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.
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.
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.
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.
D5.1 - 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.