A highly multiplexed convection flow qPCR assay and platform delivering rapid, comprehensive identification and predictive AST of pathogens causing UTIs.

项目摘要 尿路感染（UTIs）是最流行的社区和医院获得性感染之一 （每年约1000万次医疗就诊），占美国每年医疗保健支出的相当大比例， 超过60亿美元。虽然UTI病原体是很好理解的，但患者经常凭经验治疗。 缺乏可以识别UTI病原体的快速、即时的分子诊断，导致UTI患者的预后差。 抗生素管理和高UTI耐药率。 我们建议开始开发一种快速诊断检测方法和工作流程， 所有UTI病原体及其相关耐药基因，适用于床旁临床应用。 预计该测定允许更有效的UTI个性化治疗，降低UTI的发生率。 抗微生物药物耐药性和改善患者预后。 正如即将发表的《自然生物医学工程》论文所述，Torus Biosystems的qPCR系统， Synestia™已经证明了可重复的30重能力、准确的定量和SNP检测， 灵敏度低至10个基因组拷贝，周转时间小于30分钟。该消费品是 配备有嵌入式预淬灭微阵列，允许实时检测扩增 不需要打开反应室。Synestia系统的灵敏度和动态范围 已在一系列DNA输入浓度（101至105个拷贝）和阈值范围内进行了评价 发现该值依赖于输入DNA浓度的对数。该平台还 成功证明了使用对15种细菌具有特异性的多重面板进行快速细菌鉴定 物种 该第1阶段申请建议开发一个60路UTI面板，用于全面评估 在Synestia平台上30分钟内检测出泌尿病原体DNA。在接下来的第二阶段，我们将开发， 优化和验证完全集成的耗材，包括尿液样本制备（裂解和提取）， Synestia平台，并与选定的临床研究中心合作验证临床性能。球队 预计，所证明的测定将构成进一步发展的坚实基础， 用于尿路感染的商业护理点诊断测试。

Project Summary Urinary tract infections (UTIs) are among the most prevalent community- and hospital-acquired infections (~10M annual medical visits), accounting for considerable morbidity and annual US healthcare spend of greater than $6B. While UTI pathogens are well understood, patients are frequently treated empirically. The lack of rapid, point of care molecular diagnostics that can identify UTI pathogens results in poor antimicrobial stewardship and high rates of UTI drug resistance. We propose to begin development of a rapid diagnostic assay and workflow that will concurrently detect all UTI pathogens and their associated resistance genes, suitable for point of care clinical applications. This assay is anticipated to allow for more effective personalized treatment of UTIs, reducing rates of antimicrobial resistance, and improving patient outcomes. As described in an upcoming Nature Biomedical Engineering paper, the Torus Biosystems’s qPCR system, Synestia™, has demonstrated reproducible 30-plex capability, accurate quantitation and SNP detection, sensitivity down to 10 genomic copies, and turnaround times of less than 30 minutes. The consumable is equipped with an embedded pre-quenched microarray that allows for real-time detection of amplification products without opening the reaction chamber. The sensitivity and dynamic range of the Synestia system has been evaluated across a range of input concentrations of DNA (101 to 105 copies) and the threshold value was found to be dependent on the log of the input DNA concentration. The platform has also successfully demonstrated rapid bacteria identification using a multiplex panel specific for 15 bacteria species. This Phase 1 application proposes to develop a 60-plex UTI panel for comprehensive assessment of uropathogen DNA within 30 minutes on the Synestia platform. In the subsequent Phase 2, we will develop, optimize, and validate a fully integrated consumable including urine sample prep (lysis and extraction) on the Synestia platform and validate clinical performance in collaboration with select clinical sites. The team anticipates that the demonstrated assay will constitute a solid basis for further development of a commercial point of care diagnostic test for urinary tract infections.