Resistance: Global Report onSurveillance, 2014. ,
Ciprofloxacin-resistant Salmonella Kentucky in travelers, Emerg Infect Dis, vol.12, pp.1611-1612, 2006. ,
International spread of an epidemic population of Salmonella enterica serotype Kentucky ST198 resistant to ciprofloxacin, J Infect Dis, vol.204, pp.675-684, 2011. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01121157
Highly drug-resistant Salmonella enterica serotype Kentucky ST198-X1: a microbiological study, Lancet Infect Dis, vol.13, pp.672-679, 2013. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01109890
The global establishment of a highly-fluoroquinolone resistant Salmonella enterica serotype Kentucky ST198 strain, Front Microbiol, vol.4, p.395, 2013. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01115946
Drugresistant Salmonella enterica serotype Kentucky in Europe, Lancet Infect Dis, vol.14, pp.270-271, 2014. ,
Genomic and evolutionary analysis of two Salmonella enterica serovar Kentucky sequence types isolated from bovine and poultry sources in North America, PLoS One, vol.11, p.161225, 2016. ,
Early strains of multidrug-resistant Salmonella enterica serovar Kentucky sequence type 198 from Southeast Asia harbor Salmonella genomic island 1-J variants with a novel insertion sequence, Antimicrob Agents Chemother, vol.56, pp.5096-5102, 2012. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01116037
Complete nucleotide sequence of a 43-kilobase genomic island associated with the multidrug resistance region of Salmonella enterica serovar Typhimurium DT104 and its identification in phage type DT120 and serovar Agona, J Bacteriol, vol.183, pp.5725-5732, 2001. ,
Characterization of variant Salmonella genomic island 1 multidrug resistance regions from serovars Typhimurium DT104 and Agona, Antimicrob Agents Chemother, vol.46, pp.1714-1722, 2002. ,
Emergence of Salmonella genomic island 1 (SGI1) among Proteus mirabilis clinical isolates in Dijon, France, J Antimicrob Chemother, vol.68, pp.1750-1756, 2013. ,
Genomic resistance island AGI1 carrying a complex class 1 integron in a multiply antibioticresistant ST25 Acinetobacter baumannii isolate, J Antimicrob Chemother, vol.70, pp.2519-2523, 2015. ,
The Salmonella genomic island 1 is an integrative mobilizable element, Mol Microbiol, vol.55, pp.1911-1924, 2005. ,
The master activator of IncA/C conjugative plasmids stimulates genomic islands and multidrug resistance dissemination, PLoS Genet, vol.10, p.1004714, 2014. ,
The Salmonella genomic island 1 is specifically mobilized in trans by the IncA/C multidrug resistance plasmid family, PLoS ONE, vol.5, p.15302, 2010. ,
Salmonella genomic islands and antibiotic resistance in Salmonella enterica, Future Microbiol, vol.5, pp.1525-1538, 2010. ,
Proteus genomic island 1 (PGI1), a new resistance genomic island from two Proteus mirabilis French clinical isolates, J Antimicrob Chemother, vol.69, pp.3216-3220, 2014. ,
Emergence of Salmonella Genomic Island 1 Variant SGI1-W in a Clinical Isolate of Providencia stuartii from Egypt, Antimicrob Agents Chemother, vol.63, pp.1793-1811, 2018. ,
SGI2, a relative of Salmonella genomic island SGI1 with an independent origin, Antimicrob Agents Chemother, vol.52, pp.2529-2537, 2008. ,
Association of IS26-composite transposons and complex In4-type integrons generates novel multidrug resistance loci in Salmonella genomic island 1, J Antimicrob Chemother, vol.63, pp.282-289, 2009. ,
Novel insertion sequence-and transposon-mediated genetic rearrangements in genomic island SGI1 of Salmonella enterica serovar Kentucky, Antimicrob Agents Chemother, vol.52, pp.3745-3754, 2008. ,
SGI1-K, a variant of the SGI1 genomic island carrying a mercury resistance region, in Salmonella enterica serovar Kentucky, Antimicrob Agents Chemother, vol.51, pp.317-323, 2007. ,
ramR mutations affecting fluoroquinolone susceptibility in epidemic multidrug-resistant Salmonella enterica serovar Kentucky ST198, Front Microbiol, vol.4, p.213, 2013. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01109819
Genomic analysis of Salmonella enterica serotype Paratyphi A during an outbreak in Cambodia, Microb Genom, vol.2, p.92, 2013. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01523637
Practical value of food pathogen traceability through building a wholegenome sequencing network and database, J Clin Microbiol, vol.54, pp.1975-1983, 2016. ,
GenomeTrakr proficiency testing for foodborne pathogen surveillance: an exercise from, Microb Genom, vol.4, p.289, 2015. ,
SRST2: rapid genomic surveillance for public health and hospital microbiology Labs, Genome Med, vol.6, p.90, 2014. ,
Genome sequences of 65 Helicobacter pylori strains isolated from asymptomatic individuals and patients with gastric cancer, peptic ulcer disease, or gastritis, Pathog Dis, vol.68, pp.39-43, 2013. ,
Versatile and open software for comparing large genomes, Genome Biol, vol.5, p.12, 2004. ,
CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing, BMC Bioinformatics, vol.12, p.356, 2011. ,
Highthroughput sequencing provides insights into genome variation and evolution in Salmonella Typhi, Nat Genet, vol.40, pp.987-993, 2008. ,
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe, Nat Genet, vol.44, pp.1056-1059, 2012. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01117702
Fast gapped-read alignment with Bowtie 2, Nat Methods, vol.9, pp.357-359, 2012. ,
The sequence alignment/map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009. ,
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins, Nucleic Acids Res, vol.43, p.15, 2015. ,
a software platform for Bayesian evolutionary analysis, PLoS Comput Biol, vol.2, p.1003537, 2014. ,
Tracer v1.6, 2014. ,
beast: Bayesian evolutionary analysis by sampling trees, BMC Evol Biol, vol.7, p.214, 2007. ,
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, pp.1312-1313, 2014. ,
, Composition of macro geographical (continental) regions, geographical sub-regions, and selected economic and other groupings, 2013.
