M. Lecuit, Understanding how Listeria monocytogenes targets and crosses host barriers, Clin Microbiol Infect, vol.11, pp.430-436, 2005.

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, pp.30521-30528, 2017.

V. Goulet, C. Hedberg, L. Monnier, A. De-valk, and H. , Increasing incidence of listeriosis in France and other European countries, Emerg Infect Dis, vol.14, pp.734-774, 2008.

, European Centre for Disease Prevention and Control. Surveillance of seven priority food-and waterborne diseases in the EU/EEA. Stockholm, 2015.

E. Scallan, R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, M. A. Widdowson et al., Foodborne illness acquired in the United States-major pathogens, Emerg Infect Dis, vol.17, pp.7-15, 2011.

H. De-valk, V. Vaillant, C. Jacquet, J. Rocourt, L. Querrec et al., Two consecutive nationwide outbreaks of listeriosis in France, Am J Epidemiol, vol.154, pp.944-50, 1999.

E. J. Cartwright, K. A. Jackson, S. D. Johnson, L. M. Graves, B. J. Silk et al., Listeriosis outbreaks and associated food vehicles, Emerg Infect Dis, vol.19, pp.1-9, 1998.

K. E. Heiman, V. B. Garalde, M. Gronostaj, K. Jackson, S. Beam et al., Multistate outbreak of listeriosis caused by imported cheese and evidence of cross-contamination of other cheeses, Epidemiol Infect, vol.144, pp.1-11, 2012.

K. Jensen, A. Nielsen, E. M. Björkman, J. T. Jensen, T. Müller et al., Whole-genome sequencing used to investigate a nationwide outbreak of listeriosis caused by ready-toeat delicatessen meat, Clin Infect Dis, vol.63, pp.64-70, 2014.

R. Fretz, U. Sagel, W. Ruppitsch, A. Pietzka, A. Stöger et al., Listeriosis outbreak caused by acid curd cheese Quargel, Austria and Germany, Euro Surveill, vol.15, pp.2009-2019, 2009.

A. Leclercq, C. Charlier, and M. Lecuit, Global burden of listeriosis: the tip of the iceberg, Lancet Infect Dis, vol.14, pp.1027-1035, 2014.

V. Ferreira, M. Wiedmann, P. Teixeira, and M. J. Stasiewicz, Listeria monocytogenes persistence in food-associated environments: epidemiology, strain characteristics, and implications for public health, J Food Prot, vol.77, pp.150-70, 2014.

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, pp.3715-3727, 2013.

M. K. Thomas, R. Vriezen, J. M. Farber, A. Currie, W. Schlech et al., Economic cost of a Listeria monocytogenes outbreak in Canada, Foodborne Pathog Dis, vol.12, pp.966-71, 2008.

. Eur-lex, Access to European Union law, p.2017

, United States Department of Agriculture. Food Safety and Inspection Service. Compliance guides index

L. M. Graves and B. Swaminathan, PulseNet standardized protocol for subtyping Listeria monocytogenes by macrorestriction and pulsedfield gel electrophoresis, Int J Food Microbiol, vol.65, pp.501-509, 2001.

P. Martin, C. Jacquet, V. Goulet, V. Vaillant, D. Valk et al., Participants in the PulseNet Europe Feasibility Study. Pulsed-field gel electrophoresis of Listeria monocytogenes strains: the PulseNet Europe Feasibility Study, vol.3, pp.303-311, 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, pp.380-386, 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, p.16185, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01415883

A. J. Sabat, A. Budimir, D. Nashev, R. Sá-leão, J. Van-dijl et al., ESCMID Study Group of Epidemiological Markers (ESGEM). Overview of molecular typing methods for outbreak detection and epidemiological surveillance, Euro Surveill, vol.18, p.20380, 2013.

H. C. Bakker, M. W. Allard, D. Bopp, E. W. Brown, J. Fontana et al., Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar enteritidis, Emerg Infect Dis, vol.20, pp.1306-1320, 2014.

S. K. Sheppard, K. A. Jolley, and M. Maiden, A gene-by-gene approach to bacterial population genomics: whole genome MLST of Campylobacter, Genes (Basel), vol.3, pp.261-77, 2012.

M. 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, pp.728-764, 2013.

H. B. Bratcher, C. Corton, K. A. Jolley, J. Parkhill, and M. C. Maiden, A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes, BMC Genomics, vol.15, p.1138, 2014.

T. A. Kohl, R. Diel, D. Harmsen, J. Rothgänger, K. M. Walter et al., Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach, J Clin Microbiol, vol.52, pp.2479-86, 2014.

K. A. Jolley, D. Hill, H. B. Bratcher, O. B. Harrison, I. M. Feavers et al., Resolution of a meningococcal disease outbreak from whole-genome sequence data with rapid web-based analysis methods, J Clin Microbiol, vol.50, pp.3046-53, 2012.

M. De-been, M. Pinholt, J. Top, S. Bletz, A. Mellmann et al., Core genome multilocus sequence typing scheme for highresolution typing of Enterococcus faecium, J Clin Microbiol, vol.53, pp.3788-97, 2015.

J. Moran-gilad, K. Prior, E. Yakunin, T. G. Harrison, A. Underwood et al., Design and application of a core genome multilocus sequence typing scheme for investigation of Legionnaires' disease incidents, Euro Surveill, vol.20, pp.1-9, 2015.

A. J. Cody, N. D. Mccarthy, M. Jansen-van-rensburg, T. Isinkaye, S. D. Bentley et al., Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of wholegenome multilocus sequence typing, J Clin Microbiol, vol.51, pp.2526-2560, 2013.

, Standard operating procedure for PulseNet PFGE of Listeria monocytogenes, Centers for Disease Control and Prevention, 2013.

A. Criscuolo and S. Brisse, AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads, Genomics, vol.102, pp.500-506, 2013.

M. R. Crusoe, H. F. Alameldin, S. Awad, E. Boucher, A. Caldwell et al., The khmer software package: enabling efficient nucleotide sequence analysis, vol.4, p.900, 2015.

Y. Liu, J. Schröder, and B. Schmidt, Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data, Bioinformatics, vol.29, pp.308-323, 2013.

T. Mago? and S. L. Salzberg, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.27, pp.2957-63, 2011.

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

K. A. Jolley and M. C. Maiden, BIGSdb: scalable analysis of bacterial genome variation at the population level, BMC Bioinformatics, vol.11, p.595, 2010.

E. H. Simpson, Measurement of diversity, Nature, vol.163, p.688, 1949.

A. Severiano, F. R. Pinto, M. Ramirez, and J. A. Carriço, Adjusted Wallace coefficient as a measure of congruence between typing methods

, J Clin Microbiol, vol.49, pp.3997-4000, 2011.

G. Moore, B. Cookson, N. C. Gordon, R. Jackson, A. Kearns et al., Whole-genome sequencing in hierarchy with pulsed-field gel electrophoresis: the utility of this approach to establish possible sources of MRSA cross-transmission, J Hosp Infect, vol.90, pp.38-45, 2015.

, Address for correspondence: Marc Lecuit, Biology of Infection Unit

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