M. Chiara, M. Caruso, A. M. D?erchia, C. M. Manzari, R. Fraccalvieri et al., Comparative Genomics ofListeriaSensu Lato: Genus-Wide Differences in Evolutionary Dynamics and the Progressive Gain of Complex, Potentially Pathogenicity-Related Traits through Lateral Gene Transfer, Genome Biology and Evolution, vol.7, issue.8, pp.2154-2172, 2015.

J. Mclauchlin, C. Reese, P. Genus-listeria-;-vos, G. Garrity, D. Jones et al., Bergey's Manual of Systematic Bacteriology, pp.244-257, 2009.

R. H. Orsi and M. Wiedmann, Characteristics and distribution of Listeria spp., including Listeria species newly described since 2009, Applied Microbiology and Biotechnology, vol.100, issue.12, pp.5273-5287, 2016.

J. H. Pirie, THE GENUS LISTERELLA PIRIE, Science, vol.91, issue.2364, pp.383-383, 1940.

H. P. Seeliger,

S. Schulz and R. Klar, Chatten statt Jetten?Virtuelle Konferenzen in der Medizin, Zentralblatt für Gynäkologie, vol.123, issue.8, pp.487-493, 2001.

J. Rocourt and P. A. Grimont, Notes: Listeria welshimeri sp. nov. and Listeria seeligeri sp. nov., International Journal of Systematic Bacteriology, vol.33, issue.4, pp.866-869, 1983.

, Sections Officers and Managers as of July 1, 1983, SMPTE Journal, vol.92, issue.8, pp.866-869, 1983.

H. P. Seeliger, J. Rocourt, A. Schrettenbrunner, P. A. Grimont, and D. Jones, Listeria ivanovii sp. nov., International Journal of Systematic Bacteriology, vol.35, issue.1, pp.126-126, 1985.

R. Norton, Review, Oceania, vol.54, issue.4, pp.336-337, 1984.
URL : https://hal.archives-ouvertes.fr/hal-01532458

L. M. Graves, L. O. Helsel, A. G. Steigerwalt, R. E. Morey, M. I. Daneshvar et al., Listeria marthii sp. nov., isolated from the natural environment, Finger Lakes National Forest, International Journal of Systematic and Evolutionary Microbiology, vol.60, issue.6, pp.1280-1288, 2010.

H. E. Larsen and R. Shp, A mannitol fermenting Listeria: Listeria grayi sp

, Third international research symposium on electric contact phenomena, University of Maine, Orono, Maine, U.S.A., 6?10 June, 1966, Wear, vol.9, issue.3, p.248, 1966.

T. Bilthoven and . Netherlands,

J. Rocourt, P. Boerlin, F. Grimont, C. Jacquet, and J. C. Piffaretti, Assignment of Listeria grayi and Listeria murrayi to a Single Species, Listeria grayi, with a Revised Description of Listeria grayi, International Journal of Systematic Bacteriology, vol.42, issue.1, pp.171-174, 1992.

A. Leclercq, D. Clermont, C. Bizet, P. A. Grimont, A. Le-flèche-matéos et al., Listeria rocourtiae sp. nov., International Journal of Systematic and Evolutionary Microbiology, vol.60, issue.9, pp.2210-2214, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02663151

D. Bertsch, J. Rau, M. R. Eugster, M. C. Haug, and P. A. Lawson, Genome sequencing identifies Listeria fleischmannii subsp. coloradonensis subsp. nov., isolated from a ranch, Int J Syst Evol Microbiol, vol.63, issue.2, pp.3257-3268, 2013.

E. L. Halter, K. Neuhaus, S. Scherer, H. C. ;-den-bakker, S. Warchocki et al., Listeria floridensis sp. nov., Listeria aquatica sp. nov., Listeria cornellensis sp. nov., Listeria riparia sp. nov. and Listeria grandensis sp. nov., from agricultural and natural environments, Int J Syst Evol Microbiol, vol.63, pp.1882-1889, 2013.

D. Weller, A. Andrus, M. Wiedmann, and H. C. Den-bakker, Listeria booriae sp. nov. and Listeria newyorkensis sp. nov., from food processing environments in the USA, International Journal of Systematic and Evolutionary Microbiology, vol.65, issue.Pt_1, pp.286-292, 2015.

A. Moura, M. Tourdjman, A. Leclercq, E. Hamelin, E. Laurent et al., Real-Time Whole-Genome Sequencing for Surveillance ofListeria monocytogenes, France, Emerging Infectious Diseases, vol.23, issue.9, pp.1462-1470, 2017.

