Increasing Access to Clinical Microbiome Specimens via a Living µbiome Bank

项目摘要 在临床和基础科学两端的转化光谱的研究人员需要访问大的 进行研究的生物标本数量。而基础科学家需要标本 T0-T1转换，临床医生经常遇到困难，从患者人群中获得控制 除了在日常临床实践中遇到的问题。幸运的是，许多微生物标本 被收集用于提供常规医疗保健，并且大多数导致剩余材料完全适合用于 进一步研究使用。例如，南卡罗来纳州医科大学诊断微生物学实验室 处理数以千计的微生物拭子进行感染监测。大多数测试结果至少有75%的 剩余的样本体积通常在几天后丢弃。这是一个独特的， 及时获取标本，以便及时捕获并重新用于转化微生物组研究。在 在这个项目中，我们建议弥合研究者需要标本和常规研究之间的差距。 丢弃了宝贵的样本资产我们通过（目标1）开发一个活的微生物群银行（LµBB）系统来实现这一目标 它可以追踪精确的e表型患者队列的剩余材料的可用性， 研究人员要求这些样本和所得的微生物组测定数据用于研究。LµBB 提供端到端的工作流程，允许研究者根据临床标准从 电子健康记录，e-表型，以去识别的方式。系统的能力， 来自不同信息化程度的机构和研究者的机构间样本请求 目标2将对导弹的穿透力和复杂性进行评估。最后，我们将彻底测试整个系统， 执行几个试验样本招募请求并生成最终的研究数据。数据将 使用新设计的微生物组数据模式存储到研究数据仓库中。总的来说， 活微生物群银行将建立一个基础设施，以重新利用现有的临床微生物学为基础 标本，这将允许机构间共享翻译微生物组的材料和数据 research.此外，它还将提供一个在CTSA网络中共享标本的模式。 !

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. !