Integrating WGS data into Quantitative Microbial Risk Assessment: - PowerPoint PPT Presentation

Integrating WGS data into Quantitative Microbial Risk Assessment: Refinement of the L. monocytogenes in cold smoked salmon model Lena Fritsch Email: lena.fritsch@anses.fr

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Whole Genome Sequencing 26/04/2018

Whole Genome Sequencing • GWAS • Transcriptomics • …. (Cocolin et al. 2017) 26/04/2018

Genome wide association studies (GWAS) 26/04/2018

Genome wide association studies (GWAS) Trait 1 0 26/04/2018

Genome wide association studies (GWAS) Trait DNA sequencing 1 0 26/04/2018

Genome wide association studies (GWAS) Find associations between genetic variations and observable traits Trait DNA sequencing 1 0 26/04/2018

Genome wide association studies (GWAS) Find associations between genetic variations and observable traits Trait DNA sequencing Biomarker « X » 1 • Genes • SNPs • …. 0 26/04/2018

How to use genomic-data ? Prevalence 10.4% (EFSA, 2015) 26/04/2018

How to use genomic-data ? Prevalence 10.4% (EFSA, 2015) Searching for Biomarker « X » Genomic data 26/04/2018

How to use genomic-data ? Prevalence 10.4% (EFSA, 2015) Searching for Biomarker « X » Genomic data 26/04/2018

How to use genomic-data ? Prevalence 10.4% (EFSA, 2013) Searching for Biomarker « X » Implementation in QMRA Genomic data 26/04/2018

Objective • Cold smoked salmon model (Pouillot et al. 2007/2009)  L. monocytogenes 26/04/2018

Objective • Cold smoked salmon model (Pouillot et al. 2007/2009)  L. monocytogenes EFSA baseline+ Møller-Nielsen et al. 2017 26/04/2018

Objective • Cold smoked salmon model (Pouillot et al. 2007/2009)  L. monocytogenes GWAS Hingston et al. 2017 EFSA baseline+ Møller-Nielsen et al. 2017 26/04/2018

Objective • Cold smoked salmon model (Pouillot et al. 2007/2009)  L. monocytogenes GWAS Hingston et al. 2017 Virulence EFSA baseline+ Maury et al. 2016 Møller-Nielsen et al. 2017 26/04/2018

Dose-Response (FDA, 2003) 26/04/2018

Dose-Response (FDA, 2003) 26/04/2018

Dose-Response (FDA, 2003) 26/04/2018

But which CC correspond to which group? CC1 (Maury et al. 2016) 26/04/2018

But which CC correspond to which group? CC1 (Maury et al. 2016) 26/04/2018

But which CC correspond to which group? CC1 (Maury et al. 2016) 26/04/2018

But which CC correspond to which group? CC1 (Maury et al. 2016) 26/04/2018

Prevalence 10.4% (EFSA, 2013) 26/04/2018

Prevalence 10.4% (EFSA, 2013) Genomic data  Which CCs are present (Møller-Nielsen et al. 2017) 26/04/2018

Prevalence 10.4% (EFSA, 2013) Prevalence [%] Hypervirulent 9.2% Medium virulence 39.1% Hypovirulent 51.7% Genomic data  Which CCs are present (Møller-Nielsen et al. 2017) 26/04/2018

Prevalence 10.4% (EFSA, 2013) Prevalence [%] Hypervirulent 9.2% Medium virulence 39.1% Hypovirulent 51.7% Genomic data  Which CCs are present (Møller-Nielsen et al. 2017) 26/04/2018

Tmin (Hingston et al. 2017) • Biomarker as Genes, SNPs, … • Biomarker full length inlA  adaptation to cold temperature 26/04/2018

Tmin (Hingston et al. 2017) • Biomarker as Genes, SNPs, … • Biomarker full length inlA  adaptation to cold temperature Tmin LG Tmin HG 26/04/2018

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26/04/2018 Results Exposure 51.7% 9.2% 39.1% Hypervirulent Medium Hypovirluent 4.4 % 0.02 % 95.5 % Cases of listeriosis

Results Hypovirluent 0.02 % Exposure 51.7% 39.1% Medium 4.4 % Cases of listeriosis 9.2% Hypervirulent 95.5 % Predicted concentrations in contaminated CSS  2 times less important per 30g for « LG » strains 26/04/2018

Conclusion and perspectives • One of the first approaches (Pielaat et al. 2015) • Strong hypothesis: r-value CCs Clinical Frequency • Issue to take into account food specific prevalence • Near future  Biomarker  Accessible data • Adapting or refinement of intervention strategies 26/04/2018

