WGS for food safety management in France : Example for Listeria monocytogenes

Transcription

1 WGS for food safety management in France : Example for Listeria monocytogenes Dr. Sophie Roussel, Anses, Maisons- Alfort; France Sophie.roussel@anses.fr 1/59

2 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 2/59

3 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 3/59

4 WGS and Bioinformatic analysis capacities at Anses : Laboratory for food safety LABORATORY for FOOD SAFETY - Maisons-Alfort Physico Chemical department Pesticides and marine biotoxins Unit Identypath" national platform Microbiology department AntibioResistance Unit GAMeR Geno-Analysis Modelisation : and Risk Assessment Trace metals and minerals -Genotyping -Illunina Mi seq Central Laboratory for Veterinary Services Enteric viruses Unit Listeria team (12 persons) Salmonella-E.coli- Listeria (SEL) Unit Staphylococci, Bacillus, Clostridium and milk Unit -1. Statistician -1. Bioinformatian, -1 expert in genotyping data analysis 4/59

5 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 ; Coordinate / manage European network of 37 NRLs Stimulate partners to do typing Roadmap 5/59

6 Step 1 : Development of SOPs (Standard Operating Procedures) -Testing. -Profil interpretation -Database curation - Data and cluster analysis Comparison of PFGE SOPs between European and US partners - 6/59

7 Step 1 : Development of SOPs (Standard Operating Procedures) -Testing. -Profil interpretation -Database curation - Data and cluster analysis Comparison of PFGE SOPs between European and US partners Step 2 : Harmonisation -the French network. -the NRL network Proficiency testing trials Annual training sessions; workshops -the National public health laboratories (NPHL) network -With other EURLs 7/59

8 Step 1 : Development of SOPs (Standard Operating Procedures) -Testing. -Profil interpretation -Database curation - Data and cluster analysis Comparison of PFGE SOPs between European and US partners Step 2 : Harmonisation -the French network. -the NRL network Proficiency testing trials Annual training sessions; workshops -the National public health laboratories (NPHL) network -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 8/59

9 Step 1 : Development of SOPs (Standard Operating Procedures) -Testing. -Profil interpretation -Database curation - Data and cluster analysis Comparison of PFGE SOPs between European and US partners Step 2 : Harmonisation -the French network. -the NRL network Proficiency testing trials Annual training sessions; workshops -the National public health laboratories (NPHL) network -With other EURLs Duration :5 years Step 4 : Epidémiosurveillance improved French, European and International and PFGE-based surveillance networks 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 9/59

10 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 10/59

11 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. 11/59

12 1) The European project ( ) 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 ( ) EURL for Lm European Union Reference Laboratory for Listeria monocytogenes In close collaboration with : The EURL/NRL (in particular IT, DE) network and other Anses centers 12/59

13 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 different sources strains from the Identify the presence of molecular markers that may explain the virulence / ecophysiology differences observed within the strain populations. PhD project Anses /DTU-food ( ) 2 years-european project ( ) 18 month project -National Grant) ( ) 13/59

14 WGS : a maximal resolution typing tool for molecular surveillance and outbreak investigation? PFGE : The current international standard -Outbreak investigation Discriminatory degree Lineage Sérotype MLST PFGE WGS MLST : Global epidemiology Population biology Phylogeny WGS : Information on pathogen genomes (species identification, drug resistance, virulence, evolution ) /59

15 WGS : a roadmap to better manage the food safety 1. Stimulate all the partner networks to track and type more strains (+ historical strains) type of WGS data useful for surveillance? Research projects Molecular markers underlying evolution, host specificity, virulence, transmissioon ecophysiology 2. Design a rational typing scheme for outbreak investigation Validation by reference laboratories Define standardized nomenclature Competent authorithies : facilitate communication and data sharing between all the actors 3.Harmonization within clinical and food reference lab networks 4. Share relevant information/ databases Networking 15/59

16 A standardized (cgmlst) : intermediate between SNP-based phylogeny and MLST? Molecular methods Molecular surveillance PFGE Genotyping based surveillance No standardized nomenclature and profile interpretation difficult MLST Nomenclature standardized Central database; not enough discriminating allele-based typing scheme Wg MLST cgmlst (more discriniating than MLST)(Ruppitsch et al., 2015) ; Jolley; Miaden, 2014); Genomic-based surveillance interpretation of data easier and more accessible than PFGE Central databases (ex. BIGSDB) SNPs highly discriminatory, less standardized 16/59

17 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 17/59

18 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 Acknowledgement 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 SSI Eva Moller Nielsen Jonas Larsson Applied Math s team Sylvia Kleta Ariane Pietzka Leila Rantala Susanne Thisted Lambertz Caroliene van Heerwaarden DTU-food : FM Aarestrup R. Hendriksen CDC Peter Gerner-Smidt 18/59

19 Thank you for your attention! 19/59