Improving diagnosis of post-traumatic sepsis using plasma microbial DNA sequencing

项目摘要/摘要 该提案提出了一项为期五年的研究职业发展计划，重点是提高对 创伤后脓毒症患者血浆微生物DNA测序的研究。我是哈佛大学的外科学助理教授。 威斯康星大学麦迪逊分校，具有创伤外科的临床和研究经验，患者- 脓毒症的中心预测因子和败血症患者血浆的实验室基因组分析。我有过 组建了一支出色的导师团队，拥有传染病、无细胞DNA、基因组数据等方面的专业知识 分析和生物信息学。拟议的培训将促进我在以下各学科的发展 基因组学的翻译研究、实验室和计算方法，以及科学写作。这将是 使我能够作为一名外科医生兼科学家过渡到研究独立性，致力于改善 通过开发基于微生物基因组学的更好的诊断测试，帮助创伤患者患上脓毒症。 败血症是一种危及生命的疾病，据估计占全球死亡人数的五分之一。大致 25%的创伤患者在住院期间发生脓毒症，其中超过20%的患者死亡 在同一次住院期间。脓毒症，如果不及早发现和治疗，可能演变为感染性休克和 多器官衰竭。因此，脓毒症的治疗强调及时使用抗生素和来源。 手术/创伤患者的对照。然而，创伤患者的脓毒症的诊断是 复杂是因为全身对损伤的炎症反应类似于脓毒症。在当前的范例中， 脓毒症的确认是基于临床体征、实验室和放射学检查结果以及医学评分。 通常是在脓毒症发作后获得的。大约有200种败血症的生物标志物在 文献，但几乎所有这样的生物标记物都依赖于测量炎症反应，这在 有创伤的病人。最近的研究，包括我的初步工作，已经表明元基因组学 血浆DNA测序可以快速识别临床怀疑为脓毒症的患者的病原体，但这些 目前还没有对创伤患者进行检测的研究。为了解决这一差距，我建议开发和评估 一种基于元基因组测序的分析进入血液的微生物DNA的分析方法。我的中央 假设创伤患者体内微生物DNA水平的定量分析可以快速预测脓毒症 确定脓毒症的致病微生物，帮助缩短抗菌治疗的时间。vbl.使用 前瞻性采集创伤患者的血浆样本，我提出以下目标：1)确定 循环微生物DNA水平升高是创伤患者脓毒症的预测指标，2)评估 使用标准护理微生物学鉴定的致病微生物与检测的一致性 血浆中病原体特异性DNA，以及3)评估血浆中循环微生物DNA水平作为 用于监测抗菌药物反应的生物标志物。

PROJECT SUMMARY/ABTRACT This proposal presents a five-year research career development plan focused on improving diagnosis of post-traumatic sepsis using microbial DNA sequencing in plasma. I am an Assistant Professor of Surgery at the University of Wisconsin-Madison, with previous clinical and research experience in trauma surgery, patient- centric predictors of sepsis, and lab-based genomic analyses of plasma in patients with sepsis. I have assembled an outstanding mentorship team with expertise in infectious disease, cell-free DNA, genomic data analysis, and bioinformatics. The proposed training will enhance my development across the disciplines of translational research, laboratory and computational methods in genomics, and scientific writing. This will enable me to transition to research independence as a surgeon-scientist dedicated to improving outcomes for trauma patients with sepsis by developing better diagnostic tests based on microbial genomics. Sepsis is a life-threatening condition, estimated to cause one-fifth of all deaths worldwide. Approximately 25% of trauma patients develop sepsis during their hospital course and more than 20% of such patients die during the same hospitalization. Sepsis, if not recognized and treated early, may evolve into septic shock and multiple organ failure. Thus, the treatment of sepsis emphasizes timely initiation of antibiotics and source control in surgery/trauma patients. However, the diagnosis of sepsis in patients with traumatic injury is complicated because systemic inflammatory response to injury mimics sepsis. In the current paradigm, confirmation of sepsis is based on clinical signs, laboratory and radiographic findings, and medical scores which are usually obtained after sepsis onset. There are approximately 200 biomarkers of sepsis described in literature but nearly all such biomarkers rely on measuring inflammatory response, which is confounded in patients with trauma. Recent studies, including my preliminary work, have shown that metagenomic sequencing of plasma DNA can rapidly identify pathogens in patients with clinical suspicion of sepsis but these assays have not been investigated in trauma patients. To address this gap, I propose to develop and evaluate a metagenomic sequencing-based assay for analysis of microbial DNA shed into the blood. My central hypothesis is that quantitative analysis of microbial DNA levels in trauma patients can predict sepsis, rapidly identify the causative organism of sepsis, and help decrease the duration of antimicrobial treatment. Using prospectively collected plasma samples from trauma patients, I propose the following aims: 1) To determine if an increase in circulating microbial DNA levels is predictive of sepsis in trauma patients, 2) To assess concordance between causative organism identified using standard-of-care microbiology and detection of pathogen-specific DNA in plasma, and 3) To evaluate circulating microbial DNA levels in plasma as a biomarker for monitoring antimicrobial response.