Whole Genome Sequencing of Carbapenem-Resistant Organisms from Sink Drains and Among Adult ICU Patients at a Tertiary Academic Medical Center in Kentucky

Carbapenem-resistant organisms (CROs) in the family Enterobacteriaceae (CRE) have been classified as an urgent public health threat, the highest hazard classification given by the CDC for multi-drug resistant organisms.1 Of particular concern are CRO’s that carry carbapenemases, which have the ability to hydrolyze almost all carbapenems and â lactamase inhibitors, and in some cases convey panresistance.2-3 Furthermore, genes that encode for carbapenemases may be located on bacterial plasmids, transposons, and integrons that make them highly transmissible between Enterobacteriaceae species and other bacteria.4 Various risk factors have been implicated in the acquisition of CROs among ICU patients.5-7 A current study of CRE risk factors at UKY healthcare includes data on the outcome CRE infection/colonization, patient demographics, invasive procedures, prior medication usage, diagnoses history, and environmental factors of patient ICU units and room #’s. The proposed project would add to the current information of CRO risk factors at UKY Healthcare by determining if sink drains potentially act as an environmental reservoir for CRO transmission. Several CRO outbreak investigations have determined that sink drains act as a reservoir for CRO acquisition.8-10 Furthermore, research using whole genome sequencing has linked clinical CRO infections/colonization’s to sink drains.8,11 UK Healthcare Infection Prevention and Control (IPAC) currently perform CRO active surveillance on all adult ICU patients. This includes a peri-rectal swab upon admission and once per week thereafter. In 2018 UK’s IPAC staff sampled multiple sinks (drains and p-traps) in patient rooms on the 7th floor of Chandler Hospital. Test results revealed that ten sink drains were positive for 15 different CRO isolates. Currently, environmental and clinical CRE isolates have been stored in a -80 cryofreezer for future study. We seek to perform whole genome sequencing on all stored environmental isolates (approx. 15) matched to a subset of clinical isolates (approx. 15) that were obtained from patients that occupied rooms where we obtained environmental isolates. Whole genome sequencing will be used to determine if clinical CRO isolates are genetically identical to environmental CRO isolates. These data will be useful in assessing the role of environmental CRO in sink drains as a potential reservoir for CRO transmission. Study results will help guide UKY IPAC policies including changes to: environmental cleaning protocols (e.g., using different disinfectants, routinely disinfecting sink drains, etc.), educational initiatives for staff, patient, and visitors, and protocols regarding zones for proper placement of items and equipment. More importantly, the potential impacts of this study may include a reduction CRO acquisition and contamination among patient and occupational staff (i.e., healthcare worker) via IPAC interventions including those above. We are seeking funding to cover the cost of whole genome sequencing.