, a genetic disease that clogs the thorax with mucus, allowing invasion of opportunistic bacteria. The surgery itself at Great Ormond Street Hospital in London was uncomplicated, and its doctors blew their bloodstream with antibiotics to keep infections under control. But intravenous drugs caused severe nausea, diarrhea and anorexia in the adolescent and had to be stopped.
Within a week, the surgical wound became red with infection. It was discovered that Mycobacterium abscessus, a cousin of slow-growing tuberculosis, was proliferating in its fluids, organs and skin. Doctors tried as many antibiotics as they could, but the drugs caused liver damage and did not have much effect. "Imagine your liver rising and falling down to the groin area – this is painful," said Dr. Helen Spencer, a lung specialist responsible for the case.
In the nine months after the transplant, Spencer watched her patient switch from a sociable teen to one who only spoke in monosyllables, if any. The medical team had no hope of her recovering. She could not eat. All they could do was send her home with palliative care, so she could see her friends and her dog while she waited for death.
It was at that moment that the patient's mother brought up the idea of phage therapy. Spencer did not know much about it, but there was a hospital microbiologist, Dr. James Soothill, who worked on the virus and agreed to help.
He knew that phages had been extensively tested as therapy in the early 20th century, but that practice had largely disappeared behind the Iron Curtain. In the 1990s, when there was a small resurgence of interest in the West, he traveled to Tbilisi for what he called "a very strange meeting organized by an American startup." It was where he met Graham Hatfull, who studied the genetics of phage that attack mycobacteria.
So in late 2017, when Spencer told Soothill about this teenager's desperate situation, he sent an email to Hatfull's lab at the University of Pittsburgh. The site has become an international phage repository through a program that Hatfull has helped develop, in which university students from around the world isolate and identify phage, learning about biology, and expanding knowledge about these viruses that grow in the trillions in and around of us. Contributing to scientific literature, he believes, is much easier than most people think. "You do not have to be a rocket scientist, you do not need a Ph.D. – in fact, you do not need anything," he said. "You just need to have a spark of curiosity and you can find out something new."
That's how Muddy ended up in his freezer, along with over 10,000 other viruses. Now Hatfull agreed to find some who could help the English teenager, so Soothill sent him a stain of the bacteria that was killing her.
The problem is that phages are notoriously demanding, infecting only very specific strains of very specific bacteria. And most of the Hatfull viruses were parasites of Mycobacterium smegmatis, a totally different species from Mycobacterium abscessus that was multiplying within the patient. They needed to find versatile viruses in exactly the right way.
While sifting the jars in his freezer, he also sent members of his lab to collect even more dirt and mud. They visited flowerbeds and compost heaps, collected pieces of poop from chicken and duck farms.
But the only phage they could think would work came from the freezer. It was muddy.
His concern was that giving a single phage as a therapy would allow the bacteria to quickly develop resistance to it. He needed at least two more to make a cocktail. "We have a good one," he remembers thinking. "Where on earth will we get anything else?"
Their staff knew that they had other phages that were active against the patient's bacterial strain – they simply were not very good at killing it. Some of them slipped peacefully inside their genome; others did a little damage, but hardly made a dent in a petri dish full of insects. "With a phage that kills efficiently, all cells are dead," said Hatfull. "You can read a newspaper through the hole that is made in the grass of bacteria."
These just made little dingy spots.
So they picked out some of them and started messing with their guts. The technique they used took advantage of the microbial propensity to rearrange the genetic material – "They are willing and able to exchange their genes," Hatfull said – to erase the DNA fragments that suppressed the killing instincts of the phages. Without these pieces, they were free to breed like crazy, the asexual equivalent of rabbits, causing the host cell to explode.
For one of the viruses, they also looked for mutants among the population that proved especially efficient, using a toothpick to select the best killers in the batch.
According to Hatfull, they wiped out part of the virus' genetic code, without adding anything, to allow them to obtain these two phages through regulations on genetically modified organisms and send the cocktail live to London, where it was the first. used on the patient's external wounds and then injected into his bloodstream. During the first two days of treatment, she felt sweaty and flushed, but the doctors found no other side effects.
Slowly, the surgical wound on his chest began to close. The redness disappeared. The infected lumps in his skin flattened into scars. The bacteria disappeared from his blood serum and his phlegm, the colonies in his organs began to diminish. Almost a year later, mycobacteria are still present in some of her skin nodules, but she is eating, doing tests, learning to drive.
Spencer worries about the phage resistance they saw when they picked up the fluid from the last remaining skin fragments and tested it in the lab, so Hatfull has been looking for new viruses to add to the mix.
As electrifying as the results are for the patient and his family, and as promising as they appear for companies working with similar personalized phage therapies, the story is just that: a story, though with careful documentation on photographs, CT scans, and laboratory tests . values. It does not carry the weight of a clinical trial.
Companies are now trying to develop phage cocktails – some custom, some prepackaged, some natural, some designed – in biological drugs. Many say that studies in humans are imminent. But it is not yet clear whether companies will be able to muster the kind of evidence needed to get these treatments approved.
For Hatfull, the study does not necessarily mean that other artificial phage therapies are easy, effective, or safe. But he hopes phage will help the world's multidrug-resistant tuberculosis crisis, caused by other bacteria of the same genus. "If you could use phages to simplify, improve, shorten TB therapy, minimize the chance of antibiotic resistance, then that would be a major overall impact," he said. "This case study, kind of opens the door a little."
For Lilli Holst, who dug up Muddy as a graduate student, the excitement was more immediate. To hear that one of her phages might have prolonged someone's life gave her a "sense of bodily reverberation." After all, who expects this kind of news to come from a rotten eggplant in their parents' compost pile?