The molecular basis of the carbapenem resistance epidemic

摘要 细菌进化中的一个共同主题是抗生素耐药性的获得如何迅速改变 人类主要病原体的流行病学图景。耐碳青霉烯类肺炎克雷伯菌(CRKP)， 首次记录于1996年，现在在纽约市(NYC)的医院流行，并在全球范围内报告。CRKP 感染往往导致较差的治疗指数；因此，遏制CRKP感染的发生率现在是一项 国家优先事项。目前，三种不同类型碳青霉烯酶的CRKP疫情重叠 正在不同的大陆蔓延。加速这些流行的是碳青霉烯酶基因的能力， 寄生在接合质粒上，在肠杆菌科家族中传播。一个危急的，糟糕的 据了解，CRKP流行的一个方面是质粒介导的转移和克隆的相对贡献 传播以推动区域和全球流行病学。之前，我们使用的是全基因组测序 (WGS)剖析美国主要流行CRKP序列类型的分子流行病学和进化 (ST)258.在我们的纽约医院网络中询问携带质粒的菌株和耐药性 发现大多数ST258 CRKP菌株含有三种常见的携带特定基因的质粒之一 碳青霉烯酶的一类，KPC。这些数据表明，CRKP的传播很可能是 质粒介导的基因转移和随后的克隆传播。因此，我们假设这种流行病是 主要是由于携带独特适应于特定宿主基因的质粒的抗性的传递 背景。在目标1中，我们扩展了我们的纽约市网络，将一个大型美国财团包括在内，并研究 全美CRKP菌株和质粒的基因组流行病学。目标2建立在洞察力和 在我们之前的研究中开发的技术通过大量的 来自62个国家的临床分离株收集，目的是构建菌株的系统地理图， 质粒和碳青霉烯酶基因。为了达到这个目的，我们还将直接测试CRKP菌株的基础--质粒 不同碳青霉烯酶基因携带者传递效率的比较研究 转化成不同的菌株背景。利用在目标1和目标2中获得的强大的CRKP基因组数据，我们将 建立一种快速的分子检测方法来鉴定和跟踪临床环境中的CRKP菌株和质粒。 目标3将表征导致高水平碳青霉烯酶耐药的非碳青霉烯酶因素。 CRKP分离株，例如外膜蛋白突变，导致非常糟糕的临床结果。 基于这一特征，将选择一些对碳青霉烯酶高度耐药的菌株建立 一个新的，精心挑选的菌株小组，用于测试新的抗生素制剂。总而言之，我们的是一个创新的 有可能在CRKP流行病学领域产生重大影响的方法，关键地发展 所需的诊断平台，并探索新型抗生素对这些微生物的疗效。

Summary A common theme in bacterial evolution is how the acquisition of antibiotic resistance can rapidly change the epidemiologic landscape of major human pathogens. Carbapenem Resistant Klebsiella pneumoniae (CRKp), first documented in 1996, is now epidemic in New York City (NYC) hospitals and is reported globally. CRKp infections often result in poor therapeutic indices; thus curbing the incidence of CRKp infections is now a national priority. Currently, three overlapping CRKp epidemics with three different classes of carbapenemases are spreading in different continents. Accelerating these epidemics is the ability of carbapenemase genes, harbored on conjugative plasmids, to spread across the Enterobacteriaceae family. A critical, poorly understood aspect of the CRKp epidemic is the relative contribution of plasmid-mediated transfer and clonal dissemination to driving the regional and global epidemiology. Previously, we used whole genome sequencing (WGS) to dissect the molecular epidemiology and evolution of the main US epidemic CRKp sequence type (ST) 258. Interrogating strains and resistance harboring plasmids within our network of NYC hospitals we found that the majority of ST258 CRKp strains harbor one of three common plasmids carrying a particular class of carbapenemase enzyme, KPC. These data suggest the spread of CRKp is likely the consequence of plasmid-mediated gene transfer and subsequent clonal spread. We therefore hypothesize that this epidemic is primarily due to transmission of resistance harboring plasmids uniquely adapted to specific host genetic backgrounds. In Aim 1, we expand our NYC network to include a large US consortium and to examine the genomic epidemiology of CRKp strains and plasmids across the US. Aim 2 builds on the insights and techniques developed in our previous studies to interrogate the global epidemiology of CRKp via a large clinical isolate collection from over 62 countries, with the goal of constructing a phylogeographic map of strains, plasmids and carbapenemase genes. In this Aim we will also directly test the basis of CRKp strain-plasmid association by comparative transmission efficiency studies of different carbapenemase gene-harboring plasmids into diverse strain backgrounds. Using robust CRKp genomic data obtained in Aims 1 and 2, we will develop a rapid molecular detection assay to identify and track CRKp strains and plasmids in clinical settings. Aim 3 will characterize non-carbapenemase factors that contribute to high-level carbapenemase resistance in CRKp isolates, such as mutations in outer membrane proteins, which result in very poor clinical outcomes. Based on this characterization, some of these highly carbapenemase resistant strains will be selected to build a new, well-curated panel of strains for testing novel antibiotic agents. Taken together, ours is an innovative approach with the potential to make a substantial impact in the field of CRKp epidemiology, develop critically needed diagnostic platforms, and explore efficacy of novel antibiotics against these organisms.