Evaluating the economic and health impact of proactive genomic epidemiology in a hospital setting

BackgroundGenomic epidemiology which combines whole genome sequencing (WGS) of bacterial isolates with patient movement data, promises improved detection, prevention, and management of infection transmission, enhancing patient safety and reducing healthcare costs. However, evidence on its cost-effectiveness and clinical utility remains limited, as initial studies were restricted to selected pathogens and based on extrapolated assumptions from partial WGS data. MethodsWe conducted a 28-month observational study at Rigshospitalet, a 1 200-bed tertiary hospital in Copenhagen. The study involved collecting patient movement and WGS data for clinical isolates of 19 bacterial species, regardless of their site of isolation, or antibiotic susceptibility profile. This included sequencing of 18 940 clinical isolates from 7 760 patients. FindingsWe found that 27{middle dot}1 % of culture-positive hospitalized patients harboured a pathogen genetically related to another patients isolate. 69 % had an epidemiological link, indicating transmission between patients, with Enterococcus faecium being the most prevalent. Notably, there were 2{middle dot}2 times more transmissions of antibiotic-susceptible than resistant isolates. We estimated that prevention based on genomic epidemiology could potentially generate net savings of {euro}1{middle dot}25 million annually and avoid more than 750 disability adjusted life years (DALYs). InterpretationOur holistic, proactive genomic epidemiology approach reveals previously unexplored transmission landscapes. We discovered that transmission is widespread, varies significantly between species, and is not limited to resistant isolates. Our results highlight the potential for WGS-informed infection control, greater savings by including susceptible isolates, and an incremental cost-effectiveness ratio (ICER) classification by pathogen species. FundingNovo Nordisk Foundation, Beta.Health, Den Frie Forskningsfond