Many thanks to: Prof. Dr. J.-C. Augustin Dr. Laurent Guillier 26/04/2018

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References • Cocolin, L., Mataragas, M., Bourdichon, F., Doulgeraki, A., Pilet, M.-F., Jagadeesan, B., Rantsiou, K., Phister, T., 2017. Next generation microbiological risk assessment meta-omics: The next need for integration. International journal of food microbiology. • Cocolin, L., Membré, J.-M., Zwietering, M., 2017. Integration of omics into MRA. International journal of food microbiology. Pouillot, R., Goulet, V., Delignette ‐ Muller, M.L., Mahé, A., Cornu, M., 2009. Quantitative Risk Assessment of Listeria monocytogenes in • French Cold ‐ Smoked Salmon: II. Risk Characterization. Risk analysis 29(6), 806-819. EFSA, 2013. Analysis of the baseline survey on the prevalence of Listeria monocytogenes in certain ready ‐ to ‐ eat foods in the EU, 2010– • 2011 Part A: Listeria monocytogenes prevalence estimates. EFSA Journal 11(6). • EFSA BIOHAZ Panel, Ricci, A., Allende, A., Bolton, D., Chemaly, M., Davies, R., Fernández Escámez, P., Girones, R., Herman, L., Koutsoumanis, K., Nørrung, B., Robertson, L., Ru, G., Sanaa, M., Simmons, M., Skandamis, P., Snary, E., Speybroeck, N., Ter Kuile, B., Threlfall, J., Wahlstrom, H., Takkinen, J., Wagner, M., Arcella, D., Da Silva Felicio, M., Georgiadis, M., Messens, W., Lindqvist, R., 2018. Scientific Opinion on the Listeria monocytogenes contamination of ready-to-eat foods and the risk for human health in the EU. EFSA Journal 16(1), 173 pp. . • FDA/FSIS, 2003. Quantitative assessment of relative risk to public health from foodborne Listeria monocytogenes among selected categories of ready-to-eat foods. Food and Drug Administration, U.S. Department of Agriculture, Centers for Disease Control and Prevention. • Hingston, P., Chen, J., Dhillon, B.K., Laing, C., Bertelli, C., Gannon, V., Tasara, T., Allen, K., Brinkman, F.S., Hansen, L.T., 2017. Genotypes Associated with Listeria monocytogenes Isolates Displaying Impaired or Enhanced Tolerances to Cold, Salt, Acid, or Desiccation Stress. Frontiers in Microbiology 8. • Maury, M.M., Tsai, Y.-H., Charlier, C., Touchon, M., Chenal-Francisque, V., Leclercq, A., Criscuolo, A., Gaultier, C., Roussel, S., Brisabois, A., 2016. Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity. Nature genetics 48(3), 308-313. • Møller-Nielsen, E., Björkman, J.T., Kiil, K., Grant, K., Dallman, et al. 2017. Closing gaps for performing a risk assessment on Listeria monocytogenes in ready ‐ to ‐ eat (RTE) foods: activity 3, the comparison of isolates from different compartments along the food chain, and from humans using whole genome sequencing (WGS) analysis. EFSA Supporting Publications 14(2). • Pielaat, A., Boer, M.P., Wijnands, L.M., van Hoek, A.H., Bouw, E., Barker, G.C., Teunis, P.F., Aarts, H.J., Franz, E., 2015. First step in using molecular data for microbial food safety risk assessment; hazard identification of Escherichia coli O157: H7 by coupling genomic data with in vitro adherence to human epithelial cells. International journal of food microbiology 213, 130-138. • Pouillot, R., Hoelzer, K., Chen, Y., Dennis, S.B., 2015. Listeria monocytogenes dose response revisited—incorporating adjustments for variability in strain virulence and host susceptibility. Risk Analysis 35(1), 90-108. • Pouillot, R., Klontz, K.C., Chen, Y., Burall, L.S., Macarisin, D., Doyle, M., Bally, K.M., Strain, E., Datta, A.R., Hammack, T.S., 2016. Infectious dose of Listeria monocytogenes in outbreak linked to ice cream, United States, 2015. Emerging infectious diseases 22(12), 2113. Pouillot, R., Miconnet, N., Afchain, A.L., Delignette ‐ Muller, M.L., Beaufort, A., Rosso, L., Denis, J.B., Cornu, M., 2007. Quantitative risk • assessment of Listeria monocytogenes in French cold ‐ smoked salmon: I. Quantitative exposure assessment. Risk analysis 27(3), 683-700. 26/04/2018