Increasing Access to Clinical Microbiome Specimens via a Living µbiome Bank

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PROJECT SUMMARY Investigators at both the clinical and basic science ends of the translational spectrum need access to large number of biospecimens to conduct their research. Whereas the basic scientists require specimens to enable the T0-T1 translation, the clinicians often experience difficulties securing controls from patient populations outside of those encountered in their day-to-day clinical practice. Fortunately, many microbiology specimens are collected for the provision of routine healthcare and most result in surplus materials perfectly suitable for further research use. For example, Medical University of South Carolina Diagnostic Microbiology Lab processes thousands of microbiology swabs for infection surveillance. Most tests result in at least 75% of the specimen volume remaining as surplus and is typically discarded after a few days. This presents a unique and timely source of specimens for just-in-time capture and repurposing for translational microbiome research. In this project, we propose to bridge the gap between the investigators needing specimens and the routinely discarded valuable specimen assets. We do so by (Aim 1) developing a Living µBiome Bank (LµBB) system that tracks the availability of surplus materials for precisely e-phenotyped cohorts of patients, and allows investigators to request those samples and the resulting microbiome assay data for research use. The LµBB provides an end-to-end workflow that allows investigators to acquire specimens based on clinical criteria from the electronic health records, e-phenotype, in a de-identified manner. The capability of the system to do interinstitutional specimen request from institutions and investigators with varying degree of informatics penetration and sophistication will be evaluated in Aim 2. Finally, we will thoroughly test the entire system by performing several pilot specimen recruitment requests and generating the final research data. The data will be deposited into the research data warehouse using a newly designed schema for microbiome data. In summary, the Living µBiome Bank will establish an infrastructure rooted in re-use of existing clinical microbiology specimens, which will allow for inter-institutional sharing of materials and data for translational microbiome research. Furthermore, it will provide a model for sharing specimens across the CTSA network. !