ELUCIDATING TRANSMISSION OF PLASMIDS HARBORING BLAKPC AMONG CARBAPENEM-RESISTANT ENTEROBACTERIACEAE USING LONG-RANGE SEQUENCING

PROJECT SUMMARY/ABSTRACT:Rationale: Resistance to broad-spectrum carbapenem antibiotics has spread rapidly amongEnterobacteriaceae since the early 1990s, posing an escalating threat to medical care. While Klebsiellapneumoniae comprise the majority of CRE in the United States, recent evidence suggests that CRE are rapidlydiversifying. This reflects the ability of carbapenem resistance genes to spread to between different strains ofEnterobacteriaceae via mobile genetic elements, particularly plasmids. Despite their important infection controlimplications, the mechanisms by which these plasmids spread have not been fully elucidated. Candidate: Asan infectious diseases clinician with a masters? degree in biostatistics, Dr. Angela Gomez-Simmonds? previouspublications characterize the clinical and molecular epidemiology of CRE. Formal training in advancedbioinformatics and genomic epidemiology will be critical for the completion of the proposed research and theadvancement of her career. With primary mentor Dr. Anne-Catrin Uhlemann, she has assembled amultidisciplinary 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 tounderstand links between the bacterial evolution, resistance mechanisms, and clinical epidemiology ofmultidrug-resistant Gram-negative nosocomial pathogens. Environment: The Uhlemann laboratory atColumbia University Medical Center (CUMC) has the microbiology and sequencing tools necessary to carryout the proposed research, as well as a large retrospective collection of CRE clinical isolates from diverse sitesto perform genomic studies. CUMC has a strong track record of supporting the career development of youngphysician-scientists. Approach: We hypothesize that horizontal transfer of plasmids encoding blaKPC, thedominant carbapenem resistance gene in the United States, is an important contributor to the spread of CREwithin hospitals. To overcome limitations in previous genomics studies using traditional sequencing platformssuch as Illumina, we will perform long-range plasmid sequencing. Plasmid-mediated transmission of blaKPC willbe characterized through three aims. In Aim 1 we will systematically assess the contribution of horizontaltransfer 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 withhorizontal transfer versus clonal spread; a third control group will consist of CRE-negative patients. In Aim 3we 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 fromclinical and environmental CRE and published genomes. In addition to elucidating the role of plasmids in thediversification and spread of CRE, this research may contribute to the integration of long-range sequencing ineffective infection surveillance and control protocols to account for plasmid-mediation CRE transmission.