The Gut Microbiome in Carbapenem-Resistant Enterobacteriaceae Colonization, Persistence, Infection, and Tolerance after Lung or Liver Transplantation

项目摘要 这份重新提交的报告是为一个以患者为导向的研究事业发展奖而重新提交的，该奖项名为《勇气》 碳青霉烯类耐药肠杆菌科(CRE)微生物群的定植、持续、感染和 肺或肝移植后的耐受性。我是医学和移植感染学的助理教授 匹兹堡大学医学中心(UPMC)的疾病医生。我需要额外的培训来发展 作为翻译研究员的专业知识。我的目标是研究引起CRE的遗传特征 肺/肝移植后的肠道定植、持久性和感染，CRE的耐受现象，以及 与这些事件相关的肠道微生物区系环境。我的初步数据显示：(1)肺/肝 移植受者Cre定植的风险很高，其中一部分患者会出现持续性Cre定植 和移植后数月至数年的复发感染，(2)头孢他啶-阿维巴坦等最后使用的抗生素 可在体外诱导CRE耐受；(3)肺/肝移植后直肠CRE定植与 明显的生物失调和变形杆菌的优势。这项研究的科学前提是，长期 肺/肝移植后Cre定植是耐药Cre菌株持续存在的结果 移植后早期在肠道内定植，这一过程与粪便减少有关 变形杆菌的多样性和丰富性，并由持续的生物失调维持。为了测试这个中心 假设，我将追求以下具体目标：(1)研究纵向CRE的遗传学特征 (1b)研究这些Cre暴露于 CRE活性抗生素头孢他啶-阿维巴坦，美罗培南-瓦博巴坦，亚胺培南-释放巴坦，头孢地洛， 和粘菌素；(1c)确定肺/肝移植后CRE定植的危险因素；(2a)确定 移植后粪便微生物组图谱可以预测未来Cre的定植；和(2b和2c)定义粪便 发生CRE定植、持续和感染的微生物群环境。该项目将提供 对肺/肝移植受者基因组流行病学和肠道微生物组的新见解 CRE定植和疾病的整个谱系。拟议的工作将在以下司内进行 UPMC传染病中心和匹兹堡大学微生物组医学中心， 它们拥有细菌基因组研究和微生物和 元基因组测序。我得到了忠诚的导师的支持，他们在移植方面具有互补的专业知识 传染病、革兰氏阴性耐药、微生物组研究和生物统计学。我会拿到证书的 从事临床研究，并接受微生物组和基因组学研究方面的教学和实践培训。穿过 我的培训计划和目标，我将获得进行耐药性翻译研究所需的技能 实体器官移植受者中的细菌和这些患者的介入性微生物群试验。

PROJECT ABSTRACT This resubmission is for a Mentored Patient-Oriented Research Career Development Award entitled “The Gut Microbiome in Carbapenem Resistant Enterobacteriaceae (CRE) Colonization, Persistence, Infection, and Tolerance after Lung or Liver Transplantation.” I am an Assistant Professor of Medicine and Transplant Infectious Diseases physician at the University of Pittsburgh Medical Center (UPMC). I require additional training to develop expertise as a translational researcher. My objective is to study the genetic characteristics of CRE that cause gut colonization, persistence, and infection after lung/liver transplant, the phenomenon of tolerance in CRE, and the gut microbiota environment associated with these events. My preliminary data suggest that (1) lung/liver transplant recipients are at high risk for CRE colonization, with a subset developing persistent CRE colonization and recurrent infections months to years after transplant, (2) last resort antibiotics like ceftazidime-avibactam can induce tolerance in CRE in vitro, and (3) rectal CRE colonization after lung/liver transplant is associated with marked dysbiosis and predominance of Proteobacteria. The scientific premise of this study is that long-term CRE colonization after lung/liver transplant is a result of persistence of antibiotic-tolerant CRE isolates that colonize the gut early after transplant, a process which is associated with a reduction in stool diversity and abundance of Proteobacteria and maintained by ongoing dysbiosis. To test this central hypothesis, I will be pursuing the following specific aims: (1a) to genetically characterize longitudinal CRE isolates from these patients; (1b) to study antibiotic tolerance and resistance after exposure of these CRE to the CRE-active antibiotics ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, cefiderocol, and colistin; (1c) to identify risk factors for CRE colonization after lung/liver transplant; (2a) to determine whether post-transplant stool microbiome profiles can predict future CRE colonization; and (2b and 2c) to define the stool microbiota environment in which CRE colonization, persistence, and infection occur. This project will provide novel insights into the genomic epidemiology and gut microbiome of lung/liver transplant recipients through the entire spectrum of CRE colonization and disease. The proposed work will be conducted within the Division of Infectious Diseases at UPMC and the Center for Medicine at the Microbiome at the University of Pittsburgh, which have the computational and technical expertise required for bacterial genomic studies and microbial and metagenomic sequencing. I am supported by committed mentors with complementary expertise in transplant infectious diseases, Gram-negative resistance, microbiome research, and biostatistics. I will obtain a Certificate in Clinical Research and receive didactic and hands-on training in microbiome and genomics research. Through my training plan and aims, I will acquire the skillset required to perform translational studies of drug-resistant bacteria in solid organ transplant recipients and interventional microbiome trials in these patients.