Carbapenem-resistant bacterial colonization and infection after liver transplant

 描述（由申请人提供）：需要多方面的方法来限制碳青霉烯类耐药肠杆菌科（CRE）感染，包括肺炎克雷伯菌，这已成为全球公共卫生问题。这些多重耐药生物体与经常超过50%的高发病率和死亡率相关，因为缺乏高效和无毒的治疗方案。虽然肠内定植的CREs已被提出作为一个潜在的风险因素，感染CRE爆发期间，其实际的贡献感染仍然不完全清楚。此外，关于这些抗生素耐药生物如何在受影响宿主内从定殖转变为感染的知识存在根本性差距。本申请的长期目标是在细菌基因组水平上阐明CRE感染如何出现和传播。了解这些过程对于开发干预和实时临床监测方法以限制CRE感染在个体和群体水平上的影响至关重要。我们将把研究重点放在肝移植后CRE感染和不良结局风险非常高的患者身上。我们的核心假设是，肠道提供了一个微环境，CRE可以在其中扩展并适应小的遗传变异，随后导致感染。为了解决这些问题，我们建议对接受肝移植的成年患者进行队列研究，并在受影响的患者和整个医院内跟踪CREs。在这个前瞻性队列中，我们将在移植前招募300名患者，收集粪便样本以确定肠道定植 在移植前和移植后反复进行，并在6个月的时间内评估患者的CRE感染。我们的研究设计将允许我们执行以下目的：1）定义肝移植患者中CRE感染的定殖率和作用; 2）评价从CRE定殖到感染的宿主内演变;和3）调查CRE在肝移植和医院中的其他患者群体之间的传播。在目标1中，我们将测试 CRE定植至感染，并使用Kaplan-Meier生存分析和考克斯比例风险模型表征结局。在目标2中，我们将应用16S和全基因组测序来回答CRE定殖优势是否在感染之前发展，以及可改变的风险因素（例如某些抗生素）如何与这些适应相关。我们还将定义 定殖CRE的克隆多样性，并评估感染性分离株是否来自优势定殖克隆或获得新的毒力性状。在目标3中，我们将通过将全基因组序列分析扩展到非肝移植患者中发生的感染来评估CRE感染的院内演变和传播。我们的多学科方法是创新的，将高分辨率基因组学与详细的流行病学调查相结合，以真实的时间监测CRE感染的演变。这项研究具有重要的直接翻译影响，建立了一个框架，以跟踪多重耐药肠杆菌科的出现，并最终设计新的遏制战略CREs。

 DESCRIPTION (provided by applicant): Multifaceted approaches are needed to limit carbapenem-resistant Enterobacteriaceae (CRE) infections, including Klebsiella pneumoniae, which have emerged as a worldwide public health problem. These multidrug- resistant organisms are associated with high morbidity and mortality that often exceeds 50%, as highly effective and non-toxic treatment regimens are lacking. While intestinal colonization with CREs has been proposed as a potential risk factor for infections during CRE outbreaks, its actual contribution to infection remains incompletely understood. Moreover, there is a fundamental gap in knowledge on how these antibiotic resistant organisms transition from colonization to infection within affected hosts. The long-term goal of this application is to elucidate at the bacterial genome level how CRE infections emerge and spread. Understanding these processes is critical to developing intervention and real-time clinical monitoring approaches to limit the impac of CRE infections at an individual and population level. We will focus our study on patients after liver transplantation who are at very high risk for CRE infections and adverse outcomes. Our central hypothesis is that the intestine provides a microenvironment in which CRE can expand and adapt with small genetic variations and subsequently lead to infections. To address these questions we propose to establish a cohort study of adult patients undergoing liver transplant, and track CREs within affected patients and across the hospital. In this prospective cohort we will enroll 300 patients pre-transplant, collect stool samples to ascertain intestinal colonization pre- and repeatedly post-transplant, and assess patients for CRE infections over a 6-month period. Our study design will allow us to execute the following Aims: 1) Define the rate and role of colonization on CRE infection in liver transplant patients; 2) Evaluate the within-host evolutio from CRE colonization to infection; and 3) Investigate the spread of CRE between liver transplant and other patient populations in the hospital. In Aim 1 we will test the contribution of CRE colonization to infection and characterize outcomes using Kaplan-Meier survival analyses and a Cox proportional hazard model. In Aim 2 we will apply 16S and whole-genome sequencing to answer whether CRE colonization dominance develops prior to infection and how modifiable risk factors (e.g. certain antibiotics) relate to these adaptations. We will also define the clonal diversity of colonizing CRE and assess whether infectious isolates arise from dominant colonizing clones or acquire novel virulence traits. In Aim 3 we will assess the within-hospital evolution and spread of CRE infections by extending whole-genome sequence analyses to infections that occurred in non- liver transplant patients. Our multidisciplinary approach is innovative in its combination of high-resolution genomics with detailed epidemiological investigations to monitor the evolution of CRE infections in real time. This research is significant with direct translational impact in establishing a framework to track the emergence of multi-drug resistant Enterobacteriaceae and to ultimately devise novel containment strategies for CREs.