Abstract
Background
Clostridioides difficile infection (CDI) is a common healthcare-associated infection with limited treatment options. Omadacycline, an aminomethylcycline tetracycline, has potent ...in vitro activity against C difficile and a low propensity to cause CDI in clinical trials. We aimed to assess fecal pharmacokinetics and gut microbiome effects of oral omadacycline compared to oral vancomycin in healthy adults.
Methods
This was a phase 1, nonblinded, randomized clinical trial conducted in healthy volunteers aged 18–40 years. Subjects received a 10-day course of omadacycline or vancomycin. Stool samples were collected at baseline, daily during therapy, and at follow-up visits. Omadacycline and vancomycin stool concentrations were assessed, and microbiome changes were compared.
Results
Sixteen healthy volunteers with a mean age of 26 (standard deviation SD, 5) years were enrolled; 62.5% were male, and participants’ mean body mass index was 23.5 (SD, 4.0) kg/m2. Omadacycline was well tolerated with no safety signal differences between the 2 antibiotics. A rapid initial increase in fecal concentrations of omadacycline was observed compared to vancomycin, with maximum concentrations achieved within 48 hours. A significant difference in alpha diversity was observed following therapy in both the omadacycline and vancomycin groups (P < .05). Bacterial abundance and beta diversity analysis showed differing microbiome changes in subjects who received omadacycline versus vancomycin.
Conclusions
Subjects given omadacycline had high fecal concentrations with a distinct microbiome profile compared to vancomycin.
Clinical Trials Registration
NCT06030219.
Omadacycline, an aminomethylcycline tetracycline, was demonstrated to have a distinct and protective gut microbiome profile and similarly achieve high fecal concentrations compared to vancomycin.
Clostridioides difficile infection (CDI) causes substantial morbidity and mortality worldwide with limited antibiotic treatment options. Ridinilazole is a precision bisbenzimidazole antibiotic being ...developed to treat CDI and reduce unacceptably high rates of infection recurrence in patients. Although in late clinical development, the precise mechanism of action by which ridinilazole elicits its bactericidal activity has remained elusive. Here, we present conclusive biochemical and structural data to demonstrate that ridinilazole has a primary DNA binding mechanism, with a co-complex structure confirming binding to the DNA minor groove. Additional RNA-seq data indicated early pleiotropic changes to transcription, with broad effects on multiple C. difficile compartments and significant effects on energy generation pathways particularly. DNA binding and genomic localization was confirmed through confocal microscopy utilizing the intrinsic fluorescence of ridinilazole upon DNA binding. As such, ridinilazole has the potential to be the first antibiotic approved with a DNA minor groove binding mechanism of action.
Abstract
Background
Microbiome disruption associated with Clostridioides difficile infection (CDI) includes reduced metabolism of primary to secondary bile acids leading to increased likelihood of C. ...difficile germination and CDI recurrence. Omadacycline has potent in vitro activity against C. difficile but its effect on the microbiome is unknown. The purpose of this study was to assess changes in bile acid concentrations in healthy volunteers given omadacycline compared to vancomycin, the most common antibiotic used to treat CDI.
Methods
As part of an ongoing healthy volunteer study of adults between 18 and 40 years, subjects received a 10-day course of oral omadacycline or vancomycin. Stool samples were collected and bile acids were extracted and quantified via targeted liquid chromatography-mass spectrometry (LC-MS). For this analysis, samples collected at the end of antibiotic therapy (day 9-10) were analyzed for primary and secondary bile acids. Results were compared and visualized using R (ggplot2).
Results
Between October 2020 and December 2021, 16 healthy volunteers aged 26 ± 5 years (male: 69%; Caucasian: 31%; mean body mass index: 23.6 ± 3.8 kg/m2) were enrolled. Concentrations of primary bile acids (cholic acid and chenodeoxycholic acid) were higher in patients receiving oral vancomycin than those receiving omadacycline (Table 1). Secondary bile acids were higher in the omadacycline arm compared to vancomycin. Secondary:primary bile ratio was higher for omadacycline (0.43) than vancomycin (0.03).
Conclusion
Omadacycline preserved bile acid homeostasis in the gut to a higher extent that vancomycin, suggesting reduced microbiome dysbiosis. With potent in vitro C. difficile activity, availability as an oral and IV formulations, and favorable microbiome properties, further development of omadacycline for the treatment of CDI is warranted.
