EFFORT will establish a research programme to study the complex ecology of antimicrobial resistance and the complex interactions between bacterial communities, commensals and pathogens in animals, the food chain and the environment which reaches beyond previously conducted (international) research projects. This will be conducted by a combination of epidemiological and ecological studies using newly developed molecular and bio-informatics technologies. This will include an exposure assessment of humans from animal sources. The ecological studies on isolates will be verified by in vitro and in vivo studies. Moreover, real-life intervention studies will be conducted. Focus will be on predicting and limiting the future evolution and exposure to humans of the most clinically important resistance by synthesising different sources of information in our prediction models.
Knowledge production in EFFORT is structured into 8 interrelated scientific WPs and 2 WPs on knowledge translation. These WPs range from the broad scale of metagenomic-based research, to the epidemiology and ecology, and the public health and economic impact of antimicrobial resistance in the food chain.
The project is structured around a central data collection work package (WP1) in which all data essential for the epidemiological, ecological as well as the microbiological samples for analysis of antimicrobial resistance are obtained during the first two years of the project. The complete DNA-extracts and the bacteria identified in this work package will subsequently be used in WP2 and WP3 for further microbiological analysis, including metagenomic analysis and identification and characterization of mobile genetic elements and resistance determinants, as well as their transfer properties. The integrated phenotypic, metagenomic and genetic data, together with the risk factor and management data obtained in WP1 will be used in three work packages: focusing on the eco-epidemiology of resistance (WP4), establishing potential links between usage and resistance (WP5) and proposing and analysing intervention studies (WP6). These analyses will include the metagenomic data with the complete antimicrobial resistance determinants present in the total samples. Using the output of these three workpackages, WP7 will assess the exposure to humans through multiple routes using stochastic modelling, while WP8 will integrate the data to determine the economic impact of antimicrobial resistance. Two additional WPs on knowledge translation (WP9) and project management (WP10) will assure the dissemination both inside and outside the consortium, proper exploitation, transfer, training and the administrative and financial management of the project.
WP leader: Dik Mevius – Central Veterinary Institute (CVI) – The Netherlands
Partners involved: CVI, UUVM, UCM, ANSES, ILZLT, VION, UGent, TIHO, DTU, NVRI, NDRVI, Intomics.
WP leader: Frank Aerestrup – National Food Institute (DTU) – Denmark
Meta-genomic analysis will provide a complete quantitative determination of all known antimicrobial resistance genes present in a sample. With the considerable reduction in costs this has now become available for large scale studies. However, the technology needed is currently not available in all places and it is still not possible to foresee whether it will be routinely available in e.g. slaughterhouses. Thus, in the current project we have decided on a hierarchical analytic strategy, where comprehensive meta-genomic analysis on selected samples will form the basis for qualitative screening of a larger number of samples using arrays, and qPCR screening of a few selected resistance genes. The array and qPCR will be initiated based on the first meta-genomic analysis and adjusted during the course of the project.
The main objectives of WP2 are:
Partners involved: DTU, UUVM, CVI, BfR, UCM, NVRI, Intomics.
WP leader: Bruno Gonzalez-Zorn – Universidad Complutense de Madrid - Spain
Partners involved: UCM, UUVM, CVI, BfR, VION, ILSI
WP leader: Dick Heederik – Utrecht University – The Netherlands
Partners involved: UUVM, CVI, UGent, DTU, SAFOSO
WP leader: Jeroen Dewulf – Gent University - Belgium
Partners involved: UGent, UUVM, CVI, DTU, NVRI, SAFOSO
WP leader: Pascal Sanders – Agence nationale de sécurité de l’alimentation, de l’environnement et du travail - France
Partners involved: ANSES, VION, PorQ, ø-VET, Vetworks, BEC
WP leader: Tine Hald – National Food Institute - Denmark
Partners involved: DTU, UUVM, SAFOSO
WP leader: Helmut Saatkamp – Wageningen University – The Netherlands
The objectives of WP8 are to improve current decision making of relevant authorities through providing relevant knowledge and information for decision support, particularly on:
Partners involved: BEC, THIO
WP leader: Katharina Stärk – SAFOSO - Switzerland
Partners involved: SAFOSO, ARTTIC, UUVM, DTU, ILSI, BEC
WP leader: Jaap A. Wagenaar – Utrecht University – The Netherlands
The main objective is to set up an effective management framework for the EFFORT consortium to ensure progress of the project towards its planned objectives and respect of contractual commitments. The organisational structure, decision-making mechanisms and detailed project management activities are described in section 2.1 “Management structure and procedures”.
The specific objectives are:
Partners involved: UUVM, ARTTIC