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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