(710g) Systems Biology for Biofilm Antibiotic Tolerance

This presentation will touch on bubonic plague, a differential balance equation describing spatiotemporal gene expression, two fishing expeditions, microbial asphyxiation, spumoni ice cream, and the story of what happened on the pacemaker of an indigent alcoholic. Each of these items illuminate an aspect of the serious, unsolved problem of chronic infections stemming from microbial biofilms. One of the main reasons for the persistence of biofilm infections is the antibiotic tolerance that manifests as microorganisms aggregate and mature. Using the bacterium Pseudomonas aeruginosain model biofilm systems, the chemical, physiological, and genetic bases of biofilm antibiotic tolerance were investigated using a suite of techniques including oxygen microelectrodes, GFP-reporter strains, transcriptomics, metabolomics, mutant susceptibility assays, and mathematical modeling. Collectively, these findings, though incomplete, support a sequence of phenomena leading to biofilm antibiotic tolerance involving oxygen limitation, electron acceptor starvation and growth arrest, parallel induction of associated stress responses, and differentiation into protected cell states. Successes of this integrated approach include: i) correspondence between chemical measurements of oxygen, reaction-diffusion modeling, and gene set enrichment analysis indicating hypoxia, and ii) measurement of reduced specific growth rate in biofilms and identification of transcriptomic signatures for stationary phase and zinc starvation in the in vitrobiofilm and also in some published in vivotranscriptomic and proteomic analyses. Limitations and ongoing challenges of the approach include: i) lack of correspondence between transcriptomic and metabolic activities, 2) technical difficulty of addressing microscale physiological heterogeneity, iii) failure of in vitromodels to capture all of the physiological features of in vivoreality, iv) discrepancy between the decrease in viable plate counts following antibiotic treatment and maintenance of catabolic activity of the treated biofilm, and 4) inherent difficulty of targeting dormant bacterial cells that have deployed overlapping, redundant protective mechanisms.