Development of a Novel Whole Genome Sequencing-based Platform for Rapid Identification and Antimicrobial Profiling of Uropathogens

复杂性尿路感染是严重的或危及生命的感染，超出了一个简单的膀胱 感染，最常见于住院患者。有超过280万例复杂的 泌尿道感染，其中20%的病例进展为尿脓毒症，导致近 每年有15万人死亡。有效管理复杂的尿路感染需要快速 鉴定致病细菌病原体和相关的抗生素耐药性谱。当前 然而，护理标准是尿培养，从样本收集到可采取行动需要2-3天 产生指导患者治疗的信息。因此，迫切需要诊断工具， 允许快速鉴定尿路病原体及其抗微生物剂抗性/敏感性概况。到 为了满足这一未满足的需求，Day Zero Diagnostics（DZD）正在开发一种诊断工作流程， 基因组测序和机器学习提供高分辨率的物种识别和抗菌 耐药和敏感性分析，而无需尿液培养。这些数据将 指导循证治疗决策，以改善患者护理。本提案的目的是：（1） 证明来自尿样的各种物种的细菌DNA的超高富集，以及（2） 优化样品制备管道，在6小时或更短时间内提供可操作的结果， 复杂性尿路感染时间表拟议的具体目标，以及可量化的目标指标， 旨在在开发商业体外诊断之前证明概念验证。 在第一阶段完成后，第二阶段将集中于优化工作流程，扩展测试能力， 分析和临床验证研究。

Complicated urinary tract infections are severe or life-threatening infections that extend beyond a simple bladder infection and occur most frequently in hospitalized patients. There are over 2.8 million cases of complicated urinary tract infections in the U.S. each year, with 20% of cases progressing to urosepsis, leading to nearly 150,000 deaths each year. Effective management of complicated urinary tract infections requires the rapid identification of the causative bacterial pathogen(s) and the associated antibiotic resistance profile. The current standard of care, however, is urine culture, which requires 2-3 days from specimen collection until actionable information to guide patient treatment is generated. Hence, there is an urgent need for diagnostic tools that will allow for the rapid identification of uropathogens and their antimicrobial resistance/sensitivity profile(s). To address this unmet need, Day Zero Diagnostics (DZD) is developing a diagnostic workflow that leverages whole genome sequencing and machine learning to deliver high resolution species identification and antimicrobial resistance and susceptibility profiling from a patient sample without the need for urine culture. These data will guide evidence-based treatment decisions to improve patient care. The aims of this proposal are to (1) demonstrate ultra-high enrichment of bacterial DNA from a diverse range of species from urine samples and (2) optimize a sample preparation pipeline to deliver an actionable result in six hours or less, a clinically relevant timeframe for complicated urinary tract infection. The proposed Specific Aims, with quantifiable target metrics, are designed to demonstrate proof-of-concept in advance of the development of a commercial in vitro diagnostic. Upon Phase I completion, Phase II will focus on optimizing the workflow, expanding test capabilities, and analytical and clinical validation studies.