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Antibiotics Help C. diff Compete for Nutrients Needed to Survive & Thrive

Study finds antibiotic use alters native gut bacteria that normally compete with C. diff for nutrients.

Clostridium difficile (C. diff) remains a leading cause of health care-associated infections and continues to plague providers and patients alike. Although antibiotics are available to treat the infection, they are known to alter gut microbiota and decrease the body's natural resistance to colonization. Furthermore, many patients go on to experience recurrence.

Although the mechanisms that drive colonization resistance are not well-understood, a new study conducted by researchers from North Carolina (NC) State University offers some insight.

“Our latest work suggests that the microbiota may provide natural resistance to C. diff colonization by competing with C. diff for nutrients in that environment; specifically, for an amino acid called proline,” corresponding author Casey Theriot, PhD, assistant professor of infectious disease at NC State, said in a recent statement. By altering native gut bacteria that normally would compete with C. diff for nutrients, antibiotic use essentially provides C. diff with a feast, allowing it to grow.

The researchers feel that these findings could potentially lead to the development of probiotics that can help restore the body’s “good” bacteria in the gut or to inform better strategies to prevent infection from happening altogether.

The harmful impact of antibiotic use on the microbiome proved to be a hot topic at last year's 5th Annual International C. diff Awareness Conference and Health Expo, consistently coming up in conversation among attendees.

“The antibiotics we use to treat C. diff also cause what we might describe as collateral damage to the gut microbiome,” Richard Vickers, PhD, chief scientific officer of R&D at Summit Therapeutics told Contagion® at the conference. “We know the gut microbiome, that community of bacteria that live within our gastrointestinal tract, is absolutely fundamental to the pathogenesis of C. diff infection. And so, if it’s in a normal, healthy state, then that protects us from C. diff developing.”

However, antibiotics to treat C. diff alter indigenous gut microbiota, and without those diverse bacteria, resistance to colonization decreases; this loss significantly alters the metabolic environment of the gut, specifically the composition and concentration of “host-derived” metabolites.

Using a mouse model, Dr. Theriot and postdoctoral fellow, Joshua Fletcher, infected antibiotic-treated mice with C. diff and monitored their gut environment at 0, 12, 24, and 30 hours postinfection. To identify which nutrients the bacteria were ‘eating,’ the team conducted metabolomic and RNA sequencing analysis at those 4 different time intervals. Through metabolomics, the team was able to “trace the abundance of nutrients in the gut,” while the RNA analysis “indicated which genes in the C. diff were active in metabolizing nutrients,” according to the statement. Their 2-tiered approach found that early on in the colonization process, C. diff uses specific amino acids and carbohydrates to grow.

“We already know that in order for C. diff to produce toxin, which mediates disease in the gut, it has to grow at high levels,” Dr. Theriot told our sister publication MD Magazine. “In order to grow to high levels, it requires nutrients, specifically proline and other amino acids.”

The researchers found that proline and other proline-rich metabolites in the gut microbiome of the mice increased in number after antibiotic use. When the team introduced C. diff to the mice, the bacteria were able to grow to high levels and produce toxin.

“This finding is interesting because we now have a metabolic target to go after,” Dr. Theriot told MD Mag. “And so, we can design a targeted probiotic strain that is able to outcompete C. diff in the gut for amino acids, specifically proline.”

The research suggests that proline and other proline-rich metabolites are “important for growth during the early stages of C. diff colonization,” she said.

The team isn’t stopping there; future mechanistic studies will investigate the factors that could be working to supply proline to C. diff in the gut. They hope to identify where the proline is coming from so that they could "shut it down," she said.