Model used in the article: Assessment of the risk of salmonellosis linked to the consumption of liquid egg products made from internally contaminated shell eggs initially stored at 65°F (18°C) compared to 45°F (7°C). Journal of Food Protection, 2020. doi: 10.4315/0362-028X.JFP-19-376

Régis Pouillot,¹ Wayne Schlosser,² Jane M. Van Doren,^1* Sherri B. Dennis,¹ Janell R. Kause<sup>2

1</sup>U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740, USA; and

²Office of Public Health Science, Food Safety and Inspection Service, U.S. Department of Agriculture, 1400 Independence Avenue S.W., Washington, D.C. 20250, USA

Disclaimer

Access to the model is provided to enhance understanding of the methods we used in conducting the risk assessment. Please refer to the risk-assessment report regarding limitations and conclusions of the risk assessment model and results.
Responsibility for the interpretation and use of the model and of the accompanying documentation lies solely with the user. Third parties' use of or acknowledgment of the system and its accompanying documentation, including through the suggested citation, does not in any way represent that FDA, USDA, or JIFSAN endorses such third parties or expresses any opinion with respect to their statements.

Suggested Citation

Régis Pouillot, Wayne Schlosser, Jane M. Van Doren, Sherri B. Dennis, and Janell R. Kause, “Assessment of the risk of salmonellosis linked to the consumption of liquid egg products made from internally contaminated shell eggs initially stored at 65°F (18°C) compared with 45°F (7°C).” Journal of Food Protection. https://doi.org/10.4315/0362-028X.JFP-19-376.
Model code available at https://www.foodrisk.org/resources/display/202. 

General concept

The model is developed in three steps

1. Simulate pre-process egg contamination according to preferred storage scenarios using the FSIS Shell Egg Model (“ShellEggModel2019.xlsm” Microsoft Excel™ with embedded Visual Basic model);
2. Simulate vats of egg white, egg yolk and whole eggs using the results of the previous simulation (“BuildTheVat.R”: R code (R Development Core Team 2019));
3. Evaluate the risk from egg products made from these vats using the adapted FSIS Liquid Egg Model (“SERA_Liquid_Egg2019.xls” Microsoft Excel™ with embedded Visual Basic model).

Preliminary

Download the 3 files (found in the Download section at bottom of page), preferably in the same directory:

• “ShellEggModel2019.xlsm”
• “BuildTheVats20181109.R”
• “SERALiquidEgg_ProductsModel2019.xlsm”

Simulate pre-process egg contamination

1. Open the “ShellEggModel2019.xlsm” file (using Microsoft Excel™). This file is basically a copy of the file distributed with the FSIS 2005 risk assessment (FSIS 2005) with a specific set of parameters. Please refer to the documentation on that model for further details. Note: you have to Enable macros to run the model.
2. Set-up some parameters for your simulation (see Table 1).
• The parameters that were modified from the FSIS 2005 risk assessment and that were held constant in the 2020 runs are in red cells;
• The parameters that were modified from the FSIS 2005 risk assessment and that were used for the various simulations of the 2020 runs are in yellow cells.

Table 1 : parameter set-up to duplicate the 2020 runs.

Step	Simulations name	Parameter	Cell Reference	Value
Layer House	FSIS (2005) Baseline for layer house	Mean temperature in Layer house	F54	=LN(75)
		Std Dev temperature in Layer House	G54	0.15
		Minimal time in Layer House	F64	0
		Maximal time in Layer house	G64	0.5
	Limit Egg Safety Final Rule	Mean temperature in Layer house	F54	=LN(75)
		Std Dev temperature in Layer House	G54	0.0001
		Minimal time in Layer House	F64	1.5
		Maximal time in Layer house	G64	1.5
On Farm	75 F alternative	Mean temperature On Farm	F55	=LN(75)
		Std Dev temperature On Farm	G55	0.0001
	45 F alternative	Mean temperature On Farm	F55	=LN(45)
		Std Dev temperature On Farm	G55	0.0001
	Storage Time before processing: x days (example 5 days)	Minimal time on Farm	F65	x (example 5)
		Maximal time on Farm	G65	x (example 5)

3. Click on the “Run Model” button (close to cell M64).
4. Wait for the code to run. Note: it might take a long time. During the run, the screen may freeze (irresponsive). If this occurs, don’t worry; the simulation is still running;
5. Close Microsoft Excel™ (the following step won’t work if the file is open).

(Note: the simulation size we used for the manuscript was 100,000 simulations. You could do some shorter runs for tests by changing cell D8)

Simulate the vats

1. “Source” the file “BuildTheVats.R” with the R software. This will simulate (by default) the contamination of 50,000 - 350,000 lb vats of egg white, egg yolk and whole eggs originating from the scenario you run in the previous step.
2. You will need R and the “readxl” library available on https://cran.r-project.org/
   Note: The ShellEggModel2019.xlsm should be placed in the R session working directory.
• To change the working session directory in R: File → Change dir…
• To change the working session directory in RStudio: Session -> Set Working directory…
• To change the working in the R console: use the function setwd()
3. The output will be placed in a CSV file named “Simul.csv” in the R session working directory.

Assess the risk linked to liquid egg products

1. Open the Microsoft Excel™ VBA spreadsheet: “SERALiquidEgg_ProductsModel2019.xlsm”. Note: you have to Enable macros to run the model.
2. Click on the “Click here to continue” Button
3. Open the file " Simul.csv" created by the previous process.
4. Copy - Paste the values (columns A to D) from " Simul.csv" to the tab "EggContamination" from "SERALiquidEgg_ProductsModel2019.xlsm",
5. Go to the summary tab and click on the button “Click Here to Input Values from the Model”.
6. Choose the number of iterations you wish to run a simulation (We used 10,000 iterations for convergence. A more reasonable number of simulations should be used for trial runs),
7. Click on “Run Model”,
8. Wait for the code to run. Note: it might take a very long time. During the run, the screen may freeze (irresponsive). If this occurs, don’t worry; the simulation is still running.
9. The results will be provided in the “Summary” tab.

References

FSIS (2005). Risk Assessments of Salmonella Enteritidis in Shell Eggs and Salmonella spp. in Egg Products., United States Department of Agriculture - Food Safety Inspection Service.

Pouillot, R., Schlosser, W., Van Doren, J.M., Dennis, S.B., Kause, J.R. (2020) Assessment of the risk of salmonellosis linked to the consumption of liquid egg products made from internally contaminated shell eggs initially stored at 65°F (18°C) compared to 45°F (7°C). Journal of Food Protection, 2020. doi: 10.4315/0362-028X.JFP-19-376

R Development Core Team. (2019). "R: a language and environment for statistical computing."   Retrieved March 20, 2019, from http://www.R-project.org.