Exploring novel microbial metabolites and drugs for inhibiting Clostridioides difficile

Abstract

Clostridioides difficile is an enteric pathogen that can cause a range of illnesses from mild diarrhea to pseudomembranous colitis and even death. This pathogen often takes advantage of microbial dysbiosis provoked by antibiotic use. With the increasing incidence and severity of infections, coupled with high recurrence rates, there is an urgent need to identify innovative therapies that can preserve the healthy state of the gut microbiota. In this study, we screened a microbial metabolite library against C. difficile . From a collection of 527 metabolites, we identified 18 compounds with no previously identified antimicrobial activity and metabolites that exhibited potent activity against C. difficile growth. Of these 18 hits, five drugs and three metabolites displayed the most potent anti- C . difficile activity and were subsequently assessed against 20 clinical isolates of C. difficile . These potent agents included ecteinascidin 770 (minimum inhibitory concentration against 50% of isolates [MIC 50 ] ≤0.06 µg/mL); 8-hydroxyquinoline derivatives, such as broxyquinoline and choloroquinaldol (MIC 50 = 0.125 µg/mL); ionomycin calcium salt, carbadox, and robenidine hydrochloride (MIC 50 = 1 µg/mL); and dronedarone and milbemycin oxime (MIC 50 = 4 µg/mL). Unlike vancomycin and fidaxomicin, which are the standard-of-care anti- C . difficile antibiotics, most of these metabolites showed robust bactericidal activity within 2–8 h with minimal impact on the growth of representative members of the normal gut microbiota. These results suggest that the drugs and microbial metabolite scaffolds may offer alternative avenues to address unmet needs in C. difficile disease prevention and treatment. IMPORTANCE The most frequent infection associated with hospital settings is Clostridioides difficile , which can cause fatal diarrhea and severe colitis, toxic megacolon, sepsis, and leaky gut. Those who have taken antibiotics for other illnesses that affect the gut's healthy microbiota are more susceptible to C. difficile infection (CDI). Recently, some reports showed higher recurrence rates and resistance to anti- C. difficile , which may compromise the efficacy of CDI treatment. Our study is significant because it is anticipated to discover novel microbial metabolites and drugs with microbial origins that are safe for the intestinal flora, effective against C. difficile , and reduce the risk of recurrence associated with CDI.