Researchers Pursue a Targeted Treatment for Colitis-Causing Bacteria

By Thomas Crocker
Monday, July 20, 2020

Current antibiotic treatments for Clostridioides difficile infection (CDI), which causes the chronic, degenerative disease colitis, eliminate beneficial bacteria in the gut along with the harmful pathogen. Researchers at North Carolina State University (NCSU) have taken the first step toward developing a therapy that attacks C. difficile while sparing other microbes.

Notoriously difficult to resolve, CDIs are responsible for an estimated 500,000 illnesses annually in the U.S., according to the CDC. Antibiotic use — the primary risk factor for CDI — alters the composition of the gut microbiome, making conditions for infection favorable. Antibiotics are also the standard treatment for CDI. That may contribute to recurrent infections, which occur in about 30% of cases, NCSU researchers report.

“Patients with recurrent CDI typically require a fecal microbiota transplant [FMT] to clear it, but we do not know the long-term consequences of giving a FMT to patients,” says Casey Theriot, PhD, Associate Professor of Infectious Disease at NCSU College of Veterinary Medicine. “This is evident from recent deaths due to transfer of antibiotic-resistant bacteria in donor stool. C. difficile continues to be on the CDC’s most urgent threat list today. Therefore, it will be important to develop novel, non-antibiotic treatments that target this pathogen while sparing the rest of the gut microbiota for clearance.”

Theriot and colleagues recently demonstrated proof of concept for just such a therapy.

“We are trying to develop and test new, innovative therapeutics for Clostridioides difficile infection. These new therapies are specific to the pathogen, largely sparing the rest of the gut microbiota.”
— Casey Theriot, PhD, Associate Professor of Infectious Disease at NCSU College of Veterinary Medicine

Tapping the Potential of Genome Editing

Working with startup company Locus Biosciences, Theriot and colleagues in the NCSU Veterinary Medicine and Agriculture and Life Sciences colleges used genome-editing technology CRISPR-Cas to target C. difficile using a specially engineered virus called a bacteriophage. The team used the bacteriophage to deliver a CRISPR cargo designed to destroy C. difficile using Cas3 proteins.

“The very nature of CRISPR-Cas systems is to provide DNA-encoded, RNA-mediated, nucleic acid targeting as part of the adaptive immune system in bacteria,” the authors write. “Conveniently, this immune system can be reprogrammed to target the host chromosome rather than an invasive bacteriophage or plasmid, leading to lethal cleavage of the genome by the CRISPR-Cas machinery. Our approach here was to deliver a CRISPR array containing a self-targeting sequence, which redirects the endogenous Cas machinery toward the genome, using CRISPR phage as a delivery vector.”

Precise targeting of C. difficile is crucial to preserving colonization resistance, which is the gut microbiota’s natural defense mechanism against harmful pathogens, according to Theriot. Antibiotic use subjects beneficial bacteria in the gut to continuous disturbance, making CDI recurrence more likely.

A Successful First Step

In vitro tests and in vivo tests in C. difficile-infected mice demonstrated the effectiveness of the team’s novel therapy — the CRISPR-Cas systems destroyed the target bacteria, although the treatment did not eliminate all of the C. difficile bacteria in the mice. Rather, the CRISPR-Cas systems temporarily reduced the mice’s bacterial load. Two days after receiving treatment, C. difficile levels in the mice rebounded. Results of the study were published in mBio, a journal of the American Society for Microbiology.

Demonstrating the ability to reduce C. difficile levels in mice, albeit temporarily, is an important step on the road to developing a viable treatment. Now, the researchers’ goal is to permanently prevent infection recurrence, which they hope to accomplish by adjusting the bacteriophage.

“Novel therapeutics that are tailored to one’s gut microbiota are on the horizon for CDI and other infectious diseases,” Theriot says. “Right now, I think the most important thing that physicians can continue to do is practice prudent use of antibiotics, as our next big challenge will be combatting antibiotic-resistant pathogens in the hospital setting. We need to be innovative when developing future therapeutics.”

AGA: Probiotic Use Support Evidence Largely Lacking

Probiotics are popular, but there is not enough evidence to recommend using them to treat most gastrointestinal disorders, according to new American Gastroenterological Association (AGA) guidelines.

The AGA conducted a comprehensive review of the medical literature and concluded there is little evidence to support many Americans’ belief that probiotics benefit digestive health, with three exceptions:

  • Prevention of Clostridioides difficile infection (CDI) in children and adults
  • Prevention of necrotizing enterocolitis — a disease characterized by inflammation of the colon — in premature, low birth weight babies
  • Management of pouchitis, inflammation of a pouch created during surgery for ulcerative colitis.

These are the only conditions for which the AGA supports the use of certain probiotics, per standards published in the journal Gastroenterology. According to the guidelines, there is insufficient evidence to support the use of probiotics to treat CDI, ulcerative colitis, Crohn’s disease and irritable bowel syndrome. Patients taking probiotics for those conditions may wish to consider discontinuing, the AGA recommends. The organization does not recommend using probiotics to treat acute infectious gastroenteritis in children. The new guidelines provide a basis for gastroenterologists and other clinicians to discuss the evidence surrounding probiotic use with patients. The AGA advises gastroenterologists to suggest probiotics to patients only when they seem certain to benefit.