Clinical-Stage, Oral β-Lactamase Enzyme to Prevent Clostridium difficile Infection Triggered by Antibiotic-Mediated Gut Microbiome Disruption

Background: Antibiotic-mediated disruption of the gut microbiome can lead to serious infections such as Clostridium difficile (CDI). SYN-004, in Phase 2 clinical testing, is a β-lactamase enzyme for oral use with certain IV β-lactam antibiotics intended to preserve the gut microbiome by inactivating antibiotics in the GI tract. The β-lactamase strategy for microbiome protection from both IV and orally-delivered antibiotics was explored using pig models of antibiotic-mediated gut dysbiosis.

Methods: The β-lactamase was produced in E. coli and the clinical formulation, SYN-004, was manufactured as enteric-coated pellets for duodenal release. Pig models (20 kg, n=5 per cohort) of ceftriaxone- (CRO; IV, 30 mg/kg, SID) and amoxicillin- (AMX; PO, 20 mg/kg, BID) +/- SYN-004 (PO, 75 mg, QID) mediated gut dysbiosis were established. Fecal DNA whole genome shotgun sequence analyses assessed microbiome preservation and systemic antibiotic absorption was quantified by HPLC or LC/MS. New formulations of the β-lactamase, engineered to be released in the GI tract at a point distal to oral antibiotic absorption but proximal enough to protect the microbiome, were tested in vitro.

Results: In pigs, SYN-004 protected the gut microbiomes from IV CRO and oral AMX (see figure). CRO serum levels were unaffected by SYN-004. In contrast, no systemic AMX was detected in the presence of SYN-004, suggesting that the β-lactamase degraded AMX prior to its absorption. Therefore, pH-dependent release formulations, designed to release enzyme more distally in the GI tract, were produced and tested in vitro. Dissolution analyses demonstrated no leakage at pHs below the target and the expected release profiles. The most promising formulations are being scaled up for evaluation with oral AMX in pigs.

Conclusion: SYN-004 protected the gut microflora in pigs from damage caused by IV CRO, further supporting the SYN-004 clinical program focused on microbiome protection in humans. New formulations to target enzyme release distal to AMX absorption displayed the expected in vitro release profiles and are being tested in pigs. SYN-004 has the potential to become the first therapy designed to protect the microbiome from certain antibiotics and to prevent antibiotic-associated diarrhea and CDI.