Global Trends in Typhoid and Paratyphoid Fever, Clinical Infectious Diseases, vol.50, issue.2, pp.241-247, 2010. ,
DOI : 10.1086/649541
URL : https://academic.oup.com/cid/article-pdf/50/2/241/942101/50-2-241.pdf
Gastroenteritis, Clinical Infectious Diseases, vol.50, issue.6, pp.882-891, 2010. ,
DOI : 10.1086/650733
Global burden of invasive nontyphoidal Salmonella disease, Emerg Infect Dis, vol.201021, issue.16, 2015. ,
Invasive nontyphoidal Salmonella disease, Current Opinion in Infectious Diseases, vol.24, issue.5, pp.484-493, 2011. ,
DOI : 10.1097/QCO.0b013e32834a9980
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277940
Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa, Nature Genetics, vol.4, issue.11, pp.1215-1236, 2012. ,
DOI : 10.1093/bioinformatics/btn529
Outbreak of salmonella dublin infection in France, Euro Surveill, vol.1, issue.2, pp.9-10, 1995. ,
SUMMARY, Epidemiology and Infection, vol.7, issue.03, pp.1-6 ,
DOI : 10.1093/molbev/mst197
Role of Salmonella Typhi Vi Antigen and Secretory Systems on Immune Response, Current Pharmaceutical Design, vol.22, issue.41, pp.6251-6260, 2016. ,
DOI : 10.2174/1381612822666160829142308
Role of antigens and virulence factors of Salmonella enterica serovar Typhi in its pathogenesis, Microbiological Research, vol.167, issue.4, pp.199-210, 2012. ,
DOI : 10.1016/j.micres.2011.08.001
The Role of the st313-td Gene in Virulence of Salmonella Typhimurium ST313, PLoS ONE, vol.6, issue.1, p.84566, 2014. ,
DOI : 10.1371/journal.pone.0084566.s003
Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype, Genome Research, vol.19, issue.12, pp.2279-87, 2009. ,
DOI : 10.1101/gr.091017.109
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Research, vol.18, issue.5, pp.821-830, 2008. ,
DOI : 10.1101/gr.074492.107
URL : http://genome.cshlp.org/content/18/5/821.full.pdf
The RAST Server: Rapid Annotations using Subsystems Technology, BMC Genomics, vol.9, issue.1, p.75, 2008. ,
DOI : 10.1186/1471-2164-9-75
URL : https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-9-75?site=bmcgenomics.biomedcentral.com
Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-60, 2009. ,
DOI : 10.1093/bioinformatics/btp324
URL : https://academic.oup.com/bioinformatics/article-pdf/25/14/1754/605544/btp324.pdf
The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2087, 2009. ,
DOI : 10.1093/bioinformatics/btp352
URL : https://academic.oup.com/bioinformatics/article-pdf/25/16/2078/531810/btp352.pdf
jModelTest: Phylogenetic Model Averaging, Molecular Biology and Evolution, vol.25, issue.7, pp.1253-1259, 2008. ,
DOI : 10.1093/molbev/msn083
URL : https://academic.oup.com/mbe/article-pdf/25/7/1253/3543852/msn083.pdf
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, Molecular Biology and Evolution, vol.30, issue.12, pp.2725-2734, 2013. ,
DOI : 10.1093/molbev/mst197
URL : https://academic.oup.com/mbe/article-pdf/30/12/2725/19498310/mst197.pdf
BLAST+: architecture and applications, BMC Bioinformatics, vol.10, issue.1, p.421, 2009. ,
DOI : 10.1186/1471-2105-10-421
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-10-421?site=bmcbioinformatics.biomedcentral.com
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, vol.192, issue.1, p.402, 2011. ,
DOI : 10.1128/JB.01144-09
URL : https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-12-402?site=bmcgenomics.biomedcentral.com
Salmonella enterica serovar Dublin strains which are Vi antigen-positive use type IVB pili for bacterial self-association and human intestinal cell entry, Microbial Pathogenesis, vol.35, issue.6, pp.279-84, 2003. ,
DOI : 10.1016/j.micpath.2003.08.001
Molecular cloning of the ViaB region of Salmonella typhi, FEMS Microbiology Letters, vol.90, issue.1, pp.53-59, 1991. ,
DOI : 10.1111/j.1574-6968.1991.tb05124.x
