Managing the shift in the paradigm operated by the new technologies in the integrated surveillance of food-borne diseases

Risk assessment and communication in the food chain: EFSA and the European National Authorities. Models of collaboration.

Ministero della Salute, Roma – 10 December 2018

Gaia ScaviaIstituto Superiore di Sanità, Rome (Italy)Dep. Food Safety, Nutrition and Veterinary Public Healthgaia.scavia@iss.it

Vucciria - R. Guttuso, 1974

Integrated surveillance of foodborne pathogens: Salmonella serovars in human salmonellosis acquired in the EU, across

different food, animal and meat sectors by source, EU, 2016

EFSA, 2013

Integrated surveillance of foodborne pathogens:

the role of microbial subtyping

http://ec.europa.eu/food/food/biosafety/salmonella/docs/vision-paper_en.pdf.

2012

Molecular epidemiology of foodborne diseases: the EU vision paper (2012)

Molecular epidemiology of foodborne diseases (2013-2014)

Database on molecular testing of foodborne hazards from food and animal source (2014)

Traditional methods for molecular characterization of foodborne pathogens: PFGE, MLVA....

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80-100 $ per Bacterial Genome

A new era: the advent of Next Generation Sequencing techiniques

DNA DNA Library WGS Bioinformatic

Analysis Assembly, MLST

cgMLST/wgMLST

Isolate

Shift in the paradigm operated by the new technologies: Whole Genome Sequencing (WGS)

