Whole Genome Sequencing (WGS) for food safety management in France: Example for Listeria monocytogenes

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WGS for food safety management in France :

Example for Listeria monocytogenes

Dr. Sophie Roussel, Anses, Maisons-Alfort; France

[email protected]

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Anses-presentation

12 Laboratories -18 sites

Laboratory for Food Safety

Biological agents than can affect foodsafety and quality in a public health goal

Better control the food quality andhygiene from the food industry to foodservices,

Risk assessment analysis

Reference and research Scientific and technical expertises Monitoring and epidemio-surveillance

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WGS and Bioinformatic analysis capacities at Anses The WGS national plateform

3 Bioinformaticiansfull time

-2 technicians

-1 Ion Proton TM, -2 High Seq

-3 Mi seq-1 Pacbio

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WGS and Bioinformatic analysis capacities at Anses : Laboratory for food safety

Pesticides and

marine biotoxins

Unit

Trace metals and

minerals

Physico Chemical

department

AntibioResistance

Unit

GAMeR Geno-Analysis

Modelisation : and Risk

Assessment

Identypath"

national platform

Central

Laboratory for

Veterinary

Services

Microbiology department

Enteric

viruses Unit

Staphylococci,

Bacillus,

Clostridium and

milk Unit

Salmonella-E.coli-

Listeria

(SEL) Unit

LABORATORY for FOOD SAFETY - Maisons-Alfort

-1. Statistician-1. Bioinformatian , -1 expert in genotyping data analysis

-Genotyping-Illunina Mi seq

Listeria team(12 persons)

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Listeria monocytogenes AnsesTeam strains of food, feed, environment, animal

Detection-Enu meration, Ecophysiology,Predictive MicrobiologyMolecular typing Epidemiosurveillace

National Reference Lab (NRL) since 2001

French network partners

European Reference Lab (EURL) since 2006

(DG SANTE) Regulation EC 776/2006 ; https://eurl-listeria.anses.fr

Coordinate / manage European

network of 37 NRLs

Stimulate partners to do typing

Roadmap

https://eurl-listeria.anses.fr/

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-

-Testing . -Profil interpretation-Database curation - Data and cluster analysis

Comparison of PFGE SOPs between European and US partners

Step 1 : Development of SOPs (Standard Operating Procedures)

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-the French network . -the NRL network Proficiency testing trialsAnnual training sessions; workshops

-the National public health laboratories(NPHL) network

-With other EURLs




Step 2 : Harmonisation

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-With other EURLs



Step 3 : Molecular PFGE databases

-European typing databases



-EFSA-ECDC database : PFGE data from human and no human isolates

-EURL : curator of the non-human isolates

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-With other EURLs

French, European and International and PFGE-based

surveillance networks



Step 3 : Molecular PFGE databases

-European typing databases


Step 4 : Epidémiosurveillanceimproved

Duration :5 years


-EFSA-ECDC database : PFGE data from human and no human isolates

-EURL : curator of the non-human isolates

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Dispatch of PFGE protocols -Communication

In 2015 : among the French / partner network : No lab is using WGS for the surveillance in routine.

Among the European NRL network :1 lab use WGS (PHE)21/37 NRLs carry out PFGE -Some NRLs don’t type at all

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Assess WGS technology as a typing tool

Within two different analytic development projects Similar aims :

• 1. Develop WGS harmonized protocols at each of the steps ofthe process

• 2. Backwards comparability between WGS and PFGE :

Set up of a EU wide relevant strain/ genome collection

Set a cut-off for WGS among the genetic diversity of L.monocytogenes

Cluster definition : assess the genetic distance betweenepidemiologically related / not-epidemiologically relatedstrains.

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COllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe

-Coordinator : DTU-Food, (Franck Aarestrup’s team)-29 European partners ; 15 Work packages-Anses : Maisons-alfort laboratory for food safety ; Anses WGS platform (Ploufragan, Brittany).