Disclosures
Kevin W. Garey, PharmD, MS, Acurx Pharmaceuticals: Grant/Research Support|Paratek Pharmaceuticals: Grant/Research Support|Seres Therapeutics: Grant/Research Support|Summit Pharmaceuticals: Grant/Research Support.
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•A qPCR assay that targets MAA synthetase gene C of Microcystis was developed.•Ecology of Mycosporine-like amino acids (MAA) of cyanobacteria was studied.•Shinorine is the major MAA ...type from the Microcystis isolates and water samples.•MAA-producing Microcystis significantly decreased when UV irradiation decreased.•MAA-producing Microcystis might be ecologically advantageous under high UV conditions.
Mycosporine-like amino acids (MAAs) are UV-absorbing metabolites found in cyanobacteria. While their protective role from UV in Microcystis has been studied in a laboratory setting, a full understanding of the ecology of MAA-producing versus non-MAA-producing Microcystis in natural environments is lacking. This study presents a new tool for quantifying MAA-producing Microcystis and applies it to obtain insight into the dynamics of MAA-producing and non-MAA-producing Microcystis in Lake Erie. This study first developed a sensitive, specific TaqMan real-time PCR assay that targets MAA synthetase gene C (mysC) of Microcystis (quantitative range: 1.7 × 101 to 1.7 × 107 copies/assay). Using this assay, Microcystis was quantified with a MAA-producing genotype (mysC+) in water samples (n = 96) collected during March-November 2013 from 21 Lake Erie sites (undetectable − 8.4 × 106 copies/ml). The mysC+ genotype comprised 0.3–37.8% of the Microcystis population in Lake Erie during the study period. The proportion of the mysC+ genotype during high solar UV irradiation periods (mean = 18.8%) was significantly higher than that during lower UV periods (mean = 9.7%). Among the MAAs, shinorine (major) and porphyra (minor) were detected with HPLC-PDA-MS/MS from the Microcystis isolates and water samples. However, no significant difference in the MAA concentrations existed between higher and lower solar UV periods when the MAA concentrations were normalized with Microcystis mysC abundance. Collectively, this study’s findings suggest that the MAA-producing Microcystis are present in Lake Erie, and they may be ecologically advantageous under high UV conditions, but not to the point that they exclusively predominate over the non-MAA-producers.
Abstract
Background
Omadacycline is an aminomethylcycline tetracycline with potent in vitro activity against C. difficile (CD) and a low propensity for CD infection (CDI) in clinical trials. In ...addition to potent in vitro activity, ideal properties of anti-CDI antibiotics include favorable effects on bile acids and short-chain fatty acids (SCFA). The aim of this study was to compare bile acid and SCFA changes in healthy volunteers given oral omadacycline versus vancomycin.
Methods
This was a phase 1 healthy volunteer study in 16 adults randomized to an oral 10-day course of either omadacycline or vancomycin. Stool samples were collected daily with metagenomics performed targeting the V4 region of the 16S ribosomal RNA gene using the Miseq platform (Illumina). Stool samples collected at baseline, during therapy, and follow-up visits were used for this functional omics evaluation. Targeted bile acids and SCFA quantification were performed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The final concentration of each gut metabolome was normalized by the corresponding stool sample weight.
Results
Both antibiotic groups showed a significant decrease in alpha diversity during therapy. Primary bile acids increased in vancomycin-treated subjects which was not observed in the omadacycline group although secondary bile acids diminished equally. Fecal SCFA concentrations of butyrate decreased in both groups while acetate and propionate were preserved in the omadacycline group compared to vancomycin.
Conclusion
Both omadacycline and vancomycin demonstrated changes in the gut microbiome with omadacycline showing favorable effects on bile acids and SCFA. These results provide mechanistic understandings on the anti-CDI properties of omadacycline.
Disclosures
Anne J. Gonzales-Luna, PharmD, BCIDP, Cidara Therapeutics: Grant/Research Support|Ferring Pharmaceuticals: Personal Fees|Paratek Pharmaceuticals: Grant/Research Support|Seres Therapeutics: Grant/Research Support Kevin W. Garey, MS;PharmD, Paratek Pharmaceuticals: Grant/Research Support
Abstract
Background
Ibezapolstat (IBZ) is a non-absorbable antimicrobial currently in phase 2 clinical trials for the treatment of Clostridioides difficile infection (CDI). In vitro and human studies ...have shown potent activity of IBZ against C. difficile but selective activity against other beneficial Gram-positive gut microbiota shown to reduce the risk of recurrent CDI. As the target DNA Pol IIIC enzyme is present in most Gram-positive species, the reasons for this selectivity are unclear. The purpose of this study was to assess the selectivity of IBZ against Gram-positive gut commensal microbiota.
