http://tiny.cc/faowgsworkshop Potential usefulness of genome sequencing technology on food safety management - France. Presentation from the FAO expert workshop on practical applications of Whole Genome Sequencing (WGS) for food safety management - 7-8 December 2015, Rome, Italy.

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WGS for food safety management
in France :
Example for Listeria monocytogenes
Dr. Sophie Roussel, Anses, Maisons-
Alfort; France
Sophie.roussel@anses.fr

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Anses-presentation
12 Laboratories -18 sites
Laboratory for Food Safety
Biological agents than can affect food
safety and quality in a public health goal
Better control the food quality and
hygiene from the food industry to food
services,
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 Bioinformaticians
full 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 Microbiology
Molecular 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

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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 trials
Annual training sessions;
workshops
-the National public health laboratories
(NPHL) network
-With other EURLs
-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)
Step 2 : Harmonisation

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-the French network .
-the NRL network
Proficiency testing trials
Annual training sessions;
workshops
-the National public health laboratories
(NPHL) network
-With other EURLs
-Testing .
-Profil interpretation
-Database curation
- Data and cluster analysis
Comparison of PFGE SOPs between
European and US partners
Step 3 : Molecular PFGE
databases
-European typing databases
Step 1 : Development of SOPs
(Standard Operating Procedures)
Step 2 : Harmonisation
-EFSA-ECDC database : PFGE data from
human and no human isolates
-EURL : curator of the non-human
isolates

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-the French network .
-the NRL network
Proficiency testing trials
Annual training sessions;
workshops
-the National public health laboratories
(NPHL) network
-With other EURLs
French, European and
International and PFGE-based
surveillance networks
-Testing .
-Profil interpretation
-Database curation
- Data and cluster analysis
Comparison of PFGE SOPs between
European and US partners
Step 3 : Molecular PFGE
databases
-European typing databases
Step 1 : Development of SOPs
(Standard Operating Procedures)
Step 4 : Epidémiosurveillance
improved
Duration :5 years
Step 2 : Harmonisation
-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 of
the 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 between
epidemiologically related / not-epidemiologically related
strains.

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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 Anses
centers
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 and
clinical strains ;
 Explore the genetic diversity of strain populations in France and
in Europe
 Assess the epidemiological relationship of strains from the
different sources
 Identify the presence of molecular markers that may explain
the virulence / ecophysiology differences observed within the
strain 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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14
WGS : a maximal resolution typing tool for molecular
surveillance and outbreak investigation ?
WGS : Information on
pathogen genomes (species
identification, drug
resistance, virulence,
evolution…).
MLST : Global epidemiology
Population biology
Phylogeny
SérotypeLineage MLST PFGE WGS
Discriminatory degree
PFGE : The current international
standard -Outbreak
investigation

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WGS : a roadmap to better manage the food safety…
Research projects
Molecular markers underlying
evolution, host specificity,
virulence, transmissioon
ecophysiology…
1. Stimulate all the
partner networks to
track and type more
strains (+ historical
strains)
3.Harmonization within
clinical and food reference
lab networks
4. Share relevant
information/
databases
Networking
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
standardized
nomenclature
Validation by
reference
laboratories

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A standardized (cgMLST) : intermediate between
SNP-based phylogeny and MLST ?
Molecular
surveillance
Molecular
methods
Genotyping –based
surveillancePFGE
SNPs
MLST
allele-based typing scheme
Wg MLST –cgMLST (more
discriniating than
MLST)(Ruppitsch et al., 2015) ;
Jolley; Miaden, 2014);
Genomic-based
surveillance
Nomenclature standardized
Central database; not enough
discriminating
interpretation of data easier
and more accessible than
PFGE
Central databases (ex.
BIGSDB)
highly discriminatory, less
standardized
No standardized
nomenclature 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 large
national / international surveillance networks.
• The replacement of PFGE with a new WGS-based method must be
conducted gradually to avoid the loss of precious historic
information 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 Henri
Trinh-Tam Dao
Karol Romero
Jean-François Mariet
Damien Michelon
Benjamin Félix
Renaud Lailler , david Albert
Maisons-Alfort Food Safety
laboratory
Michel-Yves Mistou
Laurent Guillier
Nicolas Randomski
Arnaud Felten
Olivier Firmesse
Anses WGS Platform
Yannick Blanchard
EURL Lm coordination
Bertrand Lombard
Adrien Asséré ; Marie-Christine Salvi
Food NRL network, in particular (AT, BE, DE,
FI, IE, IT, NL, SE)
Vicdalia Aniela Acciari
Nadine Botteldoorn
Els Biesta-Peters
Bernadette Hickey
Luigi Iannetti
DTU-food :
FM Aarestrup
R. Hendriksen
SSI
Eva Moller Nielsen
Jonas Larsson
CDC
Peter Gerner-Smidt
Applied Math’s team
Sylvia Kleta
Ariane Pietzka
Leila Rantala
Susanne Thisted Lambertz
Caroliene van Heerwaarden

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Thank you for your attention !