2) The EURL project on WGS typing(2015-2017)

In close collaboration with :The EURL/NRL (in particular IT, DE) network and other Ansescenters

1) The European project(2015-2020)

EURL for Lm

European Union Reference

Laboratory for

Listeria monocytogenes

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Assess the typing potential of WGS /research projects

Overview of the genetic structure of populations of food andclinical strains ;

Explore the genetic diversity of strain populations in France andin Europe

Assess the epidemiological relationship of strains from thedifferent sources

Identify the presence of molecular markers that may explainthe virulence / ecophysiology differences observed within thestrain populations.

PhD project Anses /DTU-food (2013-2016)

2 years-European project (2014-2016)

18 month project -National Grant) (2015-2017)

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WGS : a maximal resolution typing tool for molecularsurveillance and outbreak investigation ?

WGS : Information on pathogen genomes (species

identification, drugresistance, virulence,

evolution…).

MLST : Global epidemiology

Population biology

Phylogeny

SérotypeLineage MLST PFGE WGS

Discriminatory degreePFGE : The current international

standard -Outbreak

investigation

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WGS : a roadmap to better manage the food safety…

Research projectsMolecular markers underlying

evolution, host specificity, virulence, transmissioon

ecophysiology…

1. Stimulate all the partner networks to track and type more strains (+ historical

strains)

3.Harmonization withinclinical and food reference

lab networks

4. Share relevant information/

databasesNetworking

Competent authorithies: facilitate

communication and data sharing between all the

actors

2. Design a rational typing

scheme for outbreak

investigation

type of WGS data useful for surveillance ?

Define standardizednomenclature

Validation by reference

laboratories

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A standardized (cgMLST) : intermediate between SNP-based phylogeny and MLST ?

Molecularsurveillance

Molecularmethods

Genotyping –basedsurveillancePFGE

SNPs

MLST

allele-based typing scheme Wg MLST –cgMLST (more discriniating thanMLST)(Ruppitsch et al., 2015) ; Jolley; Miaden, 2014);

Genomic-basedsurveillance

Nomenclature standardizedCentral database; not enoughdiscriminating

interpretation of data easier and more accessible than PFGECentral databases (ex. BIGSDB)

highly discriminatory, less standardized

No standardizednomenclature and profile interpretation difficult

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Perspectives : WGS in France /Europe– replacement of PFGE ?

• Easier to replace PFGE with WGS at the local level than in largenational / international surveillance networks.

• The replacement of PFGE with a new WGS-based method must beconducted gradually to avoid the loss of precious historicinformation generated over many years.

• Underscored by the continued use of PFGE.

• In French lab/ European countries with limited financial ressources,PFGE will probably prevail in the coming years

• But these labs may rapidly adopt WGS once it is practical to use

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Acknowledgement

SEL Unit Listeria team - molecular typing team Clémentine HenriTrinh-Tam DaoKarol RomeroJean-François MarietDamien MichelonBenjamin FélixRenaud Lailler , david Albert

Maisons-Alfort Food Safety

laboratoryMichel-Yves MistouLaurent GuillierNicolas RandomskiArnaud FeltenOlivier Firmesse

Anses WGS PlatformYannick Blanchard

EURL Lm coordinationBertrand LombardAdrien Asséré ; Marie-Christine Salvi

Food NRL network, in particular (AT, BE, DE, FI, IE, IT, NL, SE) Vicdalia Aniela AcciariNadine BotteldoornEls Biesta-PetersBernadette HickeyLuigi Iannetti

DTU-food :FM AarestrupR. Hendriksen

SSIEva Moller NielsenJonas Larsson

CDCPeter Gerner-Smidt

Applied Math’s team

Sylvia KletaAriane PietzkaLeila RantalaSusanne Thisted LambertzCaroliene van Heerwaarden

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Thank you for your attention !

Education

Whole Genome Sequencing (WGS) for food safety management in France: Example for Listeria monocytogenes