The bacterium Clostridioides difficile (C. diff) may be smaller than a pinhead, but it presents a massive issue for hospitals. According to Lynn Bry, MD, PhD, of the Department of Pathology, it has become the most prevalent hospital-associated infection worldwide.
“About 20 percent of patients who contract C. diff develop a recurrent disease that fails to respond to antibiotics, said Bry. “Over the decades, we’ve learned about the cause and mechanisms of action of this serious infection. Now, the field is turning to focus on the cure.”
Estimated to affect half a million hospital patients yearly, C. diff infections can occur in a person’s intestinal tract after they receive antibiotics. These treatments often eradicate most of the bacteria in a person’s gut microbiome and leave only species with resistance to the antibiotic, such as C. diff. While between 5 and 10 percent of healthy individuals carry C. diff in their gut, problems arise when the bacterium faces little competition and proliferates. The microbe releases toxins into the gut environment, which cause a disease called pseudomembranous colitis (inflammation and death of colon tissue) in about 8 percent of patients. In addition, the infection can occasionally lead to severe problems, including death, if left unchecked.
The story of C. diff research at the Brigham stretches back to the 1970s. Today, thanks to computational biology and international collaborations, researchers are defining cures and clinical programs to prevent C. diff infections — progress that would not have been possible without the groundwork laid more than 40 years ago.
The “Slide Rule” Era
Andrew Onderdonk, PhD, an anaerobic and clinical microbiologist of the Department of Pathology, first isolated C. diff in 1978 after he linked its toxins to a rash of colitis cases among patients prescribed the antibiotic clindamycin, used to treat wound infections.
Originally unsure of the origins of the colitis cases, he and colleagues hypothesized the illness could be an immune response to clindamycin. Only after transferring microbiota samples among clindamycin-dosed hamsters — chosen for their similar response to the antibiotic as humans — did he discover the colitis’ contagious nature, meaning it was caused by a pathogen rather than the immune system.
The presence of toxins in intestinal cultures from both hamsters and humans indicated to Onderdonk that a genus of bacteria known as Clostridium was responsible for the illness. By isolating and selecting among different bacteria from animals fed clindamycin and infecting healthy hamsters with only one species of Clostridium, he narrowed the colitis culprit to C. diff.
“We didn’t have computers back then; we still did lots of work with slide rules,” said Onderdonk, who added that although his team’s computational methods were crude by today’s standards, the scientific strategy for isolating C. diff was “spot on.”
Vancomycin, a commonly prescribed antibiotic, provided the first effective treatment for C. diff infection. However, C. diff exhibited pesky resistance to conventional drug treatments.
“Around 2003, we realized people were continuing to get severely sick with C. diff,” said Onderdonk. “We came to find that mutations in one gene allowed it to produce more toxins, so it was still a player in hospitals.”
Fecal Microbiota Transplantation: An Antibiotic-Free Treatment
Today, fecal microbiota transplantation (FMT) provides treatment for recurrent cases of C. diff infection. In this procedure, a patient is treated with stool rich in microbes from a healthy individual, which helps reestablish a robust microbiome and resolves the disease in 65 to 95 percent of patients.
First performed in 2012 at the Brigham, FMT was pioneered by Jessica Allegretti, MD, MPH, of the Departments of Gastroenterology, Hepatology, & Endoscopy and Internal Medicine. In the first few years the Brigham offered the treatment, she acted as a “one woman show,” personally screening donors of the patient’s choosing for major medical issues and possible pathogens in the blood and stool.
“This screening process was very costly and labor intensive, but it was the only option we had back then,” said Allegretti.
To streamline the donor process, she partnered with OpenBiome, a nonprofit stool bank located in Cambridge, Massachusetts, in 2014. The organization assumed collecting, screening and processing of samples. Though OpenBiome will likely close its doors next year, shuttered by the pandemic, Allegretti expressed hope that the Brigham may soon develop its own internal stool bank.
Allegretti described FMT as a safe process when performed correctly, though she noted some issues with its implementation. Since the procedure lacks U.S. Food and Drug Administration approval, the donor screening process may vary from institution to institution. She cited a 2019 case where two immunocompromised patients received FMT containing a resistant strain of E. coli as evidence for the need for standardization and regulation of the procedure. She added she is still investigating the long-term safety of FMT, as questions remain concerning the risk of diseases or disorders it might introduce to a patient. She has partnered with the American Gastroenterological Association and the National Institutes of Health to follow FMT patients for 10 years post-procedure to collect further safety data. So far, no safety signals have been identified.
“We know FMT is safe in most patient populations, but I think we can make it even safer,” she said.
