Narrow-Spectrum Antibiotic May Reduce C. difficile Risk


Study results show at a molecular level how fidaxomicin selectively targets these bacteria, while sparing others in the gut microbiome.

Narrow-spectrum antibiotics that kill just 1 or a few species of bacteria, such as, could help minimize the risk of collateral damage, which can cause individuals to become more prone to drug-resistant strains and reinfection, according to the results of a study from Rockefeller University.

Antibiotics kill the pathogens for which they are prescribed but at the same time kill beneficial bacteria, which changes the composition of the gut microbiome. Investigators examined fidaxomicin, which is used to treat Clostridium difficile, a common health care-associated infections.

The findings showed how, at a molecular level, fidaxomicin selectively targets C. difficile while leaving other bacteria alone.

Investigators hope these results, which are published in Nature, could pave the way for development of narrow-spectrum antibiotics against other pathogens.

“I want people, scientists, and doctors to think differently about antibiotics,” Elizabeth Campbell, PhD, a research associate professor at Rockefeller, said in a statement. “Since our microbiome is crucial to health, narrow-spectrum approaches have an important part to play in how we treat bacterial infections in the future.”

Physicians have been using broad-spectrum antibiotics to treat C. difficile for years, and fidaxomicin, which the FDA approved in 2011, is a relatively new alternative. Fidaxomicin targets an enzyme called the RNA polymerase (RNAP), which the bacterium uses to transcribe DNA to RNA.

Investigators visualized C. difficile RNAP using cryo-electron microscopy, a powerful imaging technique that can reveal the 3D shape of molecules and capture the drug molecule and its target in action. Their goal was to understand exactly why fidaxomicin selectively inhibits RNAP in C. difficile and not in most other bacteria.

A challenge that investigators faced was the ability to produce large amounts of C. difficile, because it does not grow in the presence of oxygen. However, with the use of Escherichia coli, investigators could more easily produce C. difficile RNAP in a lab.

Investigators were able to generate images of C. difficile RNAP locked with fidaxomicin at near-atomic resolution. They found that fidaxomicin wedges into a hinge between 2 subunits of RNAP and jams open the enzyme’s pincer. This prevents it from grabbing on to generic material and starting the transcription process.

With closer examination of the points of contact between fidaxomicin and RNAP, investigators were able to identify 1 amino acid on the RNAP that binds to fidaxomicin but is absent in the main groups of gut microbes. In a genetically altered version of C. difficile, the bacteria lacked this amino acid, and investigators found it was undisturbed by fidaxomicin, just like the other common bacteria in the gut.

Bacteria that had the amino acid added to the RNAP became sensitive to fidaxomicin, investigators found.

These findings suggest that this amino acid, among about 4000 amino acids of the robust and essential transcription machine, is susceptible to fidaxomicin, which makes the drug able to kill the harmful bacteria.

By further examining the RNAP structure, investigators can design antibiotics that target each pathogen more effectively and selectively.


How a narrow-spectrum antibiotic takes aim at C. Diff. EurekAlert. News release. April 6, 2021. Accessed April 8, 2022.

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