Co-funded by
the European Union

Public Deliverables

D9.8 - Final EFFORT conference

This deliverable reports on the EFFORT final conference entitled “Antimicrobial Resistance in the Food Chain - from Science to Policy” which was held from 26 to 28 November 2018 in Utrecht, the Netherlands.

UUVM - the project coordinator, ARTTIC, SAFOSO and ILSI were in charge of organising the conference with the support of the consortium partners. All partners contributed to the promotion of the conference through their network and by advertisements on their corporate websites.The conference attracted nearly 250 participants among them were veterinarians, policy makers, microbiologists and researchers in the field of antimicrobial resistance and food safety.

This report summarises the scope and objectives of this event, which is part of the EFFORT project dissemination plan and provides an overview of the conference content. The deliverable is structured in two main sections: The first part presents the organisation of the conference, from the definition of the objectives to its implementation. The second part describes the programme and the dissemination material used to promote the conference.

Additionally, one document is annexed to this deliverable: the conference booklet that was handed out to all participants, which includes the conference programme, biographies of the speakers and the titles of the posters shown during the event.

D9.7 - List of EFFORT lay publications and news items

During the EFFORT-project, various project partners were involved in informing the livestock sector at large, as well as the general public, on relevant experiences, new insights and other newsworthy information. Although not core-science, such dissemination was regarded important and valuable, both in terms of dissemination research findings as well as a justification of allocating public funds. The aim of this Deliverable is to provide an overview of the main lay publications and other (lay) news items generated by partners of the EFFORT project.

D9.6 - List of EFFORT scientific publications

Dissemination and promotion activities are one of the main tasks of the EFFORT Project (2013-2018). These activities were carried out by the whole consortium, with a supportive role of Work Package 9. In the first year of the project a compilation was made of all potential papers deriving from the EFFORT consortium to prevent overlap. A procedure for consultation of papers with review has been implemented. The EFFORT scientific publications were registered in different time intervals and documented in different Periodic Reports. All scientific publications were registered in Periodic Report 3 and 4. In total 11 peer-reviewed scientific papers have been published and 5 of them are still in press as part of the EFFORT Project. The increase in scientific publications between Periodic Report 1 and 4 could be affected by the availability of the project’s results during this time frame. Out of eleven scientific publications published so far, a mean H-index impact of 121 was achieved and nine papers appeared in journals belonging to quartile Q1 (one in Q2, one in Q3). These are indications of outstanding scientific impact.

D9.5 - Policy round table 2

The final Policy Round Table of the EFFORT project was organized as part of the EFFORT International Conference taking place in Utrecht November 28th 2018. It was arranged in the format of a podium discussion, enabling the audience of the EFFORT International Conference to participate in the discussions. The round table session consisted of two sections, one with brief presentations by the Policy Round Table members and a second section with a panel discussion format. The members of the Policy Round Table represented a range of stakeholders including, the veterinary authorities at national and European level, the food industry, a multi-stakeholder platform and a European agency on food security. Relevant topics about AMR in the policy context were discussed such as financial incentives in AMR interventions and potential alternatives to antibiotics. Overall, the Policy Round Table permitted to disseminate the results of the project to policy makers and to share varied views and suggestions about AMR policy.

D9.4 - Workshop on Optimised Surveillance Designs

According to the description of work, a 2-day-workshop for up to 50 participants was planned to be organized by SAFOSO in collaboration with DTU and with the contribution of UUVM, BEC, UGent, DTU and ARTTIC on the use of metagenomics data for the design of efficient AMR surveillance. This workshop was the second component of a training package provided by the EFFORT project, the first being delivered online by e-Learning. This e-Learning course was developed by DTU for a Coursera Massive Open Online Course (MOOC) on Metagenomics applied to surveillance1. One third of the workshop content was a review of online materials and the remaining two thirds contained new content to provide hands-on training. The target group for the workshop was persons from Member States competent authorities responsible for antimicrobial resistance (AMR) monitoring, including veterinary services, food safety authorities and reference laboratories, as well as academic experts in the field. The workshop took place in Tallinn on 19th-20th March, 2018, and was organized as a satellite to the Society for Veterinary Epidemiology and Preventive Medicine (SVEPM) Conference in order to reach as many relevant parties as possible.

