Real-Time Genomic Surveillance for Enhanced Healthcare Outbreak Detection and Control: Clinical and Economic Impact

Current methods are insufficient alone for outbreak detection in hospitals. Real-time genomic surveillance offers the potential to detect otherwise unidentified outbreaks. We initiated and evaluated the Enhanced Detection System for Healthcare-associated Transmission (EDS-HAT), a real-time genomic surveillance program for outbreak detection and mitigation.

This study was conducted at UPMC Presbyterian Hospital from November 2021 to October 2023. Whole genome sequencing (WGS) was performed weekly on healthcare-associated clinical bacterial isolates to identify otherwise undetected outbreaks. IP&C interventions were implemented in real-time based on identified transmission. A clinical and economic impact analysis was conducted to estimate infections avoided and net cost savings.

There were 3921 bacterial isolates from patient healthcare-associated infections that underwent WGS, of which 476 (12.1%) clustered into 172 outbreaks (size 2-16 patients). Of the outbreak isolates, 292 (61.3%) had an identified epidemiological link. Among the outbreaks with interventions, 95.6% showed no further transmission on the intervened transmission route. The impact analysis estimated that, over the 2-year period, 62 infections and 4.8 deaths were avoided, with gross cost savings of $1,011,146, and net savings of $695,706, which translates to a 3.2-fold return on investment. Probabilistic sensitivity analysis showed EDS-HAT was cost saving and more effective in 98% of simulations.

Real-time genomic surveillance enabled the rapid detection and control of outbreaks in our hospital and resulted in patient and economic benefits. This study demonstrates the feasibility and effectiveness of integrating genomic surveillance into routine infection prevention practice, offering a paradigm shift in healthcare outbreak detection and control.