Multidirectional dynamic risk assessment for ESBL source attribution

Authors:

Eduardo de Freitas Costa, Thomas Hagenaars, Anita Damme-Korevaar, Mike Brouwer, and Clazien de Vos

Aims:

The main objective of the project is to model a multidirectional dynamic risk assessment source attribution for ESBL. A risk assessment approach is used to answer the following questions:

• i) Estimate the number of human ESBL colonization attributed to the livestock sector;

• ii) Interventions in the food chain (here: chicken consumption), and in which step interventions contribute most to reducing the number of human colonization;

• iii) Contribution of broiler flock farms with high antimicrobial usage to the public health burden of ESBL colonization.

The paper is available online:

Instrucitons to reproduce the results of the paper

Using RStudio:

1 Download the files to a local or cloud folder. The best option is to download all files zipped;

2 Unzip and open the R project "MADRA.Rproj";

3 In R, you can open the file\

• "main.R" \

4 Always load the packages before running the model. The model may take a long time to run;

5 Note that two folders were created into the working directory:

• Output/chicken: Stores the results of the baseline (scenario1), uncertainty, what-if analysis simulation, final prevalence, and table 4;

• Figures/chicken: Stores the graphs obtained in the paper;