D9.3 - Training on Metagenomics and Bioinformatics

EFFORT developed a blended training on the use of metagenomics in surveillance of pathogens and AMR with the aims to 1) highlight the potential of metagenomics in a global, integrated surveillance context, 2) demonstrate its applicability by providing hands-on training on a surveillance case-study and 3) raise awareness for and initiate a discussion on the factors that may bias metagenomics surveillance results. The course consisted of a four-module e-learning component delivered one month (February 2018) ahead of the face-to-face component. The latter was a one and half day hands-on workshop (March 2018). DTU led the development of the e-learning component. It was subjected to feedback by volunteers from among the EFFORT consortium before its release to the registered workshop participants. After the workshop, the e-learning was revised by the instructors and its content was extended, before its stand-alone launch as a massive open online course (MOOC) in the platform Coursera, end of May 2018.

This document describes the development of the e-learning component: content, delivery and evaluation by the participants.

D9.9 - 2016 Scientific Session on EFFORT Progress

Several members of the EFFORT consortium have presented the topic of antimicrobial resistance in the food chain at IAFP’s European Symposium on Food Safety organised in Athens, on the 11-13 May 2016. A session dedicated to "Antimicrobial Resistance in the Food Chain" was held on Thursday 12th May 13:30-15:00. The purpose of this session to 50 participants was to give an overview of the problem of antimicrobial resistance in the food chain. The session featured speakers from the WHO and from scientist that are involved in EFFORT; one from the food industry, and an academic scientist.

D9.2 - EFFORT Policy Round Table 1

The first EFFORT policy round table, which main goals were i. to disseminate the project work plan to critical stakeholders in the area of antimicrobial resistance and ii. to obtain feedback on it from these same stakeholders,  was divided in two editions; one on September 8th and one on 16th, 2014. Representatives of a range of organizations were present, with different affiliations, including academia, non-profit, industry and policy making. For the edition on the 8th, mostly stakeholders with no commercial interest were invited; for the edition on the 16th, stakeholders had in common a “social responsible entrepreneurship”.

The webinars were recorded, and a link to the recording as well as a related discussion is available in the Project LinkedIn group.

D9.1 - EFFORT Public Website

The EFFORT Public web site is part of the dissemination activities and as a consequence its design, realisation and updates have been assigned to WP9 – Project dissemination and training, led by SAFOSO.

The current document is only intended as accompanying deliverable documentation for the website. It describes how the site has been designed and details the initial content of the site, which has been approved by the partners of the consortium.

D8.4 - Chain Model and Report on Analysis of Strategies (for pigs and broilers)

Processes that occur beyond-farm level have a substantial influence on the final microbiological quality of the meat as well, either negative or positive (ref). Beyond-farm measures can be effective in further reducing the risk of AMR by reducing the overall pathogen level of carcasses, e.g. monitoring and surveillance systems, cleaning and disinfection measures and decontamination measures. In this regard, studies mostly address the transfer and prevalence of certain pathogens, such as Campylobacter and Salmonella on the carcass (Duggan et al., 2010; Piras et al., 2014), the effect of specific measures on the prevalence of pathogens on the carcass (Morild et al., 2011; Pipek et al., 2006). There are few risk assessment studies considering the transfer of Salmonella and Campylobacter in the whole pig and broiler meat chains (Hill et al., 2016; Nauta et al., 2005; Simons et al., 2016; Swart et al., 2016). But most studies address only one part of the chain.

However, decision-making regarding beyond-farm measures is complex. That is, because such measures vary in their effect and costs associated along the supply chain. Besides, the benefits of measures often occur in a different stage of the supply chain than where the costs are made. From a decision-making point of view, a paramount issue is the cost-effectiveness of such measures both at each single stage and in the supply chain as a whole. In other words, the ultimate question is how to minimize the risk of AMR to humans at the lowest costs along the supply chain. There are some studies that address the cost of measures to reduce Campylobacter contamination in the chicken meat chain (Mangen et al., 2005) and cost-effectiveness of reducing Salmonella contamination in the meat supply chain (van der Gaag et al., 2004). Also, Lawson et al., 2009 studied the cost-effectiveness of different decontamination measures in the slaughterhouse. A cost-effectiveness study of measures to decrease the overall pathogen level of the carcass considering all stages of the chain lacks.

Hence, the aim of the study was to evaluate the cost-effectiveness of the different prevention and control measures beyond-farm stages in the pig supply chain, i.e. transport, lairage, slaughter and processing.