SIMMAP: stochastic character mapping of discrete traits on phylogenies, BMC Bioinformatics, vol.7, p.88, 2006. ,
Phytools: an R package for phylogenetic comparative biology (and other things), Methods Ecol Evol, vol.3, pp.217-223, 2012. ,
, , 2010.
Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2120, 2014. ,
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SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J Comput Biol, vol.19, pp.455-477, 2012. ,
Scaffolding pre-assembled contigs using SSPACE, Bioinformatics, vol.27, pp.578-579, 2011. ,
Toward almost closed genomes with GapFiller, Genome Biol, vol.13, p.56, 2012. ,
ABACAS: algorithm-based automatic contiguation of assembled sequences, Bioinformatics, vol.25, pp.1968-1969, 2009. ,
Prokka: rapid prokaryotic genome annotation, Bioinformatics, vol.30, pp.2068-2069, 2014. ,
ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes, Antimicrob Agents Chemother, vol.58, pp.212-220, 2014. ,
Roary: rapid large-scale prokaryote pan genome analysis, Bioinformatics, vol.31, pp.3691-3693, 2015. ,
blast+: architecture and applications, BMC Bioinformatics, vol.10, p.421, 2009. ,
VFDB 2016: hierarchical and refined dataset for big data analysis-10 years on, Nucleic Acids Res, vol.44, pp.694-697, 2016. ,
PHASTEST: tools for finding prophage in bacterial genomes, Brief Bioinform, 2017. ,
ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data, BMC Genomics, vol.16, p.667, 2015. ,
Bandage: interactive visualization of de novo genome assemblies, Bioinformatics, vol.31, pp.3350-3352, 2015. ,
In silico detection and typing of plasmids using Plas-midFinder and plasmid multilocus sequence typing, Antimicrob Agents Chemother, vol.58, pp.3895-3903, 2014. ,
Identification of IncA/C plasmid replication and maintenance genes and development of a plasmid multilocus sequence typing scheme, Antimicrob Agents Chemother, vol.61, pp.1740-1756, 2017. ,
Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica, PLoS One, vol.9, p.87991, 2014. ,
Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa ,
, Nat Genet, vol.44, pp.1215-1221, 2012.
Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona, PLoS Genet, vol.9, p.1003471, 2013. ,
Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter-and intracontinental transmission events, Nat Genet, vol.47, pp.632-639, 2015. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02043698
Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever, Proc Natl Acad Sci, vol.111, pp.12199-12204, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01104820
Genomescale rates of evolutionary change in bacteria, Microb Genom, vol.2, p.94, 2016. ,
IncA/C plasmid carrying bla(NDM-1), bla(CMY-16), and fosA3 in a Salmonella enterica serovar Corvallis strain isolated from a migratory wild bird in Germany, Antimicrob Agents Chemother, vol.59, pp.6597-6600, 2015. ,
Nucleotide sequence of IS26, a new prokaryotic mobile genetic element, Nucleic Acids Res, vol.11, pp.6319-6330, 1983. ,
Movement of IS26-associated antibiotic resistance genes occurs via a translocatable unit that includes a single IS26 and preferentially inserts adjacent to another IS26, MBio, vol.5, pp.1801-01814, 2014. ,
Fluoroquinolone resistance in Salmonella: insights by wholegenome sequencing, Microb Genom, 2018. ,
Population dynamics and antimicrobial resistance of the mostprevalent poultry-associated Salmonella serotypes, Poultry Sci, vol.96, pp.687-702, 2017. ,
Fitness benefits in fluoroquinolone-resistant Salmonella Typhi in the absence of antimicrobial pressure, Elife, vol.2, p.1229, 2013. ,
Clinically relevant mutant DNA gyrase alters supercoiling, changes the transcriptome, and confers multidrug resistance, MBio, vol.4, pp.273-286, 2013. ,
Destabilization of IncA and IncC plasmids by SGI1 and SGI2 type Salmonella genomic islands, Plasmid, pp.51-57, 2016. ,
A toxin antitoxin system promotes the maintenance of the IncA/C-mobilizable, Salmonella genomic island 1. Sci Rep, vol.6, p.32285, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01413543
Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella, Proc Natl Acad Sci, vol.115, pp.2614-2623, 2018. ,