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This manual provides guidance for reporting antimicrobial resistance in food‐producing animals and foodstuffs derived therefrom under the framework of Directive 2003/99/EC and Commission Implementing Decision (EU) 2020/1729. The objective is to harmonise and streamline Member States reporting to ensure that the antimicrobial resistance data collected are relevant and easy to analyse at the European Union level. Detailed guidelines are provided for reporting data and completing the free‐text forms. This guidance typically applies to Salmonella spp., indicator commensal Escherichia coli, Campylobacter coli and Campylobacter jejuni, and the animal populations and food categories to be reported on. Guidance is also provided on indicator Enterococcus and meticillin‐resistant Staphylococcus aureus. The manual notably includes specific guidance for reporting mandatory data on Salmonella spp. and commensal indicator E. coli producers of extended‐spectrum beta‐lactamases (ESBLs)/AmpCs/carbapenemases obtained from the harmonised routine monitoring, and ESBL‐/AmpC‐/carbapenemase‐producing E. coli derived from specific monitoring. This manual is specifically aimed at guiding the reporting of information deriving from the year 2023. [ABSTRACT FROM AUTHOR]

This manual provides guidance for reporting antimicrobial resistance under the framework of Directive 2003/99/EC and Commission Implementing Decision (EU) 2020/1729 in food‐producing animals and foodstuffs derived thereof. The objective is to harmonise and streamline the reporting made by the Member States to ensure that the antimicrobial resistance data collected are relevant and easy to analyse at the European Union level. Detailed guidelines are provided for the reporting of data and text forms. This guidance typically applies to Salmonella spp., indicator commensal Escherichia coli, Campylobacter coli and Campylobacter jejuni, and the animal populations and food categories to be reported on. Guidance is also provided on indicator Enterococcus and meticillin‐resistant Staphylococcus aureus. The manual notably includes specific guidance for reporting mandatory data on Salmonella spp. and commensal indicator E. coli producers of ESBLs/AmpCs/carbapenemases obtained from the harmonised routine monitoring, and ESBL‐/AmpC‐/carbapenemase‐producing E. coli derived from specific monitoring. This manual is specifically aimed at guiding the reporting of information deriving from the year 2022. [ABSTRACT FROM AUTHOR]

This manual provides guidance for reporting antimicrobial resistance under the framework of Directive 2003/99/EC and Commission ImplementingDecision 2020/1729/EU in food‐producing animalsand foodstuffs derived thereof. The objective is to harmonise and streamline the reporting made by the Member States to ensure that the antimicrobial resistance data collected are relevant and easy to analyse at the European Union level. Detailed guidelines are provided for the reporting of data and text forms. This guidance typically applies to Salmonellaspp., indicator commensal Escherichia coli, Campylobacter coli andCampylobacter jejuni, and the animal populations and food categories to be reported on. Guidance is also provided on indicatorEnterococcus and meticillin‐resistant Staphylococcus aureus. The manual notably includes specific guidance for reporting mandatory data on Salmonella spp. and commensal indicatorE. coli producers of ESBLs/AmpCs/carbapenemases obtained from the harmonised routine monitoring, and ESBL‐/AmpC‐/carbapenemase‐producing E. coliderived from specific monitoring.This manual is specifically aimed at guiding the reporting of information deriving from the year 2021. [ABSTRACT FROM AUTHOR]

This manual provides guidance for reporting antimicrobial resistance under the framework of Directive 2003/99/EC and Commission ImplementingDecision 2013/652/EU in food‐producing animalsand foodstuffs derived thereof. The objective is to harmonise and streamline the reporting made by the Member States to ensure that the antimicrobial resistance data collected are relevant and easy to analyse at the European Union level. Detailed guidelines are provided for the reporting of data and text forms. This guidance typically applies to Salmonellaspp., Campylobacter coli andCampylobacter jejuni, and the animal populations and food categories to be reported on. Guidance is also provided on indicator commensalEscherichia coli, indicatorEnterococcus and meticillin‐resistant Staphylococcus aureus. The manual notably includes specific guidance for reporting mandatory data on Salmonella spp. and commensal indicatorE. coli producers of ESBLs/AmpCs/carbapenemases obtained from the harmonised routine monitoring, and ESBL‐/AmpC‐/Carbapenemase‐producing E. coliderived from specific monitoring,as well as voluntary data on specific monitoring of carbapenemase‐producers.This manual is specifically aimed at guiding the reporting of information deriving from the year 2019. [ABSTRACT FROM AUTHOR]

This technical report of the European Food Safety Authority (EFSA) presents guidance to reporting European Union (EU) Member Statesand non‐Member States in data transmission using extensible markup language (XML) data transfer covering the reporting of isolate‐based quantitative antimicrobial resistance data, as well as reporting of prevalence data on zoonoses and food‐borne contaminants, food‐borne outbreak data, animal population data and disease status data.For data collection purposes, EFSA has created the Data Collection Framework (DCF)application. The present report provides data dictionaries to guide the reporting ofinformation deriving from 2019 under the framework of Directive 2003/99/EC, Regulation (EU) 1375/2015, Regulation (EU) 854/2004 and Commission Implementing Decision 2013/652/EC.The objective is to explain in detail the individual data elements that are included in the EFSA data models to be used for XML data transmission through the DCF. In particular, the data elements to be reported are explained, including information about the data type, a reference to the list of allowed terms and any additional business rule or requirement that may apply. [ABSTRACT FROM AUTHOR]