D8.1 - Development of aggregated impact parameters and data-collection at the animal and farm level

It is known that farm husbandry and management influence the health status and welfare quality of the animals in the flocks and herds. At the same time the spread of resistant bacteria is partly influenced by the amount of antimicrobial usage within a flock or herd, which is influenced by the animal health and welfare status. The aim of the deliverable is to develop an Index, composed of different indirect and direct on-farm parameters, to determine the relation between farm husbandry and management system on the one hand, and the risk factors for the transmission of AMR on the other. The ultimate aim is to provide a parameter that allows to determine the potential impact of the animal health and welfare quality of food animal herds and flocks on the magnitude of antimicrobial resistance and on the spread of resistant bacteria and/or resistance genes at herd/flock level.


D6.3 - Implementation of interventions and follow-up of impacts on antimicrobial usage, economic and technical parameters, and resistance

In two countries (France and the Netherlands), 59 farrow-to-finish pig farms were recruited and monitored by 22 veterinarians. Fifty farms were included in the antimicrobial usage analysis. The action plans contained four domains (disease management, drug stewardship, farm management, farmer knowledge) and covered different stages (sows and gilts, suckling piglets, post-weaning pigs, fatteners). Most of the proposed actions concerned sows and gilts, piglets and post-weaning pigs. A significant reduction in antimicrobial usage was observed over time and after the implementation of action plans. No intervention-, time- or country-related fixed effect was found to have a significant effect on the mortality rates recorded either in weaners or fatteners. Unfortunately, the difference in the recording systems for animal production parameters between the two countries impaired our capacity to analyse other zootechnical data. Antimicrobial resistance did not change significantly between the two sampling times.

The two studies have shown that antimicrobial usage is affected by the tailored intervention proposed and followed up by veterinarians without impairing the zootechnical indicators monitored. An overall reduction in antimicrobial usage was observed on all farms throughout the study period. For further studies, the implementation of information tools to collect, share and analyse the data between the different stakeholders should improve these tailor-made interventions. The development of a time series design and data analysis should also be promoted to extract new knowledge from each individual case.

D6.1 - EFFORT Review Intervention

Title: Systematic review on available knowledge about interventions along the food chain

The purpose of this document is to review interventions which, either alone, or in combination, have been implemented, and to identify which ones are effective in reducing antibiotic prescription in pig and poultry production. The review is limited to the two animal species which will be targeted by intervention in EFFORT. Information collected in this review will help the design of the assessment decision tool and the intervention study in pig and poultry farms. 

D5.4 - Position Paper on Surveillance of Microbial Resistance on the Basis of (meta-)Genomic Approaches

Surveillance of antimicrobial resistance (AMR) is globally primarily based on methods that identify the antimicrobial resistance of bacteria by culture methods followed by phenotypic testing of susceptibility. For these methods there are different options, like the agar diffusion assay (semi-quantitative) and the quantitative methods yielding the Minimal Inhibitory Concentration (MIC) of the isolate for selected antimicrobials; these techniques are the agar dilution assay, the broth dilution assay and the smaller version of the latter, the broth microdilution assay. There is currently a shift towards the use of molecular methods. This can be methods that are used to characterize an isolated bacterium (micro-arrays to detect resistance genes) or Whole Genome Sequencing (WGS) followed by ‘’fishing’’ for resistance genes, or methods that are based on sequencing the entire so-called microbiome, all genetic material present in a sample, followed by identifying the resistance genes in the entire pool of sequences. This method is called metagenomics and it provides information about microbial DNA without culturing the micro-organisms. The phenotypic methods are well established, standardized around the world and considered as an important tool for epidemiological and clinical determination of susceptibility. WGS is evaluated in several studies, including the EFFORT project, and this approach is considered as reliable to replace the phenotypic methods. Advantage is the additional information that is obtained for each isolate. The comparison of costs between WGS and phenotypic methods is debated. Metagenomics, although powerful for research, is not yet ready for implementation in routine surveillance systems. Amongst the issues to be solved are inter-lab variability, the sensitivity for low prevalent genes, and the interpretation of the output of the technique for risk managers.

D5.1 - Quantification of AM usage, Biosecurity and Welfare

D5.1 - Quantitative description of the antimicrobial consumption, biosecurity and welfare in the different animal production systems and countries

Antimicrobial usage data is available for pigs and poultry from all participating countries. Since some of these data will be further updated as the result of ongoing quality improvement and data analysis, the results presented in this deliverable are preliminary. Furthermore, results on biosecurity and animal welfare are presented for pigs and poultry. 

