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Study Gives Insight Into Fidaxomicin’s Gut-Sparing Activity in Clostridioides difficile


Fidaxomicin, now commonly used to treat Clostridioides difficile infection, selectively targets the bacterium while sparing crucial gut commensals that protect against colonization. However, knowledge gaps in the molecular basis of its narrow-spectrum activity remain.

Researchers of a new paper have targeted the basis for why a commonly used macrolide antibiotic for Clostridioides difficile infections (CDI) is able to target infection with minimal effect on the gut.

Fidaxomicin, now commonly used to treat CDI, selectively targets the bacterium while sparing crucial gut commensals that protect against C difficile infections. However, knowledge gaps in the molecular basis of its narrow-spectrum activity remain.

In their paper, the researchers created a cryo-electron microscopy structure of C difficile RNA polymerase in complex with fidaxomicin, finding a single amino-acid residue in the zinc-binding-domain of the RNAP β′ subunit that serves as a sensitizing determinant for fidaxomicin.

C difficile is a Gram-positive, spore-forming, and toxin-producing intestinal bacterium that causes severe diarrhea. With a rise in infections caused by highly pathogenic variants, the CDC has designated C difficile an “urgent threat,” highlighting the need for effective treatment. While broad-spectrum antibiotics, such as vancomycin, have historically been used to treat CDI, they have been found to also negatively impact the gut microbiome and in turn allow for recurrent CDI.

“Although wide-spectrum antibiotics are broadly effective therapies, our results highlight the advantages of narrow-spectrum antibiotics to treat intestinal infections and probably other bacterial infections,” commented the researchers. “Treatment by narrow-spectrum antibiotics would reduce widespread antibiotic resistance and reduce the side effects caused by the collateral eradication of the beneficial bacteria in the gut microbiome. Using a similar approach to the one applied here, further elucidation of diverse bacterial RNAP structures and mechanisms can provide a blueprint for designer antibiotics that leverage natural microbial competition to combat pathogens more effectively.”

Using the outer-membrane weakener SPR741—a well-characterized outer-membrane weakener related to natural antibiotic colistin produced by a Firmicute—the researchers explored whether fidaxomicin resistance is dependent on the outer-membrane alone, the lack of positive charge residue on RNAP alone, or a combination of the 2. They found that both factors contributed to fidaxomicin resistance in E.coli in vivo, which the researchers said is relevant to the gut microbiome.

The group noted that while the exact presence of outer-membrane weakeners in the gut microbiome are unknown, there are other natural antibiotics generated by competing microbes in addition to colistin and medicinal antibiotics are often leveraged in combination.

“Conversely, a positively charged sensitizer (as found in CDI and Mtb) is crucial for conferring Fdx [fidaxomicin] sensitivity. Thus our studies enable the rational optimization of Fdx, depending on the target pathogen. For example, one might be able to substitute the phenolic oxygen with a stronger acid to treat Gram-positive pathogens or with a basic group to treat Gram-negative pathogens.”


Cao X, Boyaci H, Chen J, Bao Y, Landick R, Campbell E. Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile. Nature. Published online April 6, 2022. doi: 10.1038/s41586-022-04545-z

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