Data sources on animal diseases: Methodology on mapping the data sources on animal diseases in European Union Member States

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1 TECHNICAL REPORT APPROVED: 14 December 2018 doi: /sp.efsa.2018.en-1530 Abstract Data sources on animal diseases: Methodology on mapping the data sources on animal diseases in European Union Member States European Food Safety Authority (EFSA) Mapping the data sources on animal diseases, in each European Union (EU) Member State, is one of the activities of EFSA s SIGMA 1 project. The aim of this activity is to identify the central competent authorities responsible for managing the data on animal diseases and animal populations in each Member State. Initially EFSA is focusing on three diseases (on which Animal Health and Plant Health Unit is currently working): African swine fever, avian influenza and lumpy skin disease; and on the corresponding affected animal populations: swine, poultry and bovines, respectively. This technical report describes the details of the methodology implemented by EFSA for the mapping of the data sources in each EU Member State. In order to collect all the information needed, EFSA launched an online questionnaire, through the EUSurvey application, to the 28 EU Member States. The information received was assessed and validated in close collaboration with each country. The results of this activity will be published separately per Member State as a technical report where the Country Card for each one will be included. This `Country Card summarises the information related to the central competent authorities responsible for the data on animal diseases (data on outbreaks, surveillance activities and laboratory results) and on animal populations (bovines, swine, poultry). European Food Safety Authority, 2018 Key words: SIGMA, Country Card, data mapping, animal diseases, animal populations Requestor: EFSA Question number: EFSA-Q Correspondence: ALPHA@efsa.europa.eu 1 EFSA (European Food Safety Authority), SIGMA A comprehensive animal disease data collection approach. EFSA Supporting publication 2018:EN pp. Available online: EFSA Supporting publication 2018:EN-1530

2 Acknowledgements: EFSA wishes to thank the following for the support provided to this scientific output: Sotiria-Eleni Antoniou, Frank Verdonck, Gabriele Zancanaro, Alessandro Broglia, Inmaculada Aznar and also Andrea Buselli and Kanoatkhon Umurzokova, for their contributions in the questionnaire and for their technical support on the EUSurvey. Suggested citation: EFSA (European Food Safety Authority), Data sources on animal diseases: Methodology on mapping the data sources on animal diseases in European Union Member States. EFSA supporting publication 2018:EN pp. doi: /sp.efsa.2018.en-1530 ISSN: European Food Safety Authority, 2018 Reproduction is authorised provided the source is acknowledged. 2 EFSA Supporting publication 2018:EN-1530

3 Table of contents Abstract Introduction Background and terms of reference as provided by the requestor Methodology Prior information provided to the Member States Questionnaire The EUSurvey application Results outputs... 8 Glossary Abbreviations Appendix A Data sources mapping questionnaire EFSA Supporting publication 2018:EN-1530

4 1. Introduction 1.1. Background and terms of reference as provided by the requestor The European Commission is asking EFSA for scientific and technical support in the epidemiological analysis of animal disease outbreaks, i.e. African swine fever (mandates M , M , M , M ), lumpy skin disease (mandates M , M , M ) and avian influenza) and in the assessment of the surveillance data, i.e. Echinococcus multilocularis (mandates M , M ) and avian influenza (mandate M ). For this purpose, in recent years EFSA has been performing ad hoc data collections, gathering specific information on outbreaks, surveillance activities, laboratory results, animal populations related to these diseases (i.e. poultry, domestic pigs, cattle and wildlife such as wild boar) and the establishments where these animals are kept (see Figure 1). Figure 1: Data sharing between EU Member States and EFSA Currently, the data are not completely harmonised and their submission is not automated. Data transmission is now mainly done via exchange of Excel or xml files, which is time consuming, prone to mistakes and misreporting of variables. EFSA, therefore, decided to initiate a process of data model harmonisation and technical development on data submission, validation, analysis and reporting, across the different data collection activities, which are focused on the animal diseases and populations, under the name of the SIGMA project. SIGMA has been planned as a three year project (24 November 2018 to 30 September 2020) with three main phases as described in the event report 2. 2 EFSA (European Food Safety Authority), SIGMA A comprehensive animal disease data collection approach. EFSA Supporting publication 2018:EN pp. Available online: EFSA Supporting publication 2018:EN-1530