To quantify antimicrobial usage in a standardized manner the treatment incidence measure (TI) was used. The TI expresses how many animals per 1000 receive a daily dose of an antimicrobial. This measure was applied both on the data of the group treatments and the purchased products. Defined Daily Dose animal (DDDvet), Used Daily Dose animal (UDDvet) and Defined Course Dose animal (DCDvet) values were used to calculate the TIs. This allows to evaluate the effect of the different quantification systems.

D4.2 - Quantification of the relationship between human, animal and environmental resistance patterns and determinants in two sentinel occupational populations (pig and poultry)

First results indicate that the animal microbiome involves a wide range of resistance genes. Abundance of several of these genes is associated with the use of antimicrobials on the farm-level. These results give additional weight to already existing evidence of associations between the use of antimicrobials and antimicrobial resistance in animals. Results of human resistomes support the possibility of transmission of resistance from animals to humans, but the extent of transmission from animals to humans and the role of occupational or environmental exposure requires further analyses and can not only be answered by observational studies as included in the EFFORT project.

D3.4 - Intervention strategies that influence horizontal gene transfer and stability of antimicrobial resistance genes in the food chain

Antimicrobial resistance is widely accepted as a major concern for Public Health. Despite being a natural process, it is well recognized that the application of antibiotics in human and veterinary medicine, agriculture and aquaculture contribute to the generation, spread and persistence of antibiotic resistance due to selective pressure. In this process, transfer of antimicrobial resistance genes between bacteria is of utmost relevance. Along the food chain, from farm to fork, bacteria undergo several stresses and processes, that are intended to limit the bacterial viability. However, some of these processes can, as we suggest here, increase the transfer of AMR genes, and should be therefore used with care. Finally, we tested a molecule, a fatty acid, that was able to inhibit transfer of AMR genes between bacteria, being thus a promising tool to limit spread of resistance in the food chain, for example as a food additive in animals.

D3.2 - EFFORT catalogue of plasmids associated with AMR in Europe

An important factor in the dissemination of antimicrobial resistance is the ability of bacteria to transfer resistance determinants horizontally. Important bacterial tools for horizontal transmission of resistance determinants are plasmids.

 In this deliverable a literature based inventory has been made summarizing the distribution of resistance plasmids and associated resistance genes from human and animal sources in Europe.


D2.5 - Antimicrobial resistance gene profiles identified in the metagenomic sequence data

Task 2.5 comprised the metagenomic characterisation of 540 herd-level faecal samples collected from farms in nine European countries. Samples from pigs, broilers, veal calves, turkeys and rainbow trout were analysed based on DNA sequence identity to genes encoding antimicrobial resistance (AMR). The resulting herd-level AMR profiles display distinct differences between the different host animal species and also between some countries of origin. The most apparent trend is that the AMR profiles of mammalian host species (pig, veal) differ substantially when compared to avian profiles (broiler, turkey): mammalian hosts present a higher total AMR load as well as a different, less varied AMR gene composition.

The AMR profile data described in this report is available to all consortium members and has been a central part of some studies that have been published in peer-reviewed academic journals. The in-depth study of AMR in pig and broiler metagenomes by Munk et al. (2018), as well as Van Gompel et al.’s (2019) look into the relations between resistance, antimicrobial use and biosecurity in pig herds are two examples.

D2.4 - Metagenomic Sequence Data of Antimicrobial Resistance Genes in DNA from faeces, foods and the environnement

This document contains a description of how the first metagenomic sequencing of faecal samples collected within the EFFORT pilot project was performed.

The document is composed of a section describing the experimental procedures and the sequencing ending with a results section such as examples of results from the pilot project samples. These results include brief analysis of the antibiotic resistance genes detected in DNA from both poultry and pig samples, sequenced on the MiSeq, and resistance genes detected in pig samples, sequenced on the HiSeq.

D2.3 - A Web-Based Analytic Tool for Identification of Antimicrobial Resistance Genes and Mobile Genetic Elements in Genomic Data

Currently, the tool looks for DNA fragments from bacterial genomes, from DNA sequences annotated in GenBank as plasmids, and from resistance genes from the ResFinder database. Following the advice of the experts in the EFFORT consortium, additional databases of genetic elements of interest can be added, or elements currently sought by the tool may be better characterised.