Methods
Using stool samples and microbiome data from the phase 2a CDI study, concentration changes in certain Gram-positive commensals were analyzed by qPCR over time in patients with CDI given IBZ. Gram-positive isolates were cultured from stool, speciated, and MIC determined. AlphaFold2-enabled drug docking was used to assess in silico differences in drug-binding residue sites predictive of IBZ binding across a large range of Gram-positive bacteria isolated from the stool.
Results
From the phase 2a study, relative abundance of Firmicutes and concentrations of certain species (Clostridium leptum and Clostridium coccoides groups) increased while on IBZ therapy. Thirty-six strains were isolated from Families Clostridiaceae (n=25), Enterococcaceae (n=3), Lachnospiraceae (n=3), and Peptostreptococcaceae (n=5). MIC50/90 values averaged 1.5/3.0 ug/mL (geometric mean) for strains isolated at baseline and early therapy (days 1-3) and 12/126 ug/mL for samples taken later on therapy and three-day follow-up. Two strains isolated at day 30 follow-up were < 2 ug/mL and another was >128 ug/mL. All C. difficile strains were IBZ susceptible (MIC<2 ug/mL). Using a protein sequence alignment from more than 500 Firmicute PolC sequences, potential contact points of interest were identified that helped explain the selectivity of Ibezapolstat.
Conclusion
Increased Firmicute abundance and concentration may be explained by selection of non-susceptible Firmicute species during therapy. Distinct IBZ drug-binding residues in the Pol IIIC enzyme may explain this selectivity. Structural biology experiments will confirm these results.
Disclosures
Eugenie Basseres, PhD, Accurx: Grant/Research Support Kevin W. Garey, PharmD, MS, Acurx: Grant/Research Support|Ferring: Advisor/Consultant|Paratek: Grant/Research Support
Abstract
Background
Ibezapolstat (IBZ) is a non-absorbable antimicrobial currently in phase 2 clinical trials for the treatment of Clostridioides difficile infection (CDI). In vitro and human studies ...have shown potent activity of IBZ against C. difficile but selective activity against other beneficial Gram-positive gut microbiota shown to reduce the risk of recurrent CDI. As the target DNA Pol IIIC enzyme is present in most Gram-positive species, the reasons for this selectivity are unclear. The purpose of this study was to assess the selectivity of IBZ against Gram-positive gut microbiota.
Methods
Using stool samples and microbiome data from the phase 1 and 2 studies, changes in proportional abundance of gut microbiome species were analyzed over time in healthy volunteers or patients with CDI given IBZ. Using a separate collection of gut microbiota species, MIC determinations against a variety of Gram-positive gut species were assessed by broth microdilution.
Results
Baseline gut microbiota from healthy volunteers were primarily Firmicutes, Bacteroidetes, or Actinobacteria. Actinobacteria increased in abundance after starting IBZ (primarily Bifidobacteriales or Coriobacteriales) and persisted for the entire dosing period. In comparison to the phase 1 study, the phase 2a CDI study baseline microbiota had a lower proportion of Actinobacteria and Firmicutes and increased Bacteroidetes. In CDI patients, Actinobacteria increased in abundance after starting IBZ (primarily Coriobacteriales) followed within 2-3 days by decreased abundance of Bacteroidetes, and an increased abundance of Lachnospiraceae and Ruminococcaceae. Using isolated gut microbiota species, IBZ was inactive (MIC >64 µg/mL) against representative Actinobacteria (Bifidobacteriaceae and Coriobacteriaceae) and certain Firmicutes (Lachnospiraceae and Lactobacillaceae) but highly active against strains of C. difficile (MIC<2 µg/mL).
Conclusion
Microbiome changes with IBZ were dependent on underlying composition of the baseline microbiome but consistently demonstrated increased abundance of Actinobacteria after starting therapy. IBZ microbiome data coupled with in vitro MIC determinations demonstrated persistence or regrowth of healthy microbiota associated with beneficial physiologic effects.
Disclosures
Kevin W. Garey, PharmD, MS, Acurx Pharmaceuticals: Grant/Research Support|Paratek Pharmaceuticals: Grant/Research Support|Seres Therapeutics: Grant/Research Support|Summit Pharmaceuticals: Grant/Research Support.
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