5 Mapping the data sources is one of its activities. More specifically it is part of the first phase of the project aiming to draw a comprehensive overview at EU level of the sources of data related to animal diseases and animal populations. As a starting point, the focus is on three diseases on which EFSA is currently working, i.e. African swine fever (ASF), avian influenza (AI) and lumpy skin disease (LSD). Within each Member State, several different authorities are involved in data collection and its management at different administrative levels (e.g. central, regional and local), using various tools (e.g. online databases, Excel or Word files, manuscripts) and different networks of people. The aim of this activity is: i) to identify the central competent authorities in the Member States that are responsible for managing the available data at national level; and ii) to describe the hierarchy and the connection between them. All this information will be summarised and presented in a set of technical reports, one per Member State, which will include a Country Card. Consequently, the Country Cards will make this information easily available and retrievable in order: i) to enhance communication and cooperation among the different organisations and authorities; ii) to facilitate the search of the competent authorities dealing with specific types of data; and iii) to understand the complexity of the data source networks within the countries. It is important to mention that the engagement of the Member States in the SIGMA project, including their participation in this mapping activity and the relevant questionnaires, is on a voluntary basis. The development of this technical report is linked to the strategic objectives to widen EFSA s evidence base and optimise access to its data, to build the EU s scientific assessment capacity and knowledge community and prepare for future risk assessment challenges (EFSA Strategy ). 2. Methodology All the data and information used for mapping the data sources on animal diseases and the related Country Cards came directly from the Member States, which were informed about the SIGMA project, its objectives and its activities Prior information provided to the Member States During the Animal Health Network meeting 4 (Parma, May 2018) with the representatives of the Member States, the SIGMA project was presented in detail. Regarding the mapping of the data sources, the Member States were informed of the necessity of identifying the authorities responsible for the management of the data related to animal diseases and populations within their countries. Member States were made aware of the specific information needed and the use of the EUSurvey questionnaire as a tool to collect it. There was also reference to the difficulties of identifying the authorities dealing with the different types of data due to the complexity of the administrative structure. The context of the questionnaire and an example of a Country Card were also presented in order to provide them with a clear idea of the work to be done and the expected results. An extensive discussion took place, the outputs of which were considered for the questionnaire and for the following activities of the SIGMA project Questionnaire In order to collect all the relevant information on the authorities responsible for the data of interest within each Member State (see Section 1), EFSA directly addressed the Member States by using an online questionnaire. For the purpose of this specific activity, a questionnaire was considered to be the most convenient way to collect information directly from the authorities in a harmonised, comparable and interpretable manner. The questionnaire included a combination of closed-ended (yes/no) and open-ended questions. It was not possible to avoid the open-ended questions due to the nature of the information 3 EFSA (European Food Safety Authority), EFSA Strategy 2020 Trusted science for safe food. Draft for public consultation. Parma, 20 pp. Available online: th meeting of the EFSA Scientific Network on Risk Assessment in Animal Health and Welfare EFSA Supporting publication 2018:EN-1530

6 requested; for instance, the names of the competent authorities. The possibility to add comments in each question was also provided, in case something needed more explanation. The questionnaire was split into three different sections requesting information on the authorities concerning the: 1) data on animal populations; 2) data on the establishments where the animals are kept; and 3) data on the diseases related to the outbreaks, the surveillance activities and the laboratory results. In the introduction, the scope of the questionnaire was clearly defined and some instructions were also provided. The questionnaire was designed so that the same set of questions could be applied to the three types of data, leading to comparable results among them (see Appendix A). The set of questions applied for each type of data aimed to gather the following information: the existence or not of a national database for the registration and the recording of the information on each type of data whether the data are recorded at individual level (per animal or per establishment) which is the central authority collecting data, if any (name of the main organisation and the exact name of the administrative authority) the link to the website of the authority the first name and the surname of the reference person in each one of these authorities the address of the reference person whether this authority is also the data owner of the data in question the data model/dictionary was requested to be uploaded if it was available. The first section was dedicated to the animal population and targeted bovines, swine and poultry populations (see Appendix A). The second section was dedicated to the establishments, targeting the places where the animals are kept. The term establishment is defined as any premises, structure, or, in the case of open-air farming, any environment or place, where animals or germinal products are kept, on a temporary or permanent basis, except for (a) households where pet animals are kept and (b) veterinary practices or clinics. It is the definition given in EU Regulation (EC) 429/2016 (Animal Health Law) 5 and used in the SIGMA project for the disease data modelling 6. Ten different types of establishment were included, in line with the SIGMA data model: farms, quarantine premises, assembly centres, markets, scientific centres, genetic centres, exhibitions, slaughterhouses, pastures and hatcheries. To avoid misunderstandings each type of establishment mentioned in the questionnaire was accompanied by the definition provided in the SIGMA data model (see Glossary). Following previous practice, the same set of questions was applied to each type of establishment (see Appendix A). In the section dedicated to the diseases, the data regarding the targeted animal diseases (LSD, ASF and AI) were divided into three main groups: i) the data related to surveillance activities; ii) the data related to the outbreaks; and iii) the data related to the laboratory results. For each group, the same set of questions was applied (see Appendix A). The questionnaire was pilot tested by EFSA by sending it to animal health and welfare (AHAW) officers, Member State representatives of the AHAW network and the members of the SIGMA Consortium who replied to the potential questions and provided their feedback. Their comments were taken into account and the relevant amendments were implemented in the final version of the questionnaire. 5 Regulation (EU) 2016/429 of the European Parliament and of the Council of 9 March 2016 on transmissible animal diseases and amending and repealing certain acts in the area of animal health ( Animal Health Law ). OJ L 84, , p European Food Safety Authority, Zancanaro G, Monguidi M, Antoniou SE, Boelaert F, Bedriova M, Saxmose Nielsen S, Gonzales Rojas J, Roberts H, Calistri P, Thulke HH, Scientific report on the SIGMA Animal Disease Data Model: A comprehensive approach for the collection of standardised data on animal diseases. EFSA Journal 2019;17(1):5556, doi: /j.efsa EFSA Supporting publication 2018:EN-1530

