Real-Time Genome Sequencing of Resistant Bacteria Provides Precision Infection Control in an Institutional Setting

ABSTRACT

The increasing prevalence of multidrug-resistant (MDR) bacteria is a serious global challenge. Here, we studied prospectively whether bacterial whole genome sequencing (WGS) for real-time MDR surveillance is technical feasible, returns actionable results, and is cost-beneficial. WGS was applied to all MDR isolates of four species (methicillin-resistant Staphylococcus aureus [MRSA], vancomycin-resistant Enterococcus faecium, MDR Escherichia coli, and MDR Pseudomonas aeruginosa) at the University Hospital Muenster, Germany, a tertiary care hospital with 1,450 beds, during two six-month intervals. Turn-around times (TAT) were measured and total costs for sequencing per isolate were calculated. After cancelling prior policies of preemptive isolation of patients harboring certain Gram-negative MDR bacteria in risk areas, the second interval was conducted. During interval I, 645 bacterial isolates were sequenced. From culture, TATs ranged from 4.4 to 5.3 days, and costs were 202.49 € per isolate. During interval II, 550 bacterial isolates were sequenced. Hospital-wide transmission rates of the two most common species (MRSA and MDR E. coli) were low during intervals I (5.8 and 2.3 %, respectively) and II (4.3 % and 5.0 %, respectively). Cancellation of isolation of non-pan-resistant MDR E. coli in risk wards did not increase transmission. When comparing sequencing costs with avoided costs mostly due to less blocked beds during interval II, we saved in excess of at least 200.000 €. Real-time microbial WGS was in our institution feasible, produced precise actionable results, helped to monitor transmission rates that remained low following a modification in isolation procedures, and ultimately saved costs.