Computational Biology and International Collaboration Advance C. diff Research
Scientists at the Brigham are developing even safer and more effective treatments for C. diff. New research, conducted by Bry, indicates that C. diff doesn’t act alone — commensals, or microbes affecting the growth of others without harming their human host, significantly modify its environment and behaviors. While some commensals augment C. diff’s environment and increase its virulence, most interesting to Bry are those that depress its toxicity.
“In a healthy gut microbiota, organisms are actively outcompeting C. diff,” said Bry. “It can’t get a foothold in the gut. It can’t grow.”
If she could identify the bacterial strains responsible for ameliorating C. diff infections, she might be able to create a cocktail of microbes targeted to treat each individual C. diff case. With fewer foreign bacterial strains entering their bodies, patients — even immunocompromised ones — might better tolerate the transplant.
Bry collaborated with computer scientist Georg Gerber, MD, PhD, of the Department of Pathology, to develop a computational model that could sift through the data to pinpoint which commensals interacted with C. diff — a far cry from the slide rules of the 1970s.
“Our computational approach goes at the problem from two levels: trying to figure out which bacteria from a complex mix might actually be protective against the pathogen,” said Gerber, “and based on that, going deep into the molecular mechanisms that drove protection.”
Using germfree mouse models in the Massachusetts Host-Microbiome Center at the Brigham, Bry’s team identified how healthy microbes could cause very different outcomes from the infection.
“To our great surprise,” said Bry, “we found one organism that provided 100 percent survival in mice indefinitely.” This microbe, Paraclostridium bifermentans (P. bifermentans), belonged to the same family as C. diff and was more metabolically active than the pathogen during infection, limiting its ability to grow and make toxin. Bry also identified another Clostridium species, Clostridium sardiniense (C. sardiniense) that affected the mice oppositely, increasing C. diff’s mortality rate. “This latter finding was critical to show that the microbiota can also worsen C. diff disease if species remaining after antibiotic exposures cross-feed the pathogen, enhancing its growth and production of toxin,” said Bry.
Through her research, Bry established collaborations with Bruno Dupuy and Johann Peliter at the Pasteur Institute and Nitin Baliga at the Institute of Systems Biology in Seattle. These scientists helped her use improved tools to genetically manipulate C. diff and develop new systems biologic models to predict the pathogen’s gene regulation in vivo. The team recently published two papers in Cell Host and Microbe detailing their findings. They have also released these resources publicly to assist groups world-wide who study C. diff.
Bringing it back to the Brigham
“We’re continuing research to look at interactions with other commensals,” said Bry, mentioning that molecular crosstalk has given the team a “robust platform” to not only study C. diff, but also other disease-causing microbes — including those associated with food allergies and traveler’s diarrhea — and to more broadly define how microbial metabolism in the gut affects human physiology.
“By using this very defined, highly effective formula, we would know what we’re putting into a C. diff patient, and how to elicit the protective activities we want to see,” said Bry.
“I don’t think we’re going to be doing whole stool FMT well into the future, which is a good thing,” commented Allegretti, who added how this new research also helps predict recurrence of C. diff infection.
“There were not only bacteria but also metabolites we could use to predict who’s going to recur and who’s not,” she said. “These novel biomarkers really help identify who’s at risk earlier.”
Gerber mentioned how P. bifermentans research “rationalizes” FMT procedures. “We don’t know the long-term risks of putting uncharacterized microbes into a patient,” he said, “and in some cases, people are actually getting other infections from FMT.”
“If we could give patients a pill with bacteria safely grown in the lab, and with just a small set of specific bacteria needed to prevent or fight off C. diff, that would really change the therapeutic landscape,” he concluded.
Besides treating C. diff symptoms, health care providers want to screen patients for C. diff to prevent future infections. Bry is implementing a surveillance program first conceptualized at the Brigham whose rollout was complicated by the pandemic. This program uses rectal swabs to screen for another pathogen, Vancomycin-resistance Enterococci, to detect carriage of toxin-producing C. diff in patients.
“Hospitals are literally flying blindly because surveillance does not currently exist for C. diff,” she said, adding that this program helps identify asymptomatic carriers of the pathogen. The Hatch family, donors to the Brigham for half a century, enabled the original pilot project and are helping to fund the interventional surveillance program.
“The microbiologic and genomic analyses for C. diff carriage have given us new tools that we’re putting into production to both prevent and better treat the disease,” said Bry.
Onderdonk commended the progress C. diff research has made since his original hamster experiments in the 1970s. “The best thing that could happen is understanding how C. diff works, and I think Lynn Bry is pretty close to that,” he said.
Forty years of C. diff research at the Brigham has taken researchers from a puzzling cause to promising cures — and Bry noted the institution’s role in the progress. “We’ve had incredible support from the Brigham,” she said, “and we’ll continue to move research in this field forward.”