Clinical and economic outcomes of genome sequencing availability on containing a hospital outbreak of resistant Escherichia coli in Australia

Xing J. Lee, Thomas M. Elliott, Patrick N. A. Harris, Joel Douglas, Belinda Henderson, Catherine Watson, David L. Paterson, Deborah S. Schofield, Nicholas Graves, Louisa G. Gordon*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Objectives: To evaluate the outbreak size and hospital cost effects of bacterial whole-genome sequencing availability in managing a large-scale hospital outbreak.

Methods: We built a hybrid discrete event/agent-based simulation model to replicate a serious bacterial outbreak of resistant Escherichia coli in a large metropolitan public hospital during 2017. We tested the 3 strategies of using whole-genome sequencing early, late (actual outbreak), or not using it and assessed their associated outbreak size and hospital cost. The model included ward dynamics, pathogen transmission, and associated hospital costs during a 5-month outbreak. Model parameters were determined using data from the Queensland Hospital Admitted Patient Data Collection (N = 4809 patient admissions) and local clinical knowledge. Sensitivity analyses were performed to address model and parameter uncertainty.

Results: An estimated 197 patients were colonized during the outbreak, with 75 patients detected. The total outbreak cost was A$460 137 (US$317 117), with 6.1% spent on sequencing. Without sequencing, the outbreak was estimated to result in 352 colonized patients, costing A$766 921 (US$528 547). With earlier detection from use of routine sequencing, the estimated outbreak size was 3 patients and cost A$65 374 (US$45 054).

Conclusions: Using whole-genome sequencing in hospital outbreak management was associated with smaller outbreaks and cost savings, with sequencing costs as a small fraction of total hospital costs, supporting the further investigation of the use of routine whole-genome sequencing in hospitals.

Original languageEnglish
Pages (from-to)994-1002
Number of pages9
JournalValue in Health
Issue number8
Publication statusPublished - 1 Aug 2020


  • agent-based modeling
  • bacterial infectious disease
  • cost consequences
  • discrete event modeling
  • healthcare associated infections

Fingerprint Dive into the research topics of 'Clinical and economic outcomes of genome sequencing availability on containing a hospital outbreak of resistant <i>Escherichia coli</i> in Australia'. Together they form a unique fingerprint.

Cite this