Theoretical, Simulation, and Experimental Approaches to Understanding Periphery Sequestration of Diffusing Chemical Species in Bacterial Biofilms as a Mechanism for Antibiotic Recalcitrance

Abstract

People with cystic fibrosis often have chronic, antibiotic resistant Pseudomonas aeruginosa biofilm infections, which are associated with worse health outcomes. This resistance has been partially attributed to periphery sequestration, where antibiotics fail to penetrate biofilm cell clusters. The physical phenomena driving this periphery sequestration have not been definitively established or modeled. This dissertation analyzed scientific literature to determine that size effects, volume-exclusion effects and attachment effects were important physical phenomena necessary to characterize chemical species diffusion in biofilms. These effects were used as the basis of a mathematical model, termed the DIVAC model, for chemical species diffusion in biofilms. It was found that this model, by allowing for spatially heterogeneous attachment site density and biofilm porosity, was able to predict periphery sequestration. Model predictions aligned with dynamic simulation results in two spatial dimensions and equilibrium results in three spatial dimensions. These simulations pointed to the importance of accounting for porosity and attachment site heterogeneity to predict both simulations results and experimental literature data on antibiotic periphery sequestration. A synthetic biofilm experimental system to test the DIVAC model was developed, and while able to replicate the size effects seen in real biofilms, was not able to replicate the volume-exclusion and attachment effects.