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Engineered Viruses Deployed to Treat Gut Infections

C. difficile in petri dish

C. difficile bacteria in petri dish (

11 Mar. 2020. Academic and industry researchers created gene-editing viruses that in lab cultures and mice killed bacteria causing often deadly intestinal infections. A team from North Carolina State University in Raleigh and other institutions, as well as the company Locus Biosciences, describe their technology in yesterday’s issue of the journal mBio.

Researchers led by NC State genomics professor Rodolphe Barrangou and veterinary medicine professor Casey Theriot are seeking better treatments for Clostridium difficile, or C. difficile, infections. According to Centers for Disease Control and Prevention, almost 224,000 C. difficile infections occurred in the U.S. in 2017, leading to 12,800 deaths. The infections are often contracted in health care facilities, such as clinics and hospitals, causing inflammation in the colon, and symptoms including watery diarrhea, abdominal pain, nausea, loss of appetite, and fever. People who have other illnesses or conditions requiring prolonged use of antibiotics, and the elderly, are at greater risk of this disease.

Barrangou, whose lab studies Crispr for therapies, and Theriot, who studies gastrointestinal disorders, investigated bacteriophages, viruses that are natural enemies of bacteria, to specifically target C. difficile in the gut. Normal broad-spectrum antibiotics, such as vancomycin, can kill C. difficile bacteria, but they also kill helpful intestinal bacteria, with relapses occurring in some 30 percent of C. difficile patients receiving conventional antibiotics.

The gene-editing technique Crispr — short for clustered, regularly interspaced short palindromic repeats — makes it possible to edit genomes of organisms by harnessing bacterial defense mechanisms that use RNA to identify and monitor precise locations in DNA. For this study, the NC State researchers genetically engineered bacteriophages, also known as phages, to target and deliver a lethal Crispr payload to C. difficile bacteria. The team engineered phages to first target only C. difficile bacteria, then deliver a destructive enzyme called Cas3 to attack the microbe. While most Crispr gene edits use an enzyme called Cas9 to edit DNA, Cas3 shreds the target DNA beyond repair, destroying in this case the C. difficile bacteria.

To prove the concept, the team tested the its engineered phages first on cells in lab cultures, then in mice induced with C. difficile infections. Results show the modified phages better target and kill C. difficile bacteria than wild-type phages, suggesting these treatments could be both safe and effective in human patients.

Barrangou is a scientific founder and chief scientist at Locus Biosciences, a biotechnology company in Morrisville, North Carolina commercializing Crispr-edited phage therapies, and both a participant and funder of this study. In January, as reported in Science & Enterprise, Locus Biosciences began enrolling participants in a clinical trial to test an antibiotic made with engineered phages for people threatened with urinary tract infections from E. coli bacteria.

While proving the concept, the researchers still need to refine the engineered phages to prevent relapses, and produce treatments that target and kill specific C. difficile strains. “This was a positive first step in a long process,” says Barrangou in a university statement. “The results of using phages to deliver Crispr payloads open up new avenues for other infectious diseases and beyond.”

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