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

J Clin Microbiol. 2016 Dec;54(12):2874-2881. doi: 10.1128/JCM.00790-16. Epub 2016 Aug 24.


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, Muenster, Germany, a tertiary care hospital with 1,450 beds, during two 6-month intervals. 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. 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 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, we saved in excess of €200,000. Real-time microbial WGS in our institution was feasible, produced precise actionable results, helped us to monitor transmission rates that remained low following a modification in isolation procedures, and ultimately saved costs.

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Cefotaxime / pharmacology
  • Ciprofloxacin / pharmacology
  • Cross Infection / microbiology
  • Cross Infection / transmission*
  • Enterococcus faecium / drug effects
  • Enterococcus faecium / genetics*
  • Enterococcus faecium / isolation & purification
  • Escherichia coli / drug effects
  • Escherichia coli / genetics*
  • Escherichia coli / isolation & purification
  • Escherichia coli Infections / transmission
  • Genome, Bacterial / genetics*
  • Gram-Positive Bacterial Infections / transmission
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Infection Control / methods*
  • Methicillin-Resistant Staphylococcus aureus / drug effects
  • Methicillin-Resistant Staphylococcus aureus / genetics*
  • Methicillin-Resistant Staphylococcus aureus / isolation & purification
  • Microbial Sensitivity Tests
  • Piperacillin / pharmacology
  • Prospective Studies
  • Pseudomonas Infections / transmission
  • Pseudomonas aeruginosa / drug effects
  • Pseudomonas aeruginosa / genetics*
  • Pseudomonas aeruginosa / isolation & purification
  • Sequence Analysis, DNA
  • Staphylococcal Infections / transmission
  • Vancomycin-Resistant Enterococci / drug effects
  • Vancomycin-Resistant Enterococci / genetics*
  • Vancomycin-Resistant Enterococci / isolation & purification


  • Anti-Bacterial Agents
  • Ciprofloxacin
  • Cefotaxime
  • Piperacillin