7 The EUSurvey application EFSA s Animal and Plant Health Unit decided to use the EUSurvey application 7 in order to collect all the data needed from the Member States. EUSurvey is the European Commission s official survey management tool, launched in Its main purpose is to create official surveys of public opinion and forms for internal communication and staff management, e.g. staff opinion surveys and forms for evaluation or registration. EUSurvey provides a wide variety of elements used in forms, ranging from the simple (e.g. text questions and multiplechoice questions) to the advanced (e.g. editable spreadsheets and multimedia elements). The application, hosted at the European Commission s Directorate-General for Informatics, is fully opensource (available free of charge) to all EU citizens, and is published under the European Union Public Licence. The EUSurvey tool can be accessed from: The survey produced is entitled Data Sources Mapping and, following the structure of the questionnaire, is divided into the Introduction and three main sections (Animal population, Establishments and Diseases). The questions have been organised in tables using the table type of question from the toolbox of the EUSurvey application. The online form allows the submitted information to be stored, amended and/or updated, whenever it is needed or requested, similar to an online database. The result of the data collection is a database in Excel format and pdf files of the replies for easy archiving. Instructions for the users on how to complete the survey were provided in the invitation letter and in the Introduction section; furthermore, Instructions to submit and retrieve the form in EUSurvey are available in and downloadable from the home page of the survey s Background documents section. A data protection note was issued describing the purpose of the survey and clarifying the processing and management of the information and the data received through this questionnaire. It has been also uploaded as `Background Documents` of the survey. To ensure access and traceability, each Member State was provided with a dedicated token (unique link) generated by the application. This particular feature provides single use/submission access, avoiding duplication and strengthening the control of the data collected. The link to access and fill in the questionnaire was sent to the national contact points for the SIGMA project. For those Member States that did not nominate a national contact point, the link was sent to the members of EFSA s Animal Health Network EFSA Supporting publication 2018:EN-1530

8 3. Results outputs The questionnaire was launched to the 28 Member States on 11 June Up until the end of November Member States had replied to the questionnaire and 19 Member States had validated their Country Card (see Table 1 and Figure 2). Table 1: Participation of the Member States in the mapping data sources activity: submission of the questionnaire and validation of the Country Cards Member States ISO Replied to the questionnaire Validation of the Country Card by the Member State Austria AT YES YES Belgium BE YES YES Bulgaria BG YES YES Croatia HR YES NO (a) Cyprus CY YES YES Czechia CZ YES YES Denmark DK YES YES Estonia EE YES YES Finland FI YES NO (b) France FR NO NO (b) Germany DE YES YES Greece EL YES YES Hungary HU NO NO (b) Ireland IE YES YES Italy IT YES YES Latvia LV YES YES Lithuania LT YES YES Luxembourg LU NO NO (b) Malta MT NO NO (b) Netherlands NL YES YES Poland PL YES YES Portugal PT YES YES Romania RO NO NO (b) Slovakia SK YES YES Slovenia SI NO NO (b) Spain ES YES YES Sweden SE YES YES United Kingdom UK YES NO (b) (a) Croatia completed all the information requested in the questionnaire but the Country Card has not been validated because an organisational reconstruction is going to take place at the beginning of (b) Has not filled in the questionnaire or has not completed all the requested information needed for the Country Cards. 8 EFSA Supporting publication 2018:EN-1530