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Strain_4_L664

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Strain_1_L827

Strain_3_L925

Strain_4_L703

Strain_2_L700

Strain_3_L163

Strain_6_L703

Strain_4_L700

Strain_1_L607

Strain_1_L659

Strain_5_L925

Strain_2_L825

Strain_3_L825b

Strain_5_L600

Strain_4_L925

Strain_2_L322

Strain_1_2_L600

Strain_1_L700

Strain_6_L199

Strain_4_L825b

Strain_1_L950

Strain_4_L527

Strain_5_L163

Strain_1_L825b

Strain_3_L792

Strain_2_L723

Strain_5_L527

Strain_5_L322

Strain_1_L322Strain_1_L723

Strain_4_L202

Strain_3_L199

Strain_3R_L712

Strain_5_L202

Strain_5_L664

Strain_4Qb_L712

Strain_2_L202

Strain_5_L950

Strain_1_L664

Strain_2Qa_L712

Strain_6_L925

Strain_6_L843

Strain_6_L723

Strain_3Qa_L712

Strain_3_L322

Strain_3_L843

Strain_1_L843

Strain_3_L600

Strain_6_L163

Strain_6_L827

Strain_6Rb_L712

Strain_5_L827

Strain_4_L199

Strain_2R_L712

Strain_3_L827

Strain_1Rb_L712

Strain_4_L783

Strain_4_L792

Strain_5_L783

Strain_2_L659

Strain_4_L723

Strain_2_L783

Strain_5Qa_L712

Strain_1_1_L600

Strain_4_L163

Strain_2_L792

Strain_2_L607

Strain_2_L163

Strain_1Qa_L712

Strain_2_L950

Strain_3Qb_L712

Strain_2_L843

Strain_1Qb_L712

Strain_3_L703

Strain_2_L664

Strain_5R_L712

Strain_5_L659

Strain_6_L659

Strain_5_L843

Strain_6R_L712Strain_6_L825

Strain_6_L825b

Strain_3_L607

Strain_4R_L712

Strain_6_L664

Strain_5_L825

Strain_4_L322

Strain_2_L825b

Strain_2Rb_L712

Strain_1_L925

Strain_2_1_L600

Strain_6Qb_L712

Strain_3_L723

Strain_3_L527

Strain_5_L607Strain_5_L792

Strain_4_L950

Strain_2_L925

Strain_1_L703

Strain_4Qa_L712

Strain_3_L700

Strain_3_L783

Strain_5_L825b

Strain_6_L783

Strain_1R_L712

Strain_6_L607

Strain_6_L527

Strain_2Qb_L712

Strain_3_L202

Strain_3_L825

Strain_6_L700

Strain_2_L703

Strain_4_L659

Strain_6_L600

Strain_1_L163

Strain_1_L527

Strain_6Qa_L712

Strain_4_L827

Strain_6_L950

Strain_4_L607

Strain_5_L199

Strain_2_L827

Strain_6_L202

Strain_5Qb_L712

Strain_4_L843

Strain_2_L199

Strain_1_L792

Strain_5_L723

Strain_6_L792

Strain_1_L783

Strain_5_L700

Strain_5Rb_L712

Strain_3_L950

Strain_1_L825

Strain_3Rb_L712

Strain_5_L703

Strain_6_L322

Strain_3_L664

Strain_1_L199

Strain_4_L600

Strain_4_L825

Strain_1_L202

Strain_2_2_L600

Achtman, M. et al. PLOS Path, 2012

• Improved genetic characterisation of the isolates • Fast detection of virulence and resistance genes• Higher genetic discrimination among isolates

Improved outbreak detection and source tracing• Better evaluation of the contribution of the food/animal sources to the burden of

illness in humans (joint multisectoral analysis) Improved identification of the control options

• Improved understanding of the evolutionary and mechanisms and ecology (metadata needed)

• Shorter time for output production and universal approach for all pathogens

EURL E.coli, 2018

Rapid diffusion of platforms for WGS analysis

on: Omicsmap.com June, 17, 2015

Source: https://www.efsa.europa.eu/it/supporting/pub/en-1432

Regional level

WGS capability in the EU

ECDC FWD NEXT expert group

• The state of deployment for use of WGS and

culture independent diagnostics in outbreaks

and surveillance for FWD pathogens

• How to support the gradual implementation

of the new technology across MSs, including

harmonised data analysis and interpretation

• Technical support needs for inter-laboratory ring

trials or other type of analytical/epidemiological

validation studies, in complement with other

international initiatives

2014

EURLs Working Group on NGS (Whole Genome Sequencing)

Appointed by The EC to promote the use of NGS across the EURLs' networks, build capacity within the EU and ensure liaison with the work of EFSA and ECDC on the WGS mandate sent by the Commission.

MEMBERSHIP

EURL E. coli (coordinator)EURL Listeria monocytogenesEURL CPSEURL SalmonellaEURL CampylobacterEURL ParasitesEURL AREURL Food borne virusesObservers: SANTE G4, EFSA, ECDC

Members of the WG agree to contribute to the coordination of activities on NGS, notably on PT schemes, WGS data analysis, etc... with a view to achieve the different tasks of the WG by 2020.

Two physical meetings per year

2017

EURLs Working Group on NGS (Tasks and Methodology)

To development of guidance documents or SOPs to support NRLs.Harmonization of the actions to build the capacity at EU level towards the use of NGS

1. Proficiency Testing: (EURL AR lead) Development of guidance documents or SOPs defining the architecture of NGS-based PT schemes in terms of methodology of PT organisation, of data to be extracted from WGS and returned to the PT provider and of how to analyse PT results by the EURLs.

2. WGS laboratory procedures: (EURLP lead) Evaluation of Nucleic acid Extraction SOPs available or developed by existing projects to validate the performances and suitability for the NRLs network.

3. Bioinformatics tools: (EURL VTEC lead) Development of guidance documents or reports on different bioinformatics tools for NGS data mining. Develop, set up, validate (if possible), and produce tutorials for bioinformatics tools and pipelines.

4. WGS Cluster Analysis: (EURL Campy lead) Development of tutorials, guidance documents defining criteria of selection of software (open source and commercial).

5. Bench marking: (EURL Listeria lead) Development of guidance document defining how to bench marking analytical methods and pipelines.

6. Trainings on NGS: (EURL CPS lead) Definition of a common structure for training events (courses, e-Learning, ad hoc training stages, organised jointly or by the single EURLs)

7. Reference and confirmatory testing using NGS: (EURL Salmonella Lead) Giving suggestions for control strains for testing pipelines; development of guidance document on the use of NGS for confirmatory testing and typing (e.g. use of NGS for Salmonella serotyping, testing for virulence genes of E. coli).

