B. Anton, N. Sergey, A. Dmitry, A. Alexey, G. Mikhail et al., SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, Journal of Computational Biology, vol.19, pp.455-477, 2012.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2120, 2014.

A. C. Camargo, D. C. Vallim, E. Hofer, N. , and L. A. , Molecular serogrouping of Listeria monocytogenes from Brazil using PCR, Journal of Food Protection, vol.79, pp.144-147, 2016.

A. C. Camargo, J. J. Woodward, D. R. Call, N. , and L. A. , Listeria monocytogenes in food-processing facilities, food contamination, and human listeriosis: the Brazilian scenario, Foodborne Pathogens and Disease, vol.14, pp.623-636, 2017.

A. C. Camargo, N. P. Castilho, D. A. Silva, D. C. Vallim, E. Hofer et al., Antibiotic resistance of Listeria monocytogenes isolated from meat-processing environments, beef products, and clinical cases in Brazil, Microbial Drug Resistance, vol.21, pp.458-462, 2015.

T. Chakraborty, M. Leimeister-wächter, E. Domann, M. Hartl, W. Goebel et al., Coordinate regulation of virulence genes in Listeria monocytogenes requires the product of the prfA gene, Journal of Bacteriology, vol.174, pp.568-574, 1992.

C. Charlier, É. Perrodeau, A. Leclercq, B. Cazenave, B. Pilmis et al., Clinical features and prognostic factors of listeriosis: the MONALISA national prospective cohort study, The Lancet Infectious Diseases, vol.17, pp.510-519, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01475849

L. Chen, J. Yang, J. Yu, Z. Yao, L. Sun et al., VFDB: a reference database for bacterial virulence factors, Nucleic Acids Research, vol.33, pp.325-328, 2005.

V. Chenal-francisque, J. Lopez, T. Cantinelli, V. Caro, C. Tran et al., Worldwide distribution of major clones of Listeria monocytogenes, Emerging Infectious Diseases, vol.17, pp.1110-1112, 2011.

P. D. Cotter, L. A. Draper, E. M. Lawton, K. M. Daly, D. S. Groeger et al.,

S. Listeriolysin, ;. A. Novel, R. J. Cain, M. K. Bielecka, and J. A. Vázquez-boland, Peptide Haemolysin Associated with a Subset of Lineage I Listeria monocytogenes, e1000144. de las Heras, vol.4, pp.118-127, 2011.

C. M. De-noordhout, B. Devleesschauwer, F. J. Angulo, G. Verbeke, J. Haagsma et al., The global burden of listeriosis: a systematic review and metaanalysis, The Lancet Infectious Diseases, vol.14, pp.1073-1082, 2014.

M. Doumith, C. Buchrieser, P. Glaser, C. Jacquet, M. et al., Differentiation of the major Listeria monocytogenes serovars by multiplex PCR, Journal of Clinical Microbiology, vol.42, pp.3819-3822, 2004.

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, pp.1792-1797, 2004.

C. Gahan and C. Hill, Listeria monocytogenes: survival and adaptation in the gastrointestinal tract, Frontiers in Cellular and Infection Microbiology, vol.4, 2014.

T. Gelbí?ová, I. Kolá?ková, R. Pant??ek, and R. Karpí?ková, A novel mutation leading to a premature stop codon in inlA of Listeria monocytogenes isolated from neonatal listeriosis, The New Microbiologica, vol.38, pp.293-296, 2015.

J. K. Haase, X. Didelot, M. Lecuit, H. Korkeala, A. et al., The ubiquitous nature of Listeria monocytogenes clones: a large-scale multilocus sequence typing study, Environmental Microbiology, vol.16, pp.405-416, 2014.

E. Harter, E. M. Wagner, A. Zaiser, S. Halecker, M. Wagner et al., The novel stress survival islet 2 (SSI-2), predominantly present in Listeria monocytogenes strains of ST121, is involved in alkaline and oxidative stress response, Applied and Environmental Microbiology, 2017.

E. Hofer, C. M. Reis, and C. B. Hofer, Sorovares de Listeria monocytogenes e espécies relacionadas, isoladas de material clínico humano, Revista da Sociedade Brasileira de Medicina Tropical, vol.39, pp.32-37, 2006.

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.

C. Kuenne, A. Billion, M. A. Mraheil, A. Strittmatter, R. Daniel et al., Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome, BMC Genomics, vol.14, p.47, 2013.

A. Leclercq, V. Chenal-francisque, H. Dieye, T. Cantinelli, R. Drali et al., Characterization of the novel Listeria monocytogenes PCR serogrouping profile IVb-v1, International Journal of Food Microbiology, vol.147, pp.74-77, 2011.

M. Lecuit, H. Ohayon, L. Braun, J. Mengaud, and P. Cossart, Internalin of Listeria monocytogenes with an intact leucine-rich repeat region is sufficient to promote internalization, Infection and Immunity, vol.65, pp.5309-5319, 1997.

M. Lecuit, S. Vandormael-pournin, J. Lefort, M. Huerre, P. Gounon et al.,

, A transgenic model for listeriosis: role of internalin in crossing the intestinal barrier, Science, vol.292, pp.1722-1725

S. Lee, T. J. Ward, D. D. Jima, C. Parsons, and S. Kathariou, The arsenic resistance Listeria genomic island LGI2 exhibits sequence and integration site diversity and propensity for three Listeria monocytogene clones with enhanced virulence, Applied and Environmental Microbiology, vol.83, pp.1189-01117, 2017.

