PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks

Abstract

Whole genome sequencing (WGS) is increasingly used to map the spread of bacterial and viral pathogens in nosocomial settings. A limiting factor for more widespread adoption of WGS for hospital infection prevention practices is the availability of standardized tools for genomic epidemiology. Here we present the Pathogen Sequencing Phylogenomic Outbreak Toolkit (PathoSPOT), which automates integration of genomic and medical record data for rapid detection and tracing of nosocomial outbreaks. To demonstrate its capabilities we applied PathoSPOT to complete genome surveillance data of 197 MRSA bacteremia cases from two hospitals during a two-year period. PathoSPOT identified 8 clonal clusters encompassing 33 patients (16.8% of cases); none of which had been recognized by standard practices. The largest cluster corresponded to a prolonged outbreak of a hospital-associated MRSA clone among 16 adults, spanning 9 wards over a period of 21 months. Analysis of precise timeline and location data with our toolkit suggested that an initial exposure event in a single ward led to infection and long-term colonization of multiple patients, followed by transmissions to other patients during recurrent hospitalizations. Overall, we demonstrate that PathoSPOT genomic surveillance enables detection of complex transmission chains that are not readily apparent from epidemiological data and that contribute significantly to morbidity and mortality, enabling more effective intervention strategies.