FastQC: a Quality Control Tool for High Throughput Sequence Data, 2010. ,
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J. Comput. Biol, vol.19, pp.455-477, 2012. ,
Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinform. Oxf. Engl, vol.30, pp.2114-2120, 2014. ,
MeDuSa: a multi-draft based scaffolder, Bioinformatics, vol.31, pp.2443-2451, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01139506
BBMap: A Fast, Accurate, Splice-Aware Aligner, 2014. ,
Whole genome and core genome multilocus sequence typing and single nucleotide polymorphism analyses of listeria monocytogenes isolates associated with an outbreak linked to cheese, united states, Appl. Environ. Microbiol, 2013. ,
Biopython: freely available Python tools for computational molecular biology and bioinformatics, Bioinformatics, vol.25, pp.1422-1423, 2009. ,
Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar enteritidis, Emerg. Infect. Dis, vol.20, pp.1306-1314, 2014. ,
A population genetics-based and phylogenetic approach to understanding the evolution of virulence in the genus Listeria, Appl. Environ. Microbiol, vol.76, pp.6085-6100, 2010. ,
Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks, Mol. Biol. Evol, vol.34, pp.997-1007, 2017. ,
ClonalFrameML: efficient inference of recombination in whole bacterial genomes, PLoS Comput. Biol, vol.11, p.1004041, 2015. ,
Genome-scale rates of evolutionary change in bacteria, Microb. Genomics, vol.2, p.94, 2016. ,
, Scientific opinion on monitoring and assesment of the public health risk of «Salmonella Typhimurium-like» strains, EFSA J, vol.8, pp.1826-1874, 2010.
MultiQC: summarize analysis results for multiple tools and samples in a single report, Bioinformatics, vol.32, pp.3047-3048, 2016. ,
First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalianand avian-hosts, BMC Microbiol, vol.17, p.222, 2017. ,
Antigenic Formulae of the Salmonella Serovars, 9th Edn. Paris: WHO Collaborating Centre for Reference and Research on Salmonella, pp.1-166, 2007. ,
QUAST: quality assessment tool for genome assemblies, Bioinformatics, vol.29, pp.1072-1075, 2013. ,
Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm, BMC Genomics, vol.14, p.800, 2013. ,
Genomic characterization of listeria monocytogenes isolates associated with clinical listeriosis and the food production environment in ireland, Genes, vol.9, p.171, 2018. ,
Utility of whole-genome sequencing of Escherichia coli O157 for outbreak detection and epidemiological surveillance, J. Clin. Microbiol, vol.53, pp.3565-3573, 2015. ,
Approximate nearest neighbors: towards removing the curse of dimensionality, the Proceedings of the Thirtieth Annual ACM Symposium on Theory of computing, pp.604-613, 1998. ,
BIGSdb: scalable analysis of bacterial genome variation at the population level, BMC Bioinformatics, vol.11, p.595, 2010. ,
GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments, Bioinformatics, vol.31, pp.3733-3741, 2015. ,
Population genomics of Mycobacterium tuberculosis in the inuit, Proc. Natl. Acad. Sci. U.S.A, vol.112, pp.13609-13614, 2015. ,
Re-emergence and amplification of tuberculosis in the Canadian Arctic, J. Infect. Dis, vol.211, pp.1905-1914, 2015. ,
Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study, Wellcome Open Res, vol.3, p.33, 2018. ,
Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts, Science, vol.341, pp.1514-1517, 2013. ,
The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, vol.20, pp.1297-1303, 2010. ,
Food-borne illnesses are not always home-grown. Nature 1-8, 2013. ,
Operational burden of implementing Salmonella enteritidis and Typhimurium cluster detection using whole genome sequencing surveillance data in England: a retrospective assessment, Epidemiol. Infect, vol.146, pp.1452-1460, 2018. ,
PulseNet international: vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance, Euro Surveill, vol.22, p.30544, 2017. ,
Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa, Nat. Genet, vol.44, pp.1215-1221, 2012. ,
Mash: fast genome and metagenome distance estimation using MinHash, Genome Biol, vol.17, p.132, 2016. ,
Roary: rapid large-scale prokaryote pan genome analysis, Bioinformatics, vol.31, pp.3691-3693, 2015. ,
Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak, Int. J. Food Microbiol, vol.274, pp.1-11, 2018. ,
Epidemiological information is key when interpreting whole genome sequence data -lessons learned from a large L egionella pneumophila outbreak in Warstein, Euro Surveill, vol.22, pp.1-10, 2013. ,
Whole genome sequencing based surveillance of L. monocytogenes for early detection and investigations of listeriosis outbreaks, Front. Public Health, vol.7, p.139, 2019. ,
Interpreting whole-genome sequence analyses of foodborne bacteria for regulatory applications and outbreak investigations, Front. Microbiol, vol.9, p.1482, 2018. ,
, R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing, 2015.
Genomic epidemiology of campylobacter jejuni transmission in Israel, Front. Microbiol, vol.9, p.2432, 2018. ,
GenomeGraphR: a user-friendly open-source web application for foodborne pathogen whole genome sequencing data integration, analysis, and visualization, PLoS One, vol.14, p.213039, 2019. ,
Numerical Taxonomy: The Principles and Practice of Numerical Classification, 1973. ,
Genome-wide recombination drives diversification of epidemic strains of Acinetobacter baumannii, Proc. Natl. Acad. Sci. U.S.A, vol.108, pp.13758-13763, 2011. ,
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, pp.1312-1313, 2014. ,
A rapid bootstrap algorithm for the RAxML web servers, Syst. Biol, vol.57, pp.758-771, 2008. ,
Beyond the SNP threshold: identifying outbreak clusters using inferred transmissions, Mol. Biol. Evol, vol.36, pp.587-603, 2019. ,
Stopping outbreaks with real-time genomic epidemiology, Genome Med, vol.6, p.104, 2014. ,
Characterization of foodborne outbreaks of salmonella enterica serovar enteritidis with whole-genome sequencing single nucleotide polymorphism-based analysis for surveillance and outbreak detection, J. Clin. Microbiol, vol.53, pp.3334-3340, 2015. ,
Identification by PCR of non-typhoidal Salmonella enterica serovars associated with invasive infections among febrile patients in mali, PLoS Negl. Trop. Dis, vol.4, p.621, 2010. ,
Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance, PeerJ, vol.5, p.3893, 2017. ,
Utilizing the public genometrakr database for foodborne pathogen traceback, Foodborne Bacterial Pathogens, pp.201-212, 2019. ,
Comparison of advanced whole genome sequence-based methods to distinguish strains of Salmonella enterica serovar Heidelberg involved in foodborne outbreaks in Québec, Food Microbiol, vol.73, pp.99-110, 2018. ,
, , 2009.
A male-specific genetic map of the microcrustacean daphnia pulex based on single-sperm whole-genome sequencing, Genetics, vol.201, pp.31-38, 2015. ,
Molecular phylogenetics: principles and practice, Nat. Rev. Genet, vol.13, pp.303-314, 2012. ,
ggtree?: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods Ecol. Evol, vol.8, pp.28-36, 2017. ,