). Estonia, G. Mandilara, ;. Shigella, . Vtec, V. Listeria et al., Alexandre Leclercq (Institut Pasteur, Biology of Infection Unit, Inserm U1117, and Paris Descartes University

C. M. De-noordhout, B. Devleesschauwer, F. J. Angulo, G. Verbeke, J. Haagsma et al., The global burden of listeriosis: a systematic review and meta-analysis, Lancet Infect Dis, vol.14, issue.11, p.25241232, 2014.

C. Charlier, É. Perrodeau, A. Leclercq, B. Cazenave, B. Pilmis et al., MONALISA study group. Clinical features and prognostic factors of listeriosis: the MONALISA national prospective cohort study, Lancet Infect Dis, vol.17, issue.5, p.28139432, 2017.

R. F. Lamont, J. Sobel, S. Mazaki-tovi, J. P. Kusanovic, E. Vaisbuch et al., Listeriosis in human pregnancy: a systematic review, J Perinat Med, vol.39, issue.3, p.21517700, 2011.

, Surveillance Atlas of Infectious Diseases. Stockholm: ECDC, p.10, 2016.

V. Goulet, L. A. King, V. Vaillant, and H. De-valk, What is the incubation period for listeriosis?, BMC Infect Dis, vol.13, issue.1, p.23305174, 2013.

J. Lundén, T. Autio, A. Markkula, S. Hellström, and H. Korkeala, Adaptive and cross-adaptive responses of persistent and nonpersistent Listeria monocytogenes strains to disinfectants, Int J Food Microbiol, vol.82, issue.3, pp.265-72, 2003.

R. Keto-timonen, R. Tolvanen, J. Lundén, and H. Korkeala, An 8-year surveillance of the diversity and persistence of Listeria monocytogenes in a chilled food processing plant analyzed by amplified fragment length polymorphism, J Food Prot, vol.70, issue.8, p.17803143, 2007.

P. Gerner-smidt, K. Hise, J. Kincaid, S. Hunter, S. Rolando et al., PulseNet USA: a five-year update, Foodborne Pathog Dis, vol.3, issue.1, p.16602975, 2006.

B. R. Jackson, C. Tarr, E. Strain, K. A. Jackson, A. Conrad et al., Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation, Clin Infect Dis, vol.63, issue.3, p.27090985, 2016.

A. Moura, A. Criscuolo, H. Pouseele, M. M. Maury, A. Leclercq et al., Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes, Nat Microbiol, vol.2, issue.2, p.27723724, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01415883

A. Moura, M. Tourdjman, A. Leclercq, E. Hamelin, E. Laurent et al., Real-Time Whole-Genome Sequencing for Surveillance of Listeria monocytogenes, France. Emerg Infect Dis, vol.23, p.28643628, 2017.

, ECDC roadmap for integration of molecular and genomic typing into European-level surveillance and epidemic preparedness -Version 2.1, pp.2016-2019, 2016.

A. Van-belkum, P. T. Tassios, L. Dijkshoorn, S. Haeggman, B. Cookson et al., European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group on Epidemiological Markers (ESGEM). Guidelines for the validation and application of typing methods for use in bacterial epidemiology

, Clin Microbiol Infect, vol.13, issue.3, p.17716294, 2007.

A. Mellmann, D. Harmsen, C. A. Cummings, E. B. Zentz, S. R. Leopold et al., Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology

, PLoS One, vol.6, issue.7, p.21799941, 2011.

M. C. Maiden, M. J. Jansen-van-rensburg, J. E. Bray, S. G. Earle, S. A. Ford et al., MLST revisited: the gene-by-gene approach to bacterial genomics, Nat Rev Microbiol, vol.11, issue.10, p.23979428, 2013.

, Expert Opinion on the introduction of next-generation typing methods for food-and waterborne diseases in the EU and EEA, 2015.

C. Nadon, I. Van-walle, P. Gerner-smidt, J. Campos, I. Chinen et al., FWD-NEXT Expert Panel. PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance, Euro Surveill, vol.22, issue.23, p.28662764, 2017.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, issue.15, p.24695404, 2014.

A. Bankevich, S. Nurk, D. Antipov, A. A. Gurevich, M. Dvorkin et al., SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J Comput Biol, vol.19, issue.5, p.22506599, 2012.

D. R. Zerbino and E. Birney, Velvet: algorithms for de novo short read assembly using de Bruijn graphs, Genome Res, vol.18, issue.5, p.18349386, 2008.

H. Li and R. Durbin, Fast and accurate long-read alignment with Burrows-Wheeler transform, Bioinformatics, vol.26, issue.5, pp.589-95, 2010.

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat Methods, vol.9, issue.4, p.22388286, 2012.

W. Ruppitsch, A. Pietzka, K. Prior, S. Bletz, H. L. Fernandez et al., Defining and evaluating a core genome multilocus sequence typing scheme for whole-genome sequence-based typing of Listeria monocytogenes, J Clin Microbiol, vol.53, issue.9, p.26135865, 2015.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J Mol Biol, vol.215, issue.3, pp.403-413, 1990.

M. M. Maury, Y. H. Tsai, C. Charlier, M. Touchon, V. Chenal-francisque et al., Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity, Nat Genet, vol.48, issue.3, p.26829754, 2016.

A. Holch, K. Webb, O. Lukjancenko, D. Ussery, B. M. Rosenthal et al., Genome sequencing identifies two nearly unchanged strains of persistent Listeria monocytogenes isolated at two different fish processing plants sampled 6 years apart

, Appl Environ Microbiol, vol.79, issue.9, p.23435887, 2013.

D. Schmid, F. Allerberger, S. Huhulescu, A. Pietzka, C. Amar et al., Whole genome sequencing as a tool to investigate a cluster of seven cases of listeriosis in Austria and Germany, Clin Microbiol Infect, vol.20, issue.5, p.24698214, 2014.

M. J. Stasiewicz, H. F. Oliver, M. Wiedmann, and H. C. Den-bakker, Whole-Genome Sequencing Allows for Improved Identification of Persistent Listeria monocytogenes in Food-Associated Environments, Appl Environ Microbiol, vol.81, issue.17, p.26116683, 2015.

R. H. Orsi, M. L. Borowsky, P. Lauer, S. K. Young, C. Nusbaum et al., Short-term genome evolution of Listeria monocytogenes in a non-controlled environment, BMC Genomics, vol.9, issue.1, p.19014550, 2008.

S. Gillesberg-lassen, S. Ethelberg, J. T. Björkman, T. Jensen, G. Sørensen et al., Two listeria outbreaks caused by smoked fish consumption-using whole-genome sequencing for outbreak investigations, Clin Microbiol Infect, vol.22, issue.7, p.27145209, 2016.

, The ECDC-EFSA molecular typing database for European Union public health protection, European Collaborative Projects (Euroreference), vol.2, pp.4-12, 2017.

N. Field, T. Cohen, M. J. Struelens, D. Palm, B. Cookson et al., Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID): an extension of the STROBE statement, Lancet Infect Dis, vol.14, issue.4, pp.341-52, 2014.

;. Efsa-biohaz-panel, A. Ricci, A. Allende, D. Bolton, M. Chemaly et al., Scientific opinion on the Listeria monocytogenes contamination of ready-to-eat foods and the risk for human health in the EU, EFSA Panel on Biological Hazards), vol.16, p.5134, 2018.

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