I. Letunic and P. Bork, Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Research, vol.44, pp.242-245, 2016.

S. Lomonaco, D. Nucera, and V. Filipello, The evolution and epidemiology of Listeria monocytogenes in Europe and the United States. Infection, Genetics and Evolution, vol.35, pp.172-183, 2015.

S. Lüth, S. Kleta, A. Dahouk, and S. , Whole genome sequencing as a typing tool for foodborne pathogens like Listeria monocytogenes -the way towards global harmonisation and data exchange, Trends in Food Science & Technology, vol.73, pp.67-75, 2018.

M. M. Maury, V. Chenal-francisque, H. Bracq-dieye, L. Han, A. Leclercq et al., Spontaneous loss of virulence in natural populations of Listeria monocytogenes, Infection and Immunity, vol.85, pp.541-00517, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-02168452

M. M. Maury, Y. Tsai, C. Charlier, M. Touchon, V. Chenal-francisque et al., Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity, Nat Genet, vol.48, pp.308-313, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-02170775

E. Milohanic, P. Glaser, J. Coppée, L. Frangeul, Y. Vega et al., Transcriptome analysis of Listeria monocytogenes identifies three groups of genes differently regulated by PrfA, Molecular Microbiology, vol.47, pp.1613-1625, 2003.

A. Moura, M. Tourdjman, A. Leclercq, E. Hamelin, E. Laurent et al.,

, Real-time whole-genome sequencing for surveillance of Listeria monocytogenes, France. Emerging Infectious Diseases, vol.23, pp.1462-1470

A. Moura, A. Criscuolo, H. Pouseele, M. M. Maury, A. Leclercq et al., Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes, Nature Microbiology, vol.2, p.16185, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01415883

E. M. Nielsen, J. T. Björkman, K. Kiil, K. Grant, T. Dallman et al., Closing gaps for performing a risk assessment on Listeria monocytogenes in ready-toeat (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, vol.14, p.1151, 2017.

M. Olier, F. Pierre, S. Rousseaux, J. Lemaître, A. Rousset et al., Expression of Truncated Internalin A Is Involved in Impaired Internalization of Some Listeria monocytogenes Isolates Carried Asymptomatically by Humans, Infection and Immunity, vol.71, pp.1217-1224, 2003.

R. H. Orsi, H. C. Bakker, and M. Wiedmann, Listeria monocytogenes lineages: Genomics, evolution, ecology, and phenotypic characteristics, International Journal of Medical Microbiology, vol.301, pp.79-96, 2011.

J. J. Quereda, O. Dussurget, M. Nahori, A. Ghozlane, S. Volant et al., Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection, Proceedings of the National Academy of Sciences, vol.113, pp.5706-5711, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01533881

M. Ragon, T. Wirth, F. Hollandt, R. Lavenir, M. Lecuit et al., A new perspective on Listeria monocytogenes Evolution, PLOS Pathogens, vol.4, p.1000146, 2008.

S. Rousseaux, M. Olier, J. P. Lemaître, P. Piveteau, and J. Guzzo, Use of PCR-Restriction Fragment Length Polymorphism of inlA for Rapid Screening of Listeria monocytogenes Strains Deficient in the Ability To Invade Caco-2 Cells, Applied and Environmental Microbiology, vol.70, pp.2180-2185, 2004.

S. Rupp, L. Aguilar-bultet, V. Jagannathan, C. Guldimann, C. Drögemüller et al., A naturally occurring prfA truncation in a Listeria monocytogenes field strain contributes to reduced replication and cell-to-cell spread, Veterinary Microbiology, vol.179, pp.91-101, 2015.

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, Journal of Clinical Microbiology, vol.53, pp.2869-2876, 2015.

S. Ryan, M. Begley, C. Hill, and C. G. Gahan, A five-gene stress survival islet (SSI-1) that contributes to the growth of Listeria monocytogenes in suboptimal conditions, Journal of Applied Microbiology, vol.109, pp.984-995, 2010.

D. Schmid, F. Allerberger, S. Huhulescu, A. Pietzka, C. Amar et al., Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches, Clinical Microbiology and Infection, vol.20, pp.350-354, 2014.

M. Scortti, L. Han, S. Alvarez, A. Leclercq, A. Moura et al., Epistatic control of intrinsic resistance by virulence genes in Listeria, PLOS Genetics, vol.14, p.1007525, 2018.
URL : https://hal.archives-ouvertes.fr/inserm-02158860

B. J. Silk, K. A. Date, K. A. Jackson, R. Pouillot, K. G. Holt et al., Invasive listeriosis in the foodborne diseases active surveillance network (foodNet), 2004-2009: further targeted prevention needed for higher-risk groups, Clinical Infectious Diseases, vol.54, pp.396-404, 2012.

V. Toledo, H. C. Den-bakker, J. C. Hormazábal, G. González-rocha, H. Bello-toledo et al., Genomic diversity of Listeria monocytogenesis isolated from clinical and non-clinical samples in Chile, Genes, vol.9, pp.1-12, 2018.

D. C. Vallim, C. Barroso-hofer, R. D. Lisba, . Victor, A. Barbosa et al., Twenty years of Listeria in Brazil: occurrence of Listeria species and Listeria monocytogenes serovars in food samples in Brazil between 1990 and 2012, BioMed Research International, vol.2015, pp.1-8, 2015.

I. Van-walle, J. T. Björkman, M. Cormican, T. Dallman, J. Mossong et al., Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, Eurosurveillance, vol.23, p.1700798, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-02168368

A. R. Wattam, D. Abraham, O. Dalay, T. L. Disz, T. Driscoll et al.,

, PATRIC, the bacterial bioinformatics database and analysis resource, vol.42, pp.581-591