R. R. Wick, L. M. Judd, C. L. Gorrie, and K. E. Holt, Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads, PLOS Computational Biology, vol.13, issue.6, p.e1005595, 2017.

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 2012.

B. J. Walker, T. Abeel, T. Shea, M. Priest, A. Abouelliel et al., Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement, PLoS ONE, vol.9, issue.11, p.e112963, 2014.

J. Chun, A. Oren, A. Ventosa, H. Christensen, D. R. Arahal et al., Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes, International Journal of Systematic and Evolutionary Microbiology, vol.68, issue.1, pp.461-466, 2018.

T. Seemann, Prokka: rapid prokaryotic genome annotation, Bioinformatics, vol.30, issue.14, pp.2068-2069, 2014.

J. Robertson and J. H. Nash, MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies, Microbial Genomics, vol.4, issue.8, 2018.

T. J. Treangen, B. D. Ondov, S. Koren, and A. M. Phillippy, The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes, Genome Biology, vol.15, issue.11, p.524, 2014.

A. J. Page, C. A. Cummins, M. Hunt, V. K. Wong, S. Reuter et al., Roary: rapid large-scale prokaryote pan genome analysis, Bioinformatics, vol.31, issue.22, pp.3691-3693, 2015.

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.

L. T. Nguyen, H. A. Schmidt, A. Von-haeseler, and B. Q. Minh, IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies, Molecular Biology and Evolution, vol.32, issue.1, pp.268-274, 2014.

M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, vol.16, issue.2, pp.111-120, 1980.

S. Whelan and N. Goldman, A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach, Molecular Biology and Evolution, vol.18, issue.5, pp.691-699, 2001.

S. Kumar, G. Stecher, and K. Tamura, MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets, Molecular Biology and Evolution, vol.33, issue.7, pp.1870-1874, 2016.

S. Erko and J. Ebers, Taxonomic parameters revisited: tarnished gold standards, Microbiol today, vol.8, pp.6-9, 2006.

M. Kim, H. S. Oh, S. C. Park, and J. Chun, Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes, International Journal of Systematic and Evolutionary Microbiology, vol.64, issue.Pt_2, pp.346-351, 2014.

L. M. Rodriguez-r and K. T. Konstantinidis, Bypassing Cultivation To Identify Bacterial Species, Microbe Magazine, vol.9, issue.3, pp.111-118, 2014.

J. Goris, K. T. Konstantinidis, J. A. Klappenbach, T. Coenye, P. Vandamme et al., DNA?DNA hybridization values and their relationship to whole-genome sequence similarities, International Journal of Systematic and Evolutionary Microbiology, vol.57, issue.1, pp.81-91, 2007.

A. F. Auch, M. Von-jan, H. P. Klenk, and M. Göker, Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison, Standards in Genomic Sciences, vol.2, issue.1, pp.117-134, 2010.

A. F. Auch, H. P. Klenk, and M. Göker, Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs, Standards in Genomic Sciences, vol.2, issue.1, pp.142-148, 2010.

J. P. Meier-kolthoff, A. F. Auch, H. P. Klenk, and M. Göker, Genome sequence-based species delimitation with confidence intervals and improved distance functions, BMC Bioinformatics, vol.14, issue.1, p.60, 2013.

Q. L. Qin, B. B. Xie, X. Y. Zhang, X. L. Chen, B. C. Zhou et al., A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights, Journal of Bacteriology, vol.196, issue.12, pp.2210-2215, 2014.

L. Halter, E. Neuhaus, K. Scherer, and S. , Listeria weihenstephanensis sp. nov., isolated from the water plant Lemna trisulca taken from a freshwater pond, Int J Syst Evol Microbiol, vol.63, issue.2, pp.641-647, 2013.

A. Hitchins, K. Jinneman, and Y. Chen, Detection of Listeria monocytogenes in foods and environmental samples and enumeration of Listeria monocytogenes in foods, Bacteriological Analytical Manual. Food and Drug Administration, p.2017

M. A. Hussey and A. Zayaitz, Endospore stain protocol. Laboratory protocols

D. P. Breakwell, R. B. Moyes, and J. Reynolds, Differential Staining of Bacteria: Capsule Stain, Current Protocols in Microbiology, vol.15, issue.1, 2009.