9 Figure 2: Map of the EU Member States for which the Country Cards had been validated by the end of November (The map was produced through mapchart.net online application). Country Cards After the submission of the EUSurvey, questions and clarifications were exchanged directly with the Member States through s. Regarding the administrative structure of the authorities and the hierarchical relations between them, the websites of the authorities and the Country Profiles 8 were reviewed by EFSA, when needed, to ensure clarity. Finally, the information received was organised and used properly to draw up the Country Cards, one per Member State, in order to present the network of the central authorities responsible for the data on animal diseases. Each card is separated into three sections: a graph with a simplified depiction of the central authorities involved with the different types of data a short text providing basic information three detailed tables presenting the central competent authorities for: i) the data on animal populations per animal species (bovines, swine and poultry); ii) the data on the establishments where live animals are kept per each type of establishment; and iii) the data per each disease (LSD, ASF, AI) on the outbreaks, the surveillance activities and the laboratory results. The administrative level of the authorities included in the cards is the one indicated by the Member States and it is different for each country, based on the input received, e.g. some of them provided more detailed information on the hierarchical connection of the authorities than others. The titles of the authorities are also those provided by the Member States without any intervention by EFSA to translate into English EFSA Supporting publication 2018:EN-1530

10 The draft cards were sent back to the Member States for revision and validation before publication. They will be published as independent technical reports, one per Member State, once all the necessary steps are fulfilled, i.e. validation of the questionnaires and validation of the Country Card. It should be mentioned that the information provided on the competent authorities refers to the administrative structure and the competences at the date of the validation by the Member State. The complexity of the data sources network within the country and consequently within the EU influences the quality of the data used for risk assessment purposes. The involvement of different central authorities with the same or a similar type of dataset overlapping each other, the absence of one central authority responsible for each one of the datasets and the absence of national databases are some of the factors which may lead to the heterogeneity, introduction of bias and inconsistency of the data, making them inappropriate for statistical analysis. A good understanding of these aspects is of great help to enhance the data flow from the EU Member States to EFSA, increasing the quality of the data and reducing the effort of the data providers EFSA Supporting publication 2018:EN-1530

11 Glossary Assembly centre Establishment Exhibition Farm Genetic centre Hatchery Holding Market Quarantine premises Scientific centre Slaughterhouse An establishment approved by the competent authority, where kept terrestrial animals are assembled from more than one establishment for a period shorter than the required residency period for the species of animals concerned, for international and national movement. (Definition of SIGMA) Any premises, structure, or, in the case of open-air farming, any environment or place, where animals or germinal products are kept, on a temporary or permanent basis, except for (a) households where pet animals are kept and (b) veterinary practices or clinics. (Regulation (EU) 429/2016) Permanent establishments where animals of domestic or wild species are kept for exhibition to the public for seven or more consecutive days a year (e.g. zoos, petting centres), with the exception of circuses and pet shops. (Definition of SIGMA) An establishment where the animals are kept by humans, since birth OR for a rearing/production period OR for the required residency period for the species of animal concerned, for commercial purposes, i.e. to breed and/or rear and/or sell animals and/or products of animal origin. Hatcheries are excluded. (Definition of SIGMA) Establishment where the animals (bovines, equines, swine, sheep, goats) are kept by humans, for the collection of germinal products. (Definition of SIGMA) An establishment which incubates and hatches eggs and supplies day-old chicks (Art 2, Council Directive 2009/158/EC of 30 November 2009 on animal health conditions governing intra-community trade in, and imports from third countries of, poultry and hatching eggs 9 ). (Definition of SIGMA) A single economical unit which undertakes agricultural activities within the economic territory of the European Union and is characterised by a single ownership. The production areas can be located in different regions. It can have two or more establishments in different locations even in different regions. (Definition of SIGMA) An establishment, registered by the competent authority, where kept terrestrial animals are assembled from more than one establishment for a period shorter than the required residency period for the species of animals concerned, for national movements. (Definition of SIGMA) An establishment where the animals are kept in isolation with no direct or indirect contact with animals outside this epidemiological unit, for the purpose of ensuring that there is no spread of one or more specified diseases while the animals in isolation are undergoing observation for a specified length of time and, if appropriate, testing and treatment. (Regulation (EU) 2016/429) Any permanent, geographically limited and approved establishment where one or more species of animal are habitually: (a) kept to perform basic or applied scientific research; or (b) bred for the purposes of such research; (c) kept to undergo veterinary medicine practices (e.g. research laboratories, veterinary hospitals, etc.). (Definition of SIGMA) An establishment used for slaughtering and dressing animals, the meat of which is intended for human consumption (Regulation (EU) 853/ ) 9 OJ L 343, , p Regulation (EC) No 853/2004 of the European Parliament and of the Council of 29 April 2004 laying down specific hygiene rules for food of animal origin. OJ L 139, , p EFSA Supporting publication 2018:EN-1530

12 Abbreviations AHAW ASF AI EFSA EU LSD Animal health and welfare African swine fever Avian influenza European Food Safety Authority European Union Lumpy skin disease 12 EFSA Supporting publication 2018:EN-1530

13 Appendix A Data sources mapping questionnaire The questionnaire which has been used is provided in this Appendix 13 EFSA Supporting publication 2018:EN-1530

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