EFSA and ECDC were requested by the European Commission to jointly evaluate the possible solutions for the collection and analysis of whole genome sequencing (WGS) data for at least Listeria monocytogenes, Salmonella and Escherichia coli by: (1) analysing the outcome of the surveys on the status of the use of WGS of food‐borne pathogens in EU/EEA countries in both the food and public health sectors; (2) conducting a consultation of relevant actors to assess state‐of‐the‐art pipelines for collecting and analysing WGS data in Europe; (3) involving relevant stakeholders to assess the needs and requirements for the analysis of WGS data and their comparability; and (4) preparing a technical report on the identification and comparison of potential solutions for the set‐up and running of a joint EFSA‐ECDC pipeline to collect and analyse WGS data. Logical components of the overall system were identified and technical requirements were prioritised and grouped according to functionality. Eleven platforms (solutions) that integrate the relevant functionalities for collecting, analysing and visualising WGS data were thoroughly described. The degree to which the requirements are met by the different solutions (as of 31 December 2018) was evaluated. The assessment made clear that no single solution meets all the critical requirements and each solution has significant gaps regarding the unmet critical requirements. Therefore, scenarios consisting of a combination of several solutions were considered. As there may be many suitable scenarios, and the choice among them will depend on strategic or financial elements that are not within the scope of this report, it contains the scientific and technical elements necessary to generate scenarios, rather proposing individual scenarios. A scenario builder is presented which includes the significant gaps for each solution/functionality and the limitations and risks to be considered when setting up a joint ECDC‐EFSA database for the collection and analysis of WGS data. [ABSTRACT FROM AUTHOR]

This manual provides guidance for reporting antimicrobial resistance under the framework of Directive 2003/99/EC and Commission Implementing Decision 2013/652/EU in food‐producing animals and foodstuffs derived thereof. The objective is to harmonise and streamline the reporting made by the Member States to ensure that the antimicrobial resistance data collected are relevant and easy to analyse at the European Union level. Detailed guidelines are provided for the reporting of data and text forms. This guidance typically applies to Salmonella spp., Campylobacter coli and Campylobacter jejuni, and the animal populations and food categories to be reported on. Guidance is also provided on indicator commensal Escherichia coli, indicator Enterococcus and meticillin‐resistant Staphylococcus aureus. The manual notably includes specific guidance for reporting mandatory data on Salmonella spp. and commensal indicator E. coli producers of ESBLs/AmpCs/carbapenemases obtained from the harmonised routine monitoring, and ESBL‐/AmpC‐/Carbapenemase‐producing E. coli derived from specific monitoring, as well as voluntary data on specific monitoring of carbapenemase‐producers. This manual is specifically aimed at guiding the reporting of information deriving from the year 2018. [ABSTRACT FROM AUTHOR]

This technical report of the European Food Safety Authority (EFSA) presents guidance to reporting European Union (EU) Member States and non‐Member States in data submission using extensible markup language (XML) data transfer covering the reporting of isolate‐based quantitative antimicrobial resistance data, as well as reporting of prevalence data on zoonoses and food‐borne contaminants, food‐borne outbreak data, animal population data and disease status data. For data collection purposes, EFSA has created the Data Collection Framework (DCF) application. The present report provides data dictionaries to guide the reporting of information deriving from 2018 under the framework of Directive 2003/99/EC, Regulation (EU) 1375/2015, Regulation (EU) 854/2004 and Commission Implementing Decision 2013/652/EC. The objective is to explain in detail the individual data elements that are included in the EFSA data models to be used for XML data transmission through the DCF. In particular, the data elements to be reported are explained, including information about the data type, a reference to the list of allowed terms and any additional business rule or requirement that may apply. [ABSTRACT FROM AUTHOR]

Whole Genome Sequencing (WGS) is becoming increasingly used in public health and food safety laboratories. To date, there is a wide variation in the level of implementation of WGS among laboratories from different sectors in different countries, the type of analysis employed and the data interpretation. To gather information on the WGS capacity of food safety/veterinary laboratories in the European Union (EU) and associated countries (EFTA), the European Commission (DG SANTE) and the European Food Safety Authority (EFSA), supported by the EU Reference laboratories (EURLs), prepared a survey among the EU/EFTA laboratory Networks for Salmonella, Listeria monocytogenes, Escherichia coli (VTEC), Campylobacter, Coagulase Positive Staphylococci, Antimicrobial Resistance and bacteriological and viral contaminants of bivalve molluscs. Questions on the general use of WGS, pathogens tackled, analysis purposes, pipelines and tools used, place of data storage and analysis, WGS research projects, needs for support, and future interest to implement WGS were addressed. By the end of 2016, WGS was already in use in reporting laboratories from 17 out of 30 EU/EFTA countries; in particular, WGS was reported to be used in all consulted EURLs, almost half of the National Reference Laboratories (44% affirmative respondents) and only few Official Laboratories (7% affirmative respondents). The main reason for not implementing WGS was the lack of capacity (budget and expertise). WGS was mainly used for outbreak investigations, followed by surveillance, and mostly for L. monocytogenes, E. coli and Salmonella analysis. Sequencing, sequence storage and analysis were mainly done 'in house'. Several WGS pipelines/platforms/tools were in use for analysis of different microorganisms and purposes. The participating laboratories expressed a general willingness for collaboration with EURLs and European institutions. This report provides a first picture of the state of the art in relation to the use of WGS in European food safety laboratories at the end of 2016. [ABSTRACT FROM AUTHOR]

This publication is linked to the following EFSA Supporting Publications articles: http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2018.EN-1368/full, http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2018.EN-1370/full, http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2018.EN-1371/full [ABSTRACT FROM AUTHOR]