A hybrid simulation model approach to examine bacterial genome sequencing during a hospital outbreak.

BACKGROUND: Hospital infection control requires timely detection and identification of organisms, and their antimicrobial susceptibility. We describe a hybrid modeling approach to evaluate whole genome sequencing of pathogens for improving clinical decisions during a 2017 hospital outbreak of OXA-181 carbapenemase-producing Escherichia coli and the associated economic effects. METHODS: Combining agent-based and discrete-event paradigms, we built a hybrid simulation model to assess hospital ward dynamics, pathogen transmission and colonizations. The model was calibrated to exactly replicate the real-life outcomes of the outbreak at the ward-level. Seven scenarios were assessed including genome sequencing (early or late) and no sequencing (usual care). Model inputs included extent of microbiology and sequencing tests, patient-level data on length of stay, hospital ward movement, cost data and local clinical knowledge. The main outcomes were outbreak size and hospital costs. Model validation and sensitivity analyses were performed to address uncertainty around data inputs and calibration. RESULTS: An estimated 197 patients were colonized during the outbreak with 75 patients detected. The total outbreak cost was US$318,654 with 6.1% of total costs spent on sequencing. Without sequencing, the outbreak was estimated to result in 352 colonized patients costing US$531,109. Microbiology tests were the largest cost component across all scenarios. CONCLUSION: A hybrid simulation approach using the advantages of both agent-based and discrete-event modeling successfully replicated a real-life bacterial hospital outbreak as a foundation for evaluating clinical outcomes and efficiency of outbreak management. Whole genome sequencing of a potentially serious pathogen appears effective in containing an outbreak and minimizing hospital costs.

Making the sunshine vitamin - How much sun exposure is needed to maintain 25-hydroxy vitamin D concentration?

Our objective was to calculate the time in the sun necessary to maintain existing 25-hydroxyvitamin D (25(OH)D) concentration at locations across Australia and New Zealand. We used a microsimulation model to estimate changes in monthly 25(OH)D concentration using data on standard erythemal dose, solar zenith angle, and climatological ozone. We estimated the number of standard vitamin D doses per 10-min interval and used a dose-response equation to determine the average time in the sun to maintain existing 25(OH)D concentration according to month and time of day. Across all locations in summer, 5-10 min outdoors between 8 a.m. and 4 p.m. on most days of the week, with 35% of the body surface area exposed, is sufficient to maintain existing 25(OH)D concentration. In winter, at mid-to-high latitudes, time outdoors during the middle of the day is required. In winter, with 10% of the body surface area exposed, greater than 45 min in the middle of the day is required in most locations to maintain existing 25(OH)D concentration. These data can be used to inform guidelines regarding maintaining vitamin D via sun exposure and may help health practitioners identify patients who may be vitamin D deficient.