EFSA Strategy: WGS for Food Safety

EFSA Strategy:WGS for Food Safety

Beatriz Guerra Senior Scientific OfficerBIOCONTAM UNIT, RASA

ECDC expert consultation on ECDC strategy to harness whole genome sequencing for cross-border outbreak and surveillanceStokholm, 19/11/2015

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DoIs:

No conflict of interest

EFSA Strategy: WGS for Food Safety

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OUTLINE

EFSA

EFSA Strategy WGS for Food Safety

Previous Scientific Opinions

Scientific Colloquium

Procurement funding

Thematic Grant funding

EUSR-AMR support

Advisory board of EU funded projects


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EFSA




Procurement funding


EUSR-AMR support



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EFSA

The mission of the European Food Safety Authority (EFSA) is to improve food safety in the European Union (EU) and ensure a high level of consumer protection.


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HOW EFSA WORKS

EFSA’s scientists evaluate, assess, advise


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FOOD SAFETY


Biological

Hazards

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The EFSA has shown an increasing interest in WGS over recent years:

EFSA STRATEGY ON WGS

EFSA 10th Anniversary Conference

EFSA Advisory Forum

Collaborations with ECDC and EURLs

Self-task mandates

20th EFSA Scientific Colloquium

Scientific grants


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EFSA




Procurement funding

Thematic Grants funding

EUSR-AMR support



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EFSA is interested in using WGS for:

Source attribution

Outbreak detection and investigation

Common source trace back investigations

Detection and surveillance of emerging pathogens

Monitoring of antimicrobial resistance

EFSA STRATEGY ON WGS

Our main interest is to use the data generated by new Sequencing technologies (WGS, Metagenomics) for Food Safety and Public Health Protection


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EFSA




Procurement funding


EUSR-AMR support



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MOLECULAR TYPING: SCIENTIFIC OPINIONS

Evaluation of molecular typing methods for major food-borne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance (self-task mandate, BIOHAZ PANEL, 2013-2015)

EFSA-Q-2013-00032: Part 1: evaluation of methods and applications

EFSA-Q-2013-00906: Part 2: surveillance and data management activities


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OUTLINE

EFSA




Procurement funding


EUSR-AMR support



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EFSA’s Scientific Colloquium on the Use of Whole Genome Sequencing (WGS) of food-borne pathogens for public health protection (Parma, June 2014)

WGS: SCIENTIFIC COLLOQUIUM

Discussion group 1: WGS of foodborne pathogens in action

Discussion group 2: Curation and analysis of WGS data: bioinformatics solutions

Discussion group 3: Cross-sectorial coordination and international cooperation


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EFSA




Procurement: L. monocytogenes in RTE foods


EUSR-AMR support



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Closing data gaps for performing RA on L. monocytogenes in “Ready to Eat Foods” (RTE). Act. 3: Molecular characterisation employing WGS of strains from different compartments along the food chain and from humans (Oct. 2014–2016: SSI/ANSES/PHE/UA)

WGS: PROCUREMENT LISTERIA IN RTE FOODS

Molecular characterisation Lm isolates: RTE foods, food chain compartments, humans

Data analyses: genetic diversity, epidemiological relationships, markers for survival/ multiplication/ cause disease

Retrospective analysis of outbreak strains: suitability of WGS as a tool in outbreak investigations?


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OUTLINE

EFSA




Procurement funding

Thematic Grants: 2 WGS projects will be funded

EUSR-AMR support



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Call launched in April 2015, GP/EFSA/AFSCO/2015/01

Aimed to competent organisations adopted by EFSA Management Board Art. 36 of EC 178/2002.

Two out six projects were selected

Total 1,000,000 € EFSA funding (50% self-funding)

Signature pending (beginning of December)

Projects will run from beginning 2016-2018

THEMATIC GRANTS, PROMOTE NETWORKING

“New approaches in identifying and characterizing microbiological and chemical hazards”


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WGS generated data could be a powerful tool for Risk assessorsi) genetic diversity, ii) epidemiological relationships, iii) putative markers conferring advantages.

BUT integration of WGS in microbial food safety routine needs:

i) time; ii) proofs of principle; iii) transnational collaboration/scientist coordination (One Health approach); iv) new analysis tools; v) translation of results into ‘plain language’.

Projects funded: concentrate on applicability and integration of WGS methods for identification and characterisation of microbial foodborne pathogens.

“Molecular approaches for identifying and characterising microbial foodborne pathogens, specifically using Whole Genome Sequence (WGS) analysis”

THEMATIC GRANTS, WGS


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EFSA




Procurement funding


EUSR-AMR: emerging resistances, clones…



EU SUMMARY REPORT ON AMR

AMR Data fromEU MSs + EEA, CH


EU SUMMARY REPORT ON AMR, EFSA DATA

2014

Mandatory: Poultry/poultry meat,Salmonella, Campylobacter, commensal E. coli

Voluntary: MRSA, Enterococcus, ESBL-specific monitoring

2015

Mandatory: cattle/beef, swine/pork meatSalmonella, Campylobacter, commensal E. coliESBL-specific monitoring

Voluntary: MRSA, Enterococcus, Carbapenemase-E. coli specific


AMR MON P2AMR MON P1


Selection of isolates:

Emerging resistances

Detection of clones

Discrepancies

Confirmation of results

Ask MSs for the isolates

Perform:

WGS, MIC re-testing

WGS analyses support phenotypical AMR data?

WGS support EUSR-AMR, EFSA DATA


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EFSA




Procurement funding


EUSR-AMR: emerging resistances, clones…



ADVISORY BOARD WGS EU FUNDED PROJECTS


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Scientific Reports available at www.efsa.europa.eu

EUSR-AMR: http://www.efsa.europa.eu/it/efsajournal/pub/4036.htm

WGS Scientific Colloquium: http://www.efsa.europa.eu/en/press/news/150216.htm

Scientific Opinions Molecular Typing:http://www.efsa.europa.eu/it/efsajournal/pub/3502.htmhttp://www.efsa.europa.eu/it/efsajournal/pub/3784.htm

Scientific Opinions AMR:http://www.efsa.europa.eu/it/efsajournal/pub/2322.htmhttp://www.efsa.europa.eu/it/efsajournal/pub/3501.htm

INFORMATION


mailto:[email protected]


http://www.efsa.europa.eu/en/press/news/150216.htm







Thank you foryour attention!

Dr. Beatriz Guerra Román, PhD Senior Scientific Officer

BIOCONTAM Unit, RASA DepartmentTel. +39 0521 036 459; Fax: +39 0521 036 0459

e-mail: [email protected]


Health & Medicine

EFSA Strategy: WGS for Food Safety