D2.2 - Sequences of resistance genes and mobile elements identified in indicator E. coli isolates

This deliverable describes the Whole Genome Sequencing (WGS) activity as performed in EFFORT on E. coli isolates from poultry (250), pigs (250), veal calves (150) and wild boars (50). To date the raw sequence data of almost all isolates are uploaded in the Sharepoint at the Compare portal at DTU. All data will be analysed in a uniform manner by DTU using the most recent databases with the purpose to identify all AMR genes, plasmid replicons and strain genotypes (eg. cgMLST). The data will be used to evaluate its potential for AMR surveillance and epidemiology.

D2.1 - DNA Protocols

The deliverable contains protocols for pooling of the collected individual faecal samples, and for DNA extraction from pooled or individual samples.

D1.5 - Farm characteristics identified

The collection of data on farm characteristics and welfare

The database that was set-up under deliverable 1.2, is now constructed with all the information from the participating countries. Data from the EFFORT descriptive and EFFORT in-depth study was collected during field campaigns using species specific questionnaires (with information about antimicrobial usage data and farm characteristics), field forms (regarding welfare data, faecal and dust samples, slaughterhouse samples) and human questionnaire data. These questionnaires and field forms accompany the different sample types taken within the scope of the study (animal faecal samples, EDCs, active air samples and a variety of slaughterhouse samples). Furthermore, phenotypical data on the E. coli strains has been collected centrally.

The document highlights the most important phases of the identification of farm characteristics, the data collection and database construction. 

D1.4 - Antibiotic Usage Data Collected

This deliverable gives an overview of the antimicrobial usage data collection process at the date of the 6th of April 2017. For all animal species, the farms have been visited in all countries and all data has been entered in EpiData. All antimicrobial usage data for pigs and poultry in all countries have been processed and are ready for quantification (D5.1). For the other animal species all antimicrobial usage data are collected and are ready to be prepared for quantification.

D1.3 - Antimicrobial Resistance in Indicator E. coli quantified

In EFFORT a full epidemiological analysis of antimicrobial resistance was conducted in a cross-section of slaughter pigs and broiler farms in nine EU countries. The sampling effort was based on 20 farms per animal species per country. Within each country 20 farms per sector were sampled. Within each farm, 25 individual faecal samples were collected for microbiological and metagenomics analysis.  

The aim of this Deliverable is to describe the results of sampling, isolation of E. coli and MIC-determinations in the cross-sectional study in pigs, poultry, veal calves, turkeys, dogs, cats, boars and fish. A statistical analysis of differences in AMR levels observed and the associations with antibiotic use will be done in WP5.

D1.2 - Database for meta-data

Full title: D1.2 - A database to collect all phenotypic and genetic resistance data and data on antimicrobial usage and farm characteristics

A common relational database structure is built in EpiData which contains all collected information regarding species specific questionnaires, animal data, environmental data and human data, such as phenotypical and genetic data on resistance, antimicrobial usage, farm characteristics and other meta-data based on the methods described in task 1.2 and questionnaires developed in task 1.4.

This dataset is aimed at performing epidemiological analyses and will contain most of the meta-data and a subset of the relevant meta-genomic dataset.

D1.1 - Species specific questionnaires to collect and quantify data on antimicrobial consumption

The objective of the EFFORT project is to investigate the epidemiology and ecology of antimicrobial resistance in food-producing animals, the (farm) environment, and food of animal origin, companion animals and wildlife to evaluate and quantify the antimicrobial resistance exposure pathways for humans. Therefore, the EFFORT researchers need to acquire data on the presence of antimicrobial resistance in indicator bacteria and on potential risk factors related to antimicrobial consumption, management practices and biosecurity measures. To get these data, cross-sectional surveys will be conducted in nine European countries (Belgium, Bulgaria, Denmark, France, Germany, Italy, The Netherlands, Poland, Spain) in various livestock sectors, companion animals, wildlife, the environment and retail meat.

Every country will collect data at pig farms, poultry farms, the environment of these farms and in retail meat stores. For the remaining animal types, sampling will be divided over three participating countries per animal type.

In order to facilitate further analysis and allow comparison across countries and food systems, it is of uttermost importance that standardised and efficient sample and data collection methods are used. Hence, common sampling protocols and data collection formats are required. The current document describes the delivery of all the sampling protocols, questionnaires and questionnaire manuals to be used by all EFFORT partners.