Bacteriophage as a predictive biomarker in chronic Pseudomonas airway disease

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PROJECT SUMMARY / ABSTRACT Despite major advances in therapy, pulmonary disease continues to dominate the clinical course of patients with cystic fibrosis (CF). All patients with CF develop chronic lung infections, with Pseudomonas aeruginosa (Pa) becoming a predominant organism in adulthood. Even in the face of chronic inhalational antibiotic therapy to target Pa in the lungs, CF patients experience intermittent pulmonary exacerbations with stepwise decline in lung function leading to eventual respiratory failure. Novel treatment strategies are urgently needed to address the damaging effects of chronic Pa in the lungs of CF patients. This will allow for all patients with CF to fully benefit of an evolving therapeutic landscape to address their defective CF gene function. I discovered the presence of the Pa filamentous (Pf) bacteriophage, in cohorts of patients with CF in Stanford and Denmark. Pf was associated with chronicity of Pa and more severe exacerbations (Burgener et al, Science Translational Medicine 2019). This constituted the first demonstration of the involvement of bacteriophage in human lung disease. This proposal aims to delve into the mechanisms behind these associations. Given the known shortcomings of chronic inhalational antibiotic therapy, I will test the hypothesis that in the lung Pf provides antibiotic tolerance and is a predictive biomarker to guide in choosing effective inhalational therapeutics. The first aim utilizes banked respiratory Pa isolates to (1a), assess antibiotic tolerance under conditions present in the lung, (1b) perform whole genome sequencing to assess for presence of antibiotic resistance genes and (1c) perform evolutionary experiments to investigate acquisition of resistance as a function of Pf. The second aim will assess Pf as a lung disease predictive biomarker in (2a) a retrospective cohort evaluating response to exacerbations therapy and (2b) perform a cross-over clinical trial to assess for differential effects of Pf on lung function. This proposal, supported by exciting and novel preliminary data, promises to provide rationale and mechanistic foundation for Pf to be used as a predictive biomarker to guide inhalational antibiotic choices in CF airway disease management. The proposed research draws upon my prior experience in clinical pulmonary medicine and growing expertise in translational research. Along with my mentors and advisory committee, I present a comprehensive career development plan for didactics and technical training in microbiology, genomics, and clinical trial design and biostatistics. This training, along with the clinical studies and experiments outlined, will allow me to develop skills crucial for my transition to an independent translational research career focused on bringing new therapies and treatment strategies for transformative management of CF lung disease.