Patient-oriented microbiome and advanced culture approaches to identifying the microbial determinants of chronic pediatric disease

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PROJECT SUMMARY/ABSTRACT The goal of this K24 is to provide salary, administrative, and research support for Lucas Hoffman, MD, PhD, to allow him to spend at least 25% of his time mentoring students, fellows, and junior faculty in patient-oriented research on the microbial determinants of chronic, pediatric diseases. This proposal will enable Dr. Hoffman to expand his translational research program, integrate trainees into the program, and provide additional protected time and resources for mentoring existing and additional trainees specifically in patient-oriented research as they work on existing translational research projects as well as new projects to emerge from this ongoing work. The proposal also provides time and infrastructure to help Dr. Hoffman enhance his mentoring skills, including classwork, new opportunities to interact with trainees, and an oversight committee specifically focused on this topic. The three ongoing, featured research projects leverage either existing resources (Project 1) or involve face-to-face interactions with patients (Projects 2 and 3) and are yielding novel questions and new resources for these and future patient-oriented studies, providing optimal opportunities for trainees: Project 1 investigates the relationship between gastrointestinal (GI) microbiomes of infants with the genetic disease cystic fibrosis (CF) with growth and other clinical outcomes during the first year of life. This project builds on our preliminary finding that young children with CF have GI dysbioses that are predicted to impact intestinal health and inflammation. As infants with CF often fail to grow adequately, and early nutritional outcomes correlate with overall disease course, identifying the mechanisms of early CF growth failure is an important and understudied topic. In this study, we are analyzing longitudinal fecal specimens and clinical data collected as part of a recently completed, multicenter clinical study of CF infant nutrition. Project 2 is an ongoing, multicenter study of variants of Staphylococcus aureus, the most common bacterial pathogen most commonly cultured from the respiratory tracts of people with CF. These variants, known as small-colony variants (SCVs), grow slowly in the laboratory and are not routinely detected by clinical laboratories. Our preliminary data indicate that SCVs commonly infect children with CF, and that they are associated with dramatically worse lung disease compared with children without SCVs. We are investigating the prevalence and clinical associations, as well as molecular mechanisms, of SCV infection in a cohort of children with CF. This study also collects bacterial isolates, linked data, and other resources for future studies. Project 3 is an ongoing, multicenter study of sputum microbiomes among children and adults with CF before, during, and after receiving a month-long treatment with inhaled tobramycin. The microbial determinants of CF lung disease and clinical responses are well-studied yet poorly understood. In this project, we are using high- throughput sequencing-based microbiome methods to identify the microbiome correlates of antibiotic response by comparing lung function changes with microbiome changes during antibiotic treatment with a single agent.