Elucidating transmission of plasmids harboring blaKPC among carbapenem-resistant Enterobacteriaceae using long-range sequencing

项目摘要/摘要： 理由：对广谱碳青霉烯类抗生素的耐药性在 自20世纪90年代初以来一直是肠杆菌科细菌，对医疗保健构成日益严重的威胁。而克雷伯氏菌 肺炎占美国慢性肺病的大部分，最近的证据表明，慢性肺病迅速 多样化。这反映了碳青霉烯类耐药基因在不同菌株之间传播的能力。 肠杆菌科通过可移动的遗传元件，特别是质粒。尽管他们的感染控制很重要 但是，这些质粒传播的机制还没有完全阐明。候选人：AS 拥有生物统计学硕士学位的传染病临床医生，Angela Gomez-Simmonds博士的 出版物描述了CRE的临床和分子流行病学特征。高级正规培训 生物信息学和基因组流行病学将对完成拟议的研究和 她事业上的进步。在主要导师安妮-卡特琳·乌尔曼博士的帮助下，她组建了一个 由多学科专家组成的咨询团队指导她的培训和研究进展。戈麦斯-西蒙兹博士的 长期目标是成为NIH资助的独立研究人员，使用下一代测序来 了解细菌进化、耐药机制和临床流行病学之间的联系 多药耐药革兰氏阴性院内病原菌。环境：乌尔曼实验室 哥伦比亚大学医学中心(CUMC)拥有必要的微生物学和测序工具 以及来自不同地点的大量CRE临床分离株的回顾收集 进行基因组研究。CUMC在支持年轻人的职业发展方面有着良好的记录 内科医生-科学家。方法：我们假设编码blaKPC的质粒的水平转移， 美国显性碳青霉烯类耐药基因，是CRE传播的重要因素 在医院内。克服以往基因组研究中使用传统测序平台的局限性 像Illumina，我们会进行长距离的质粒测序。质粒介导的blaKPC Will 通过三个目标来表征。在目标1中，我们将系统地评估横向的贡献 在2009-2016年间收集的大量CRE分离株的回顾收集中转移到CRE的传播。 在目标2中，我们将进行一项病例对照研究，以评估与以下疾病相关的独特临床危险因素 水平转移与克隆性传播；第三个对照组将由CRE阴性患者组成。在AIM 3中 我们将确定医院环境表面(如水槽)是否为blaKPC的蓄水池- 携带着质粒。系统发育分析将用于评估来自 临床和环境CRE和已发表的基因组。除了阐明质粒在细胞中的作用外， Cre的多样化和扩散，这项研究可能有助于将远程测序整合到 有效的感染监测和控制协议，以解决质粒介导的Cre传播。

PROJECT SUMMARY/ABSTRACT: Rationale: Resistance to broad-spectrum carbapenem antibiotics has spread rapidly among Enterobacteriaceae since the early 1990s, posing an escalating threat to medical care. While Klebsiella pneumoniae comprise the majority of CRE in the United States, recent evidence suggests that CRE are rapidly diversifying. This reflects the ability of carbapenem resistance genes to spread to between different strains of Enterobacteriaceae via mobile genetic elements, particularly plasmids. Despite their important infection control implications, the mechanisms by which these plasmids spread have not been fully elucidated. Candidate: As an infectious diseases clinician with a masters’ degree in biostatistics, Dr. Angela Gomez-Simmonds’ previous publications characterize the clinical and molecular epidemiology of CRE. Formal training in advanced bioinformatics and genomic epidemiology will be critical for the completion of the proposed research and the advancement of her career. With primary mentor Dr. Anne-Catrin Uhlemann, she has assembled a multidisciplinary advisory team of experts to guide her training and research progress. Dr. Gomez-Simmonds’ long-term goal is to become an NIH-funded independent researcher using next-generation sequencing to understand links between the bacterial evolution, resistance mechanisms, and clinical epidemiology of multidrug-resistant Gram-negative nosocomial pathogens. Environment: The Uhlemann laboratory at Columbia University Medical Center (CUMC) has the microbiology and sequencing tools necessary to carry out the proposed research, as well as a large retrospective collection of CRE clinical isolates from diverse sites to perform genomic studies. CUMC has a strong track record of supporting the career development of young physician-scientists. Approach: We hypothesize that horizontal transfer of plasmids encoding blaKPC, the dominant carbapenem resistance gene in the United States, is an important contributor to the spread of CRE within hospitals. To overcome limitations in previous genomics studies using traditional sequencing platforms such as Illumina, we will perform long-range plasmid sequencing. Plasmid-mediated transmission of blaKPC will be characterized through three aims. In Aim 1 we will systematically assess the contribution of horizontal transfer to the spread of CRE in a large retrospective collection of CRE isolates collected between 2009-2016. In Aim 2 we will perform a case-control-control study to assess unique clinical risk factors associated with horizontal transfer versus clonal spread; a third control group will consist of CRE-negative patients. In Aim 3 we will determine whether hospital environmental surfaces such as sink drains are reservoirs for blaKPC- harboring plasmids. Phylogenetic analyses will be used to assess links between plasmid sequences from clinical and environmental CRE and published genomes. In addition to elucidating the role of plasmids in the diversification and spread of CRE, this research may contribute to the integration of long-range sequencing in effective infection surveillance and control protocols to account for plasmid-mediation CRE transmission.