A comprehensive next generation sequencing diagnostic tool for lung infection among hospitalized patients

摘要 重症监护病房(ICU)住院的一个主要驱动因素是肺炎。免疫功能低下的患者 占ICU肺炎入院人数20%的这一群体，因普通肺炎而严重感染的风险增加 呼吸道微生物以及不容易用标准培养或治疗的条件致病菌 经验性抗生素。而感染的临床鉴定的标准做法包括广泛的培养和 非培养技术，这些测试通常需要很多天才能得出结果，而确定的致病因素是 仅在10%-40%的病例中发现。因此，患者经常接受多个疗程的抗生素治疗，而不是 识别特定的病原体以指导治疗。确定致病病原体的难度 指导适当的治疗增加了这些患者的成本和死亡率；死亡率高达30%-50%。 目前感染的黄金标准诊断依赖于数十年的技术，这些技术可能需要数周才能完成， 敏感性有限，且可由单个筛查的微生物的类型和数量有限 测试。因此，由于当前的诊断不能全面地筛选和 准确检测微生物病原体，这是改善这些疾病临床结果的重大障碍 病人。我们已经开发了全面的下一代测序(NGS)小组，用于检测和 还能检测抗微生物耐药性(AMR)和宿主免疫反应特征的微生物鉴定。 我们之前的研究已经证明了我们的诊断工具应用于低水平诊断的可行性 慢性疾病中的呼吸道感染及其对微生物和分子生物学方法的优越性 诊断。我们的NGS诊断(Dx)小组是对当前方法的重大技术创新； Dx面板使用直接来自患者的样本(而不是依赖于培养)，提供更高的灵敏度 而不是qPCR或元基因组测序方法，并筛选数以万计的其他 一次化验中的微生物。这些功能是可能的，这要归功于我们的创新设计以及专利 实验室和分析工作流程。该项目的长期目标是提供一种新的临床工具 免疫功能低下的肺部感染性并发症患者感染的检测和特征。 在这一阶段，我们将检查我们的检测方法在这种急性临床环境中使用的可行性，评估 首次使用我们的AMR和宿主免疫筛查为诊断和治疗提供支持信息 治疗指导。具体地说，我们将1)估计我们的小组提供明确检测到 临床测试失败时一个或多个病原体，2)确定使用我们的AMR配置文件替换 临床培养分离试验3)确定免疫图谱在该人群中的可行性和4)确定 侵袭性较小的鼻咽拭子是否有可能在更大的队列中进行进一步研究。总数 这种诊断的市场是一组肺炎住院患者。我们的竞争优势包括 在单一检测中提高了灵敏度、全面的微生物检测和治疗效果洞察。

ABSTRACT A major driver of intensive care unit (ICU) hospital admissions is pneumonia. The immunocompromised patient group, which makes up 20% of ICU pneumonia admissions, is at increased risk for severe infection from common respiratory organisms as well as opportunistic pathogens that cannot be easily cultured or treated with standard empiric antibiotics. While standard practice for clinical identification of infection includes extensive culture and non-culture techniques, these tests often take many days to yield results and a definitive causative agent is identified in only 10%-40% of cases. As a result, patients often receive multiple courses of antibiotics without identification of a specific pathogen to guide therapy. The difficulty in determining the offending pathogens to guide proper treatment increases both costs and mortality for these patients; mortality is as high as 30%-50%. Current gold-standard diagnostics for infection rely on decades-old technology that can take weeks to complete, have limited sensitivity, and are limited in the type and number of microbes that can be screened by a single test. Thus, a critical gap exists due to the inability of current diagnostics to comprehensively screen and accurately detect microbial pathogens, which is a significant barrier to improved clinical outcomes for these patients. We have developed a comprehensive next generation sequencing (NGS) panel for detection and identification of microbes that also detects anti-microbial resistance (AMR) and host immune response features. Our previous studies have demonstrated the feasibility of our diagnostic tool for application to low-level respiratory infections in chronic disease and its superiority to both microbiological and molecular approaches to diagnosis. Our NGS diagnostics (Dx) panel is a significant technological innovation over current methodology; the Dx panel utilizes samples directly from the patient (rather than relying on cultures), provides greater sensitivity than qPCR or meta-genomic sequencing approaches and screens for the presence of tens of thousands of other microbes in a single assay. These features are possible due to our innovative design in addition to proprietary laboratory and analysis workflows. The long-term goal of this project is to provide a novel clinical tool for detection and characterization of infections in immunocompromised patients with infectious lung complications. In this Phase I, we will examine the feasibility of our assay for use in this acute clinical setting, evaluating for the first time the use of our AMR and host immune screening to provide supportive information for diagnosis and treatment guidance. Specifically, we will 1) estimate the rate at which our panel provides a definitive detection of one or more pathogens when clinical tests fail, 2) establish the feasibility of using our AMR profile to replace clinical culture isolate tests 3) determine the feasibility of immune profiling in this population and 4) determine whether less invasive nasopharyngeal swabs have the potential for further study in a larger cohort. The total market for this diagnostic is the set of hospitalized patients with pneumonia. Our competitive advantages include improved sensitivity, comprehensive microbe detection and treatment effectiveness insights in a single assay.