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

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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.