EFSA and ECDC¶
Both EFSA and ECDC have done extensive work on how to implement whole genome sequencing for surveillance and outbreak purposes. This page is meant to collect reports and opinions from these institutions.
These institutions also have reports that specifically advice on specific pathogens, information on these are found in the species specific sections.
ECDC resources¶
- 2019 - Collection and analysis of whole genome sequencing data from food-borne pathogens and other relevant microorganisms isolated from human, animal, food, feed and food/feed environmental samples in the joint ECDC–EFSA molecular typing database
- 2019 - ECDC strategic framework for the integration of molecular and genomic typing into European surveillance and multi-country outbreak investigations
- 2018 - ECDC public health microbiology strategy 2018–2022
- 2018 - Monitoring the use of whole-genome sequencing in infectious disease surveillance in Europe 2015–2017
- 2016 - ECDC roadmap for integration of molecular typing and genomic typing into European-level surveillance and epidemic preparedness – Version 2.1, 2016-19
- 2016 - Expert opinion on whole genome sequencing for public health surveillance
- 2015 - Expert Opinion on the introduction of next-generation typing methods for food- and waterborne diseases in the EU and EEA
EFSA resources¶
- 2019 - EFSA and ECDC technical report on the collection and analysis of whole genome sequencing data from food‐borne pathogens and other relevant microorganisms isolated from human, animal, food, feed and food/feed environmental samples in the joint ECDC‐EFSA molecular typing database
- 2019 - Technical specifications on harmonised monitoring of antimicrobial resistance in zoonotic and indicator bacteria from food‐producing animals and food
- 2019 - Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms
- 2018 - INNUENDO: A cross‐sectoral platform for the integration of genomics in the surveillance of food‐borne pathogens
- 2018 - Final report of ENGAGE ‐ Establishing Next Generation sequencing Ability for Genomic analysis in Europe
- 2018 - Outcome of EC/EFSA questionnaire (2016) on use of Whole Genome Sequencing (WGS) for food‐ and waterborne pathogens isolated from animals, food, feed and related environmental samples in EU/EFTA countries
- 2018 - Use of next‐generation sequencing in microbial risk assessment
- 2014 - Scientific Opinion on the evaluation of molecular typing methods for major food‐borne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance: Part 2 (surveillance and data management activities)
- 2014 - Scientific Opinion on the evaluation of molecular typing methods for major food‐borne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance: Part 1 (evaluation of methods and applications)