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. ,
Bergey's Manual of Systematic Bacteriology, pp.244-257, 2009. ,
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. ,
THE GENUS LISTERELLA PIRIE, Science, vol.91, issue.2364, pp.383-383, 1940. ,
,
Chatten statt Jetten?Virtuelle Konferenzen in der Medizin, Zentralblatt für Gynäkologie, vol.123, issue.8, pp.487-493, 2001. ,
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.
Listeria ivanovii sp. nov., International Journal of Systematic Bacteriology, vol.35, issue.1, pp.126-126, 1985. ,
Review, Oceania, vol.54, issue.4, pp.336-337, 1984. ,
URL : https://hal.archives-ouvertes.fr/hal-01532458
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. ,
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.
,
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. ,
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
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. ,
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. ,
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. ,
Real-Time Whole-Genome Sequencing for Surveillance ofListeria monocytogenes, France, Emerging Infectious Diseases, vol.23, issue.9, pp.1462-1470, 2017. ,
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads, PLOS Computational Biology, vol.13, issue.6, p.e1005595, 2017. ,
Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 2012. ,
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement, PLoS ONE, vol.9, issue.11, p.e112963, 2014. ,
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. ,
Prokka: rapid prokaryotic genome annotation, Bioinformatics, vol.30, issue.14, pp.2068-2069, 2014. ,
MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies, Microbial Genomics, vol.4, issue.8, 2018. ,
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. ,
Roary: rapid large-scale prokaryote pan genome analysis, Bioinformatics, vol.31, issue.22, pp.3691-3693, 2015. ,
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004. ,
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. ,
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. ,
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. ,
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets, Molecular Biology and Evolution, vol.33, issue.7, pp.1870-1874, 2016. ,
Taxonomic parameters revisited: tarnished gold standards, Microbiol today, vol.8, pp.6-9, 2006. ,
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. ,
Bypassing Cultivation To Identify Bacterial Species, Microbe Magazine, vol.9, issue.3, pp.111-118, 2014. ,
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. ,
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. ,
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. ,
Genome sequence-based species delimitation with confidence intervals and improved distance functions, BMC Bioinformatics, vol.14, issue.1, p.60, 2013. ,
A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights, Journal of Bacteriology, vol.196, issue.12, pp.2210-2215, 2014. ,
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. ,
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 ,
Endospore stain protocol. Laboratory protocols ,
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
Chapter II Serotyping of Listeria monocytogenes and Related Species, Methods in Microbiology, pp.31-49, 1979. ,
Chapter II Serotyping of Listeria monocytogenes and Related Species, Methods in Microbiology, vol.13, pp.31-49, 1979. ,
Differentiation of the Major Listeria monocytogenes Serovars by Multiplex PCR, Journal of Clinical Microbiology, vol.42, issue.8, pp.3819-3822, 2004. ,
Characterization of the novel Listeria monocytogenes PCR serogrouping profile IVb-v1, International Journal of Food Microbiology, vol.147, issue.1, pp.74-77, 2011. ,
Genome-based epidemiological surveillance of Listeria monocytogenes at a global scale, Nat Microbiol, vol.2, p.16185, 2016. ,
A note on a lytic phenomenon shown by group B streptococci, Aust J Exp Biol Med Sci, vol.22, pp.197-200, 1944. ,
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
Listeria Pathogenesis and Molecular Virulence Determinants, Clinical Microbiology Reviews, vol.14, issue.3, pp.584-640, 2001. ,
, Bacteriological Analytical Manual, 2020.
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. ,
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.
,
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. ,
The Listeria monocytogenes strain 10403S BioCyc database, Database, vol.2015, 2015. ,
Data S4: Data for Fig. 12 ,
Listeria seeligeri, 2020. ,
Crystal structure of AckA from Mycobacterium paratuberculosis ATCC BAA-968 / K-10, 2011. ,
Table 10.A1.5. Demographic structure based on LWS data ,
Data S4: Gene trees from empirical data ,
,
,
,
, cornellensis strains TTU A1-0210 T, FSL F6-0970
, riparia strains FSL S10-1204 T, FSL S10-1219
,
,
, FSL S10-1186, FSL S10-1203 and FSL S10-1220
, aquatica strains FSL S10-1188 T and FSL S10-1181
,
, newyorkensis strains FSL M6-0635 T and A5-0209
, booriae strains FSL A5-0279 T and FSL A5-0281
,
,
,
,
, 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