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

高度多重对流 qPCR 检测和平台，可对引起 UTI 的病原体进行快速、全面的识别和预测 AST。

• 批准号: 10322806
• 负责人: Dmitriy Khodakov
• 金额: $ 30万
• 依托单位: TORUS BIOSYSTEMS, INC.
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-01 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10322806
• 关键词: Accounting; Affect; Antibiotic Resistance; Antibiotic Therapy; Antibiotics; Antimicrobial Resistance; Bacteria; Biological Assay; Biomedical Engineering; Cells; Chemistry; Clinical; Clinical Sensitivity; Collaborations; Community Hospitals; Complex; Convection; Cytolysis; DNA; Detection; Development; Diagnosis; Diagnostic; Diagnostic tests; Drug resistance; Fractionation; Future; Genes; Genomics; Gold; Health Care Costs; Healthcare; Infection; Infection Control; Laboratories; Medical; Molecular Diagnostic Techniques; Morbidity - disease rate; Mutation; Nature; Nosocomial Infections; Nucleic Acid Amplification Tests; Nucleic Acids; Nucleotides; Paper; Pathogen detection; Patient-Focused Outcomes; Patients; Performance; Phase; Population; Preparation; Prevalence; Rapid diagnostics; Reaction; Recovery; Recurrence; Reproducibility; Sampling; Sensitivity and Specificity; Small Business Innovation Research Grant; Solid; Specimen; System; Technology; Testing; Therapeutic; Time; TimeLine; Urinary tract infection; Urine; Uropathogen; Validation; Visit; Work; amplification detection; antimicrobial; base; clinical application; clinical research site; communicable disease diagnosis; design; detection sensitivity; diagnostic assay; diagnostic panel; diagnostic platform; improved; insight; molecular diagnostics; multi-drug resistant pathogen; pathogen; pathogenic bacteria; pathogenic fungus; personalized medicine; point of care; point-of-care diagnostics; prototype; rapid test; resistance gene; synthetic construct; Accounting; Affect; Antibiotic Resistance; Antibiotic Therapy; Antibiotics; Antimicrobial Resistance; Bacteria; Biological Assay; Biomedical Engineering; Cells; Chemistry; Clinical; Clinical Sensitivity; Collaborations; Community Hospitals; Complex; Convection; Cytolysis; DNA; Detection; Development; Diagnosis; Diagnostic; Diagnostic tests; Drug resistance; Fractionation; Future; Genes; Genomics; Gold; Health Care Costs; Healthcare; Infection; Infection Control; Laboratories; Medical; Molecular Diagnostic Techniques; Morbidity - disease rate; Mutation; Nature; Nosocomial Infections; Nucleic Acid Amplification Tests; Nucleic Acids; Nucleotides; Paper; Pathogen detection; Patient-Focused Outcomes; Patients; Performance; Phase; Population; Preparation; Prevalence; Rapid diagnostics; Reaction; Recovery; Recurrence; Reproducibility; Sampling; Sensitivity and Specificity; Small Business Innovation Research Grant; Solid; Specimen; System; Technology; Testing; Therapeutic; Time; TimeLine; Urinary tract infection; Urine; Uropathogen; Validation; Visit; Work; amplification detection; antimicrobial; base; clinical application; clinical research site; communicable disease diagnosis; design; detection sensitivity; diagnostic assay; diagnostic panel; diagnostic platform; improved; insight; molecular diagnostics; multi-drug resistant pathogen; pathogen; pathogenic bacteria; pathogenic fungus; personalized medicine; point of care; point-of-care diagnostics; prototype; rapid test; resistance gene; synthetic construct

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.

项目摘要 尿路感染（UTI）是最普遍的社区和医院的感染之一 （每年约1000万），考虑到发病率和年度医疗保健支出 大于$ 6B。虽然对UTI病原体有充分的了解，但患者经常受到经验治疗。 缺乏可以鉴定uti病原体的快速，护理分子诊断剂会导致差 抗菌药物管理和UTI药物抗性的高率。 我们建议开始开发快速的诊断测定和工作流程，以同时检测 所有UTI病原体及其相关的耐药基因，适用于护理点临床应用。 预计该测定法可以对UTI进行更有效的个性化处理，从而降低 抗菌素耐药性并改善患者预后。 如即将到来的自然生物医学工程纸中所述，圆环生物系统的QPCR系统， Synestia™已证明可重现的30个PLEX功能，准确的定量和SNP检测， 灵敏度降至10个基因组拷贝，周转时间少于30分钟。可消耗是 配备嵌入式预淬灭微阵列，可实时检测放大 没有打开反应室的产品。合成系统的灵敏度和动态范围 已经在一系列输入浓度的DNA（101至105份）和阈值中评估了 发现值取决于输入DNA浓度的对数。该平台也有 成功证明了使用15种细菌特异的多重图案鉴定的快速细菌鉴定 物种。 该第1阶段的申请提案要开发一个60季度UTI面板，以全面评估 在Synestia平台上30分钟内尿路病DNA。在随后的第2阶段，我们将发展， 优化并验证完全集成的消耗量，包括尿液样品准备（裂解和提取） 合成平台和与某些临床部位合作验证临床性能。团队 预计该证明的测定法将构成进一步发展的可靠基础 尿路感染的商业护理诊断测试。