European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2014, EFSA J, vol.13, p.4329, 2015. ,
European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2015, EFSA J, vol.14, p.4634, 2016. ,
European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2016, vol.15, p.5077, 2017. ,
The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2016, EFSA J, vol.16, p.5182, 2018. ,
SPI-23 of S. Derby: Role in adherence and invasion of porcine tissues, PLoS ONE, vol.9, p.107857, 2014. ,
Population structure and associated phenotypes of Salmonella enterica serovars Derby and Mbandaka overlap with host range, BMC Microbiol, vol.16, p.15, 2016. ,
A genomic overview of the population structure of Salmonella, PLoS Genet, vol.14, p.1007261, 2018. ,
Analysis of the baseline survey on the prevalence of Salmonella in holdings with breeding pigs in the EU, 2008 -Part A: Salmonella prevalence estimates, EFSA Journal, vol.7, 2009. ,
Salmonella Derby clonal spread from pork, Emerg. Infect. Dis, vol.11, pp.694-698, 2005. ,
Evaluation of WGS based approaches for investigating a food-borne outbreak caused by Salmonella enterica serovar Derby in Germany, Food Microbiol, 2017. ,
Non-typhoidal Salmonella in the Pig Production Chain: A Comprehensive Analysis of Its Impact on Human Health, vol.8, p.19, 2019. ,
, Food safety. Availabe online, 2015.
Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change ,
, , p.1535, 2013.
gyrA mutations associated with fluoroquinolone resistance in eight species of Enterobacteriaceae, Antimicrob. Agents Chemother, vol.42, pp.2661-2667, 1998. ,
Altitudinal migration by birds: A review of the literature and a comprehensive list of species, J. Field Ornithol, vol.88, pp.321-335, 2017. ,
Salmonellosis in wild birds, Semin. Avian Exotic. Pet. Med, vol.13, pp.50-66, 2004. ,
Bird migration routes and risk for pathogen dispersion into western Mediterranean wetlands, Emerg. Infect. Dis, vol.13, pp.365-372, 2007. ,
Structures et Organisation des Filières Volailles de Chair en Europe ,
Volaille de Chair, p.55, 2014. ,
Antimicrobial resistance and virulence determinants in European Salmonella genomic island 1-positive Salmonella enterica isolates from different origins, Appl. Environ. Microbiol, vol.77, pp.5655-5664, 2011. ,
Cadel-Six, S. Polyphyletic Nature of Salmonella enterica Serotype Derby and Lineage-Specific Host-Association Revealed by Genome-Wide Analysis, Front. Microbiol, vol.9, p.891, 2018. ,
Full-genome sequence of a novel myovirus, GF-2, infecting Edwardsiella tarda: Comparison with other Edwardsiella myoviral genomes, Arch. Virol, vol.160, pp.2129-2133, 2015. ,
The Significance of Viruses to Mortality in Aquatic Microbial Communities, Microb. Ecol, vol.28, pp.237-243, 1994. ,
, Viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. MMBR, vol.64, pp.69-114, 2000.
Viral lysis, flagellate grazing potential, and bacterial production in Lake Pavin, Microb. Ecol, vol.45, pp.119-127, 2003. ,
URL : https://hal.archives-ouvertes.fr/hal-00527524
Ecology of prokaryotic viruses, FEMS Microbiol. Rev, vol.28, pp.127-181, 2004. ,
Quality Control tool for High Throughput Sequence Data ,
Quality control and preprocessing of metagenomic datasets, Bioinformatics, vol.27, pp.863-864, 2011. ,
finished microbial genome assemblies from long-read SMRT sequencing data, Nat. Methods, vol.10, pp.563-569, 2013. ,
A whole-genome assembly of Drosophila, Science, vol.287, pp.2196-2204, 2000. ,
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, vol.27, pp.2987-2993, 2011. ,
Prokka: Rapid prokaryotic genome annotation, Bioinformatics, vol.30, pp.2068-2069, 2014. ,
Microevolution of Monophasic Salmonella Typhimurium during Epidemic, Emerg. Infect. Dis, vol.22, pp.617-624, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-01602815
Disentangling a complex nationwide Salmonella Dublin outbreak associated with raw-milk cheese consumption, Eurosurveillance, p.24, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-02005693
Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms, PLoS ONE, vol.9, p.104984, 2014. ,
The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009. ,
FastTree 2 -Approximately Maximum-Likelihood Trees for Large Alignments, PLoS ONE, vol.5, p.9490, 2010. ,
Interactive tree of life (iTOL) v3: An online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Res, vol.44, pp.242-245, 2016. ,
Remark AS R94: A Remark on Algorithm AS 181: The W-test for Normality, J. R. Stat. Soc. Ser. C (Appl. Stat.), vol.44, pp.547-551, 1995. ,
Conditions for the Effectiveness of a Preliminary Test of Variance, Am. Stat, vol.44, pp.322-326, 1990. ,
, Nontyphoidal Salmonella Infection, vol.22, pp.726-729, 2012.
Identification of acquired antimicrobial resistance genes, J. Antimicrob. Chemother, vol.67, pp.2640-2644, 2012. ,
PHASTER: A better, faster version of the PHAST phage search tool, Nucleic Acids Res, vol.44, pp.16-21, 2016. ,
, Architecture and applications. BMC Bioinform, vol.10, p.421, 2009.
Basic local alignment search tool, J. Mol. Biol, vol.215, pp.403-410, 1990. ,
, This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license, © 2019 by the authors. Licensee MDPI