, Appendix 1?chemical structure 8. Compound 3i., Curr Protoc Microbiol, vol.3, p.3

H. P. Seeliger and K. Höhne, Chapter II Serotyping of Listeria monocytogenes and Related Species, Methods in Microbiology, pp.31-49, 1979.

H. P. Seeliger and K. Höhne, Chapter II Serotyping of Listeria monocytogenes and Related Species, Methods in Microbiology, vol.13, pp.31-49, 1979.

M. Doumith, C. Buchrieser, P. Glaser, C. Jacquet, and P. Martin, Differentiation of the Major Listeria monocytogenes Serovars by Multiplex PCR, Journal of Clinical Microbiology, vol.42, issue.8, pp.3819-3822, 2004.

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, issue.1, pp.74-77, 2011.

A. Moura, A. Criscuolo, H. Pouseele, M. M. Maury, and A. Leclercq, Genome-based epidemiological surveillance of Listeria monocytogenes at a global scale, Nat Microbiol, vol.2, p.16185, 2016.

R. Christie, N. E. Atkins, and E. Munch-petersen, A note on a lytic phenomenon shown by group B streptococci, Aust J Exp Biol Med Sci, vol.22, pp.197-200, 1944.

M. M. Maury, Y. H. Tsai, C. Charlier, M. Touchon, and V. Chenal-francisque, Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity, Nat Genet, vol.48, issue.3, pp.308-313, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-02170775

J. A. Va?zquez-boland, M. Kuhn, P. Berche, T. Chakraborty, G. Dom??nguez-bernal et al., Listeria Pathogenesis and Molecular Virulence Determinants, Clinical Microbiology Reviews, vol.14, issue.3, pp.584-640, 2001.

W. Andrews, H. Wang, A. Jacobson, T. Hammack, . Bam et al., Bacteriological Analytical Manual, 2020.

J. Bille, B. Catimel, E. Bannerman, C. Jacquet, M. N. Yersin et al., API Listeria, a new and promising one-day system to identify Listeria isolates., Applied and Environmental Microbiology, vol.58, issue.6, pp.1857-1860, 1992.

R. Troxler, A. Von-graevenitz, G. Funke, B. Wiedemann, and I. Stock, Natural antibiotic susceptibility of Listeria species: L. grayi, L. innocua, L. ivanovii, L. monocytogenes, L. seeligeri and L. welshimeri strains, Clinical Microbiology and Infection, vol.6, issue.10, pp.525-535, 2000.

, Notation, Positive Definite Matrices, pp.253-254, 2009.

?. and N. ,

!. , variable between studies (possibly due to differences in incubation times and temperatures between studies)

*. , valentina strains, based on API 50 CH, produce acid from gentiobiose and Dtrehalose but not produce acid from dulcitol, L-arabitol, methyl ?-D-mannopyranoside, methyl ?-D-glucopyranoside

*. , Figure 7: An API based security system.

R. H. Orsi, T. M. Bergholz, M. Wiedmann, and K. J. Boor, The Listeria monocytogenes strain 10403S BioCyc database, Database, vol.2015, 2015.

L. Lin, Data S4: Data for Fig. 12

L. Lse and . Seeligeri, Listeria seeligeri, 2020.

L. Liv, A. Ivanovii-strain, and . Baa-678, Crystal structure of AckA from Mycobacterium paratuberculosis ATCC BAA-968 / K-10, 2011.

L. Lws and . Welshimeri, Table 10.A1.5. Demographic structure based on LWS data

L. Lma, Data S4: Gene trees from empirical data

L. Lgy,

L. Lro,

L. Lwp,

L. Lcn, cornellensis strains TTU A1-0210 T, FSL F6-0970

L. Lri, riparia strains FSL S10-1204 T, FSL S10-1219

L. Lgd,

L. Lfc, A. 24998t, and . Baa,

T. and F. F6-1019, FSL S10-1186, FSL S10-1203 and FSL S10-1220

L. Laq, aquatica strains FSL S10-1188 T and FSL S10-1181

L. Lfo,

L. Lny, newyorkensis strains FSL M6-0635 T and A5-0209

L. Lbo, booriae strains FSL A5-0279 T and FSL A5-0281

L. Lco,

L. Lgo,

L. Lth,

L. Lva and . Sp,

, All species/strains are positive for aesculin and acid production from N-acetylglucosamine, amygdalin, arbutin, D-cellobiose, D-fructose, D-mannose and salicin

, All species/strains are negative for nitrite reduction and acid production from D-adonitol, D-arabinose, glycogen, methyl ?-D-xylopyranoside