2018

ARIES: infrastructure for genomic analysis

https://aries.iss.it

GENPAT: Activity 2018

Sequenced isolates: N= 2099

Campylobacter

Listeria

Brucella

Salmonella

African Horse Sickness virus(AHSV)

Altro

Bioinformatic analysis in support of National Reference Laboratories (NRL) and Centres

LNR Listeria

LNR Brucella

LNR Campylobacter

CESME

COVEPI

National Reference Centre for Genome Sequencing of pathogeneticmicrorganisms (GENPAT): data bank & bioinformatic analysis (IZS AM)

Interoperability with other information system at national level

National Reference Centre for Genome Sequencing of pathogeneticmicrorganisms (GENPAT): data bank & bioinformatic analysis (BIOINFODB)

Routine WGS of L. monocytogenes 2017- 2018:identified clusters

The regional workflow:

• 4. 5M inhabitants

• 8 hospital laboratories

• 1 regional ref. laboratory (IZS)

• routine typing and subtyping by:

PFGE-MLVA-WGS (Salmonella)

WGS (Listeria monocytogenes)

• Joint database for human, food, animal isolates

• Salmonella: 800-900/year (humans) 800-1000/ year (other sources)

• Listeria: 20-40/year (humans)

Molecular surveillance of foodborne pathogens in Emilia-Romagna region

Many activities supporting the shift in the surveillance paradigm

• Few initiatives aimed at supporting the usability of NGS data for the purposes of risk assessment and risk management

• Need to implement a common framework by sharing the WGS-based surveillance framework background and same ‘language’

A shift in the paradigm of integrated molecular surveillance

of foodborne pathogens

CA

CA

Project title: Harmonization of the integrative molecular surveillance of foodborne pathogens of priority in the light of the technological shift towards Next Generation Sequencing (NGS).Project link to the Delphi priorities / EFSA Strategy topics

- Zoonosis (in general including bio-hazard )- Microbial food pathogensProject description:

The focus of the project will be to assist the EU in the transition of the molecular typing approach from PFGE and MLVA to NGS and will concern the foodborne pathogens included in the priority list of Dir. CE 99/2003. Objectives:To build and consolidate the capacity in the production of NGS data.To build and share knowledge on the use of NGS data to characterize foodborne microbial hazards.To increase skills and awareness in the use of NGS data in the integrative molecular surveillance of foodborne pathogens.The objectives will be achieved through the following activities:Hands-on training programs dedicated to the production, analysis and use of NGS data.Workshops to discuss: i) the experiences accumulated on NGS applied to subtype foodborne pathogens; ii) the gaps and data needs for a full application of NGS to integrative molecular surveillance of foodborne pathogens.Connection with the existing initiative at the EU level (Horizon 2020).Participation in the International Forums for the subject matter.

Aims:

• To support the shift in the molecular typing of foodborne pathogenstowards WGS

• To improve the skill and know-how of risk assessors in the use of WGS data for the integrated molecular surveillance of foodbornepathogens in view of:

• Outbreak preparedness

• Improved characterization of the risks posed to humans by the animal and food chains

• Better communication of foodborne risks to policy-makers and competent authorities

• Prioritization of the surveillance activities

• Prioritization of control options in foodborne outbreaks(improvement of risk management)

• Better communication to consumers and public opinion

• To join under the same conceptual framework all the actors involvedin the activities of risk assessment and risk management of foodborneillness with a multidisciplinary “One-Health” approach

Conclusions

• Surveillance and control of foodborne illness benefit importantly from the implementation of new technological platform for microbial WGS data production, collation, analysis and interpretation

• To fully exploit the potential benefits of these tools it is necessary to support the transition from the classical approach to a WGS-based epidemiological surveillance

• There is the need to develop a new conceptual framework for the surveillance of foodborne illness and a common language among all actors involved in the production, analysis, interpretation and communication of the information and its use for the risk assessment purposes

• Complex approach, implicating that the skills, knowledge, experiences and expertise disseminatedamong different actors and sectors of the WGS surveillance should be joined

• The RAA collaborative project aims to achieve a cultural hub to cover the existing gaps and to connectthe scientific, technological and operational aspects necessary for a multidisciplinary WGS-basedframework of surveillance of foodborne illness

• EFSA is a key partner since it represents an integral part of the technological transition process of surveillance of foodborne hazards at EU level. It is in a privileged position for catching the needs of MSsand for stimulating their empowerment.

Thank you for your attention!

Acknowledgments:

• Simonetta Bonati (Ministero della Salute)• Rossana Valentini (Ministero della Salute)• Stefano Morabito (Istituto Superiore di Sanità)• Cesare Cammà (Istituto Zooprofilattico G. Caporale)• Stefano Pongolini (Istituto Zooprofilattico Sperimentale

della Lombardia ed Emilia Romagna)