JIACRA IV Code Repository

Overview

This repository contains code and synthetic anonymised data for the Fourth Joint Inter-Agency Report on Antimicrobial Consumption and Resistance Analysis (JIACRA IV). The report focuses on the integrated analysis of antimicrobial consumption and the occurrence of antimicrobial resistance in bacteria from humans and food-producing animals in the EU/EEA.

Introduction

The JIACRA IV report aims to provide insights into antimicrobial consumption and resistance patterns in bacteria from humans and food-producing animals. This README.md file serves as a guide for users to understand and replicate the analyses performed in the report.

Repository Structure

The repository is organized into three main folders corresponding to each type of analysis:

• Univariate analysis

• Multivariate analysis

• Trend analysis

Installation

To replicate the analysis, follow these steps:

1. Clone the repository to your local machine.
2. Navigate to the respective folders to access the scripts and documentation for each analysis type.
3. Follow the instructions in each README.md file in each folder.
4. Open the corresponding .Rproj file in each folder.

Code

Detailed R scripts for each analysis type and SAS code for the trends analysis are available. These scripts are annotated for better understanding.

Data

The anonymised synthetic datasets for demonstration of the code and their corresponding structure can be found in each data subfolder.

Documentation

For detailed instructions and documentation for each analysis type, please refer to the README.md files in their corresponding subfolder.

Authors

This public repository is the result of joint collaborative efforts between experts from the European Centre for Disease Prevention and Control (ECDC), the European Food Safety Authority (EFSA), and the European Medicines Agency (EMA). Liselotte Diaz Högberg, Joana Gomes Dias, Elias Iosifidis, Vivian Leung, Gaetano Marrone, Dominique Monnet, Cèlia Ventura-Gabarro, Chiara Entradi, Vera Vlahović-Palčevski and Therese Westrell (ECDC); Marc Aerts, Pierre-Alexandre Belœil, Ernesto Liebana, Valentina Rizzi and Bernd-Alois Tenhagen (Chair) (EFSA), and Claire Chauvin, Barbara Freischem, Hector Gonzalez Dorta, Helen Jukes, Zoltan Kunsagi, Filipa Mendes Oliveira, Oskar Nilsson, Cristina Ribeiro-Silva, Chantal Quinten and Engeline van Duijkeren (EMA).

Correspondence

For questions or assistance, you can contact:

• ECDC: arhai@ecdc.europa.eu
• EFSA: zoonoses@efsa.europa.eu
• EMA: <https://www.ema.europa.eu/en/about-us/contacts/send-question-

License

This project is licensed under the EUROPEAN UNION PUBLIC LICENCE v. 1.2 EUPL © the European Union 2007, 2016. For more details consult the LICENSE file.