INNUENDO: integration of genomics in surveillance of food ...
Transcript of INNUENDO: integration of genomics in surveillance of food ...
INNUENDO: integration of genomics in
surveillance of food-borne pathogens
¹Mirko Rossi, ²João Carriço, ³Javier Garaizar, ³Joseba Bikandi, ⁴Friederike Hilbert, ⁵Saara
Salmenlinna, ⁶Marjaana Hakkinen, ⁷Monica Oleastro, ⁷Vitor Borges, the INNUENDO consortium
¹Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland; ²Faculty of Medicine, University of Lisbon, Lisbon, Portugal;
³University of Basque Country, Vitoria-Gasteiz, Autonomous Community of the Basque Country, Spain; ⁴University of Veterinary Medicine,
Vienna, Austria; ⁵Finnish National Institute for Health and Welfare, Helsinki, Finland; ⁶Finnish Food Safety Authority, EVIRA, Helsinki,
Finland; ⁷Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
To design an affordable and
sustainable diagnostic
infrastructure, the INNUENDO
consortium includes governmental
organisations, authorities and
research institutes from the food,
veterinary and human sectors, from
Finland, Estonia, Latvia, Portugal,
Basque Autonomous Community in
Spain and Austria (The Team).
Allowing project stakeholders to
assess design choices early on in the
development cycle, this
multinational collaboration in the
‘One-health’ context will ensure that
the planned infrastructure will
address the requirement for the
integration of WGS in routine
analysis in the food chain.
Ÿ Implementing whole genome sequencing (WGS) in routine surveillance and
outbreak investigations is becoming a strategic goal for many public health
authorities all over the world.
Ÿ Small countries with limited resources might not be able to succeed in
reaching this goal in the near future, pu�ing several EU member states in a
condition of inferior capabilities for outbreak detection and investigation.
Ÿ To guarantee the reinforcement of European capacities to ensure protection
of citizens against cross border health threats, EU must enable wider access
to the new methodologies.
Ÿ The potential of widespread, routine use of WGS analysis for public health
protection is essentially restricted by the absence of accessible IT framework,
and the limited skills of public health microbiologists in handling these novel
methodologies.
Ÿ An increased level of cooperation between the local, national and European
competent authorities by dedicated training, development of a common
pathogen database and validation of new approaches in microbial
characterization is warranted.
Why? What is new?
Who?
When?
How?
Ÿ Thinking small: supporting small EU countries with limited resources
Ÿ Network development and sharing data: communication protocols and centralized calculation
Ÿ The keyword is calibration: account effect of the genetic diversity in a bacterial population
accumulated over time on the final interpretation
Ÿ A pan-genome gene-by-gene approach: validation of pangenome approach in the context of
epidemiological investigation
Ÿ A consistent, flexible and portable pipeline: QA/QC; establish different analytical strategies;
hyperlink with available nomenclature servers
Ÿ Training: improve skills of public health microbiologists
DisclaimerThe conclusions, findings, and opinions expressed in this poster reflect only the view of the
INNUENDO consortium members and not the official position of the European Food Safety
Authority that is not responsible for any use that may be made of the information they contain.
The INNUENDO project has received funding from European
Food Safety Authority (EFSA), grant agreement
GP/EFSA/AFSCO/2015/01/CT2 (New approaches in identifying
and characterizing microbial and chemical hazards)
Feb 2016 May 2016 Aug 2016 Nov 2016 Feb 2017 May 2017 Aug 2017 Nov 2017 Feb 2018 May 2018 July 2018
Realtime WGS application in investigating STEC outbreaks at national level; validation of the platform and communication SOP
Guidelines for implementation of WGS in routine analysis of outbreak investigation at EU level
INNUENDO platform configuration and SOP for communication during outbreaks
Simulation of multinational outbreak
DB developing: public + ~1200 new sequences
Final reporting to EFSA
Calibration of genetic diversity: Phylogeography; microevolution analysis (farm-to-fork, outbreak); bio-tracing; Validation gene-by-gene approach
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