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Table 1 Parameter description, values and sources used in the hybrid simulation model

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

ParameterValueSource
Initialization
 Initial starting population (n)551Hospital admissions dataset
 Number of floors and wardsLevel 5 (Ward A,B,C,D); Level 2 (Ward A,B,C,D,E); SIU; GARU (Bunya, Banksia, Cassia)Building floor plans
Hospital Mechanics Sub Model
 Population entry rate, patients per day24Calibration
 Ward admission, transfers and stays asee Additional file 1: Table S1-S3Hospital admissions dataset
Susceptible-colonized sub model
 Transmission parameter βLevel 5 = 0.153, Level 2 = 0.14, SIU = 0.086, GARU = 0.086Calibration
Outbreak Management Sub Model
 No WGS, outbreak number, patients with confirmed colonization7–15Expert opinion
 No WGS, outbreak start delay, patients with confirmed colonization2–5Expert opinion
 Microbiology test processing time, days2Expert opinion
 Genome sequencing processing time, days (SD) b7 (0.5)Expert opinion
 Daily probability of patient being screenedLevel 5 = 0.041, Level 2 = 0.043, GARU = 0.055, SIU = 0.056Calibration
 Genome sequencing cost, AU$ (SD) c354.70 (53.2)Clinical records
 Microbiology test cost, AU$(SD)79.23 (11.88)MBS item 69,306, PCR cost [35]
 Bedroom cleaning cost, AU$(SD) d70 (10.5)Clinical staff
 Bed closure, AU$ (Q1-Q3)216 (147–285)Page et al., 2017 [21]
 Hourly wage for infection control nurse, AU$ (SD)40.33 (6.05)Clinical staff & Queensland Health wage rates [36]
 Executive infection control meeting e, AU$462.03 (69.3)Clinical staff & Queensland Health wage rates [36]
Increased virulence scenario
 Infection chance0.165Tischendorf et al., 2016
 Time till infection27 days [11]Tischendorf et al., 2016
 Mortality (in-hospital)0.40 (0.5)Chang et al., 2015
 Infection treatment costs, AU$$2650Chang et al., 2015
 End-of-life costs, AU$$19,696Reeve et al., 2018
Environmental contamination scenario
 ET odds-ratio for patients in contaminated beds2.65Mitchell et al., 2015
 Bed contamination length, days5–10 daysKramer et al., 2006
  1. GARU geriatric assessment and recovery unit, SIU spinal injury unit, SD standard deviation, PCR polymerase chain reaction, ET environmental transmission
  2. aGamma distribution assigned
  3. bNormal distribution assigned
  4. cComprising: sample prep 15.00, sequencing 105.00, analysis/storage 18.00, scientist 102.50, isolate handling 5.00, labor admin 33.33 biostats 75.85
  5. dHospital cleaning staff, labor hourly rate 31.24, curtains 33.00, consumables 5.00
  6. e3 senior consultants 215.10, Infection control nurse 59.03, senior admin 65.10, manager 45.81