Real time genome sequencing of resistant bacteria ensures precise infection control in an institutional setting

The increasing prevalence of multidrug-resistant (MDR) bacteria is a serious global challenge. For this reason, a recently published study (J. Clin. Microbiol. 54: 2874, 2016) prospectively analyzed whether bacterial whole-genome sequencing (WGS) for real-time MDR surveillance is technical feasible, returns actionable results, and is cost-beneficial.

During two 6-month intervals 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. More than 1,200 isolate WGS data were analyzed automatically using the Ridom SeqSphere⁺ tool developed within the framework of the PathoNGen-Trace project. Turnaround 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. Hospital-wide transmission rates of the two most common species (MRSA and MDR E. coli) were low during interval I (5.8% and 2.3%, respectively) and interval II (4.3% and 5.0%, respectively). Cancellation of isolation of patients infected with non-pan-resistant MDR E. coli in risk wards did not increase transmission. Comparing sequencing costs with avoided costs, mostly due to fewer blocked beds during interval II, €200,000 were saved in interval II.

This shows, that real-time microbial WGS was feasible, produced precise actionable results, helped to monitor transmission rates that remained low following a modification in isolation procedures, and ultimately saved costs.