In silico Analysis of Clostridium difficile Biofilm Metabolism and Treatment*

Clostridium difficile is an anaerobic bacterium responsible for recurring infections in the gastrointestinal tracts of patients previously treated with oral antibiotics that disrupt the healthy gut microbiome. Recent in vitro experiments have demonstrated the ability of C. difficile to form biofilms on surfaces. We developed a metabolic model of C. difficile biofilms to investigate the effects of biofilm formation on antibiotic treatment in vivo. The model was formulated by combining a genome-scale reconstruction of C. difficile primary metabolism with reaction-diffusion type equations for key nutrients (glucose and six essential amino acids) and the common oral antibiotic vancomycin. A very simple model of vancomycin pharmacokinetics was used to predict the efficacy of a typical treatment schedule under the assumption of a fixed thickness of the mature biofilm. Our model predicted that vancomycin will effectively eradicate biofilms of sufficiently small thickness. Once the thickness passed a critical threshold, the model predicted vancomycin treatment would fail catastrophically due to insufficient antibiotic penetration into the biofilm caused by the combination of limited diffusion and vancomycin binding to cell wall precursors. This critical biofilm thickness was shown to be very sensitive to model parameters associated with the vancomycin stool levels and killing efficiency.