Tracking plasmid spread and transmission in the hospital: A novel tool for infection prevention and control

Project Summary Despite recent progress in reducing the incidence of healthcare-associated infections (HAIs), the Centers for Disease Control and Prevention estimated that 687,000 HAIs occurred in U.S. acute care hospitals in 2015 and that the HAI prevalence on a given day was one in 30 patients. An estimated 72,000 patients died with

HAIs during their hospitalization. In addition, outbreaks in hospitals remain a serious problem but the vast majority of hospitals use antiquated and ineffective methods to detect them. We established the Enhanced Detection System for Healthcare Acquired Transmission (EDS-HAT) (R01AI127472), which combines bacterial

whole genome sequencing (WGS) surveillance (as opposed to reactive WGS) to detect outbreaks with data mining (DM) of the electronic health record (EHR) and machine learning (ML) to identify the responsible transmission routes. We have demonstrated that EDS-HAT detects both serious outbreaks that were otherwise

unrecognized and novel transmission routes and therefore now run the system in real time. Plasmids carried by bacteria frequently encode genes that confer resistance to antimicrobial agents. When patients or hospital environments are co-colonized with two bacterial species, these settings provide the opportunity for plasmid

transfer to occur from a species carrying a plasmid to one that does not. The species with the newly acquired plasmid can then be transmitted to another patient, a combination of events we call transfer to transmission (T2T). Importantly, T2T events are not captured by traditional WGS analysis or EDS-HAT. In this R21

application, we propose to leverage the success and infrastructure of EDS-HAT by developing methods for detection of T2T events and determining the potential utility of incorporating surveillance for these events into EDS-HAT. In Aim 1, we plan to develop and validate optimal laboratory and bioinformatics approaches for

real-time identification of T2T events in the hospital. In Aim 2, we will determine the feasibility and potential impact of real-time monitoring for T2T events and determining the responsible transmission routes. Actionable T2T events will be reported to our infection prevention team so that interventions can be developed to interrupt

transmission. These aims will be accomplished by a team with expertise in infectious diseases epidemiology, outbreak investigation, infection prevention and control, microbial genomics and genomic epidemiology. If successful, this research will lead to a novel infection prevention tool. The proposed research is highly

translational and will improve patient safety through incorporation of innovative genomic and computational approaches for identifying otherwise unrecognized T2T events.