Composition, Acquisition, and Distribution of the Vi Exopolysaccharide-Encoding Salmonella enterica Pathogenicity Island SPI-7, Journal of Bacteriology, vol.185, issue.17, pp.5055-65, 2003. ,
DOI : 10.1128/JB.185.17.5055-5065.2003
Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18, Nature, vol.16, issue.6858, pp.848-52, 2001. ,
DOI : 10.1093/bioinformatics/16.10.944
Survival of Vi-capsulated and Vi-deleted Salmonella typhi strains in cultured macrophage expressing different levels of CD14 antigen, FEMS Microbiology Letters, vol.147, issue.2, pp.259-65, 1997. ,
DOI : 10.1111/j.1574-6968.1997.tb10251.x
Role of the vi antigen of salmonella typhi in resistance to host defense in vitro, J Lab Clin Med, vol.108, issue.5, pp.506-522, 1986. ,
Flagellar glycosylation -a new component of the motility repertoire? Microbiology, pp.1249-62, 2006. ,
Flashy flagella: flagellin modification is relatively common and highly versatile among the Enterobacteriaceae, BMC Genomics, vol.5, issue.1, p.377, 2016. ,
DOI : 10.1093/bib/bbn017
Deadly syringes: type VI secretion system activities in pathogenicity and interbacterial competition, Current Opinion in Microbiology, vol.16, issue.1, pp.52-60, 2013. ,
DOI : 10.1016/j.mib.2012.11.009
The Type VI Secretion System Encoded in SPI-6 Plays a Role in Gastrointestinal Colonization and Systemic Spread of Salmonella enterica serovar Typhimurium in the Chicken, PLoS ONE, vol.5, issue.7, p.63917, 2013. ,
DOI : 10.1371/journal.pone.0063917.s001
The Type VI Secretion System Encoded in Salmonella Pathogenicity Island 19 Is Required for Salmonella enterica Serotype Gallinarum Survival within Infected Macrophages, Infection and Immunity, vol.81, issue.4, pp.1207-1227, 2013. ,
DOI : 10.1128/IAI.01165-12
SUMMARY, Epidemiology and Infection, vol.7, issue.11, pp.2430-2439, 2016. ,
DOI : 10.1093/bioinformatics/btp352
Inducible prophages contribute to Salmonella virulence in mice, Molecular Microbiology, vol.118, issue.1, pp.167-76, 1999. ,
DOI : 10.1016/0378-1119(85)90120-9
Identification of GtgE, a Novel Virulence Factor Encoded on the Gifsy-2 Bacteriophage of Salmonella enterica Serovar Typhimurium, Journal of Bacteriology, vol.184, issue.19, pp.5234-5243, 2002. ,
DOI : 10.1128/JB.184.19.5234-5239.2002
Identification and Characterization of Novel Salmonella Mobile Elements Involved in the Dissemination of Genes Linked to Virulence and Transmission, PLoS ONE, vol.27, issue.7, p.41247, 2012. ,
DOI : 10.1371/journal.pone.0041247.s011
The salmonella dublin virulence plasmid mediates systemic but not enteric phases of salmonellosis in cattle, Infect Immun, vol.63, issue.7, pp.2755-61, 1995. ,
Stress induction of the virulence proteins (SpvA, ?B, and -C) from native plasmid pSDL2 of salmonella dublin, Infect Immun, vol.61, issue.2, pp.705-718, 1993. ,
Helicobacter pylori ??-Glutamyl Transpeptidase Is a Pathogenic Factor in the Development of Peptic Ulcer Disease, Gastroenterology, vol.139, issue.2, pp.564-73, 2010. ,
DOI : 10.1053/j.gastro.2010.03.050
Inhibition of T-Cell Proliferation by Helicobacter pylori ??-Glutamyl Transpeptidase, Gastroenterology, vol.132, issue.5, pp.1820-1853, 2007. ,
DOI : 10.1053/j.gastro.2007.02.031
The PagN protein of Salmonella enterica serovar Typhimurium is an adhesin and invasin, BMC Microbiology, vol.8, issue.1, p.142, 2008. ,
DOI : 10.1186/1471-2180-8-142
The PagN protein mediates invasion via interaction with proteoglycan, FEMS Microbiology Letters, vol.297, issue.2, pp.209-225, 2009. ,
DOI : 10.1111/j.1574-6968.2009.01666.x
URL : https://academic.oup.com/femsle/article-pdf/297/2/209/19621988/297-2-209.pdf
Identification of an outer membrane protein of Salmonella enterica serovar Typhimurium as a potential vaccine candidate for Salmonellosis in mice, Microbes and Infection, vol.15, issue.5, pp.388-98, 2013. ,
DOI : 10.1016/j.micinf.2013.02.005
Salmonella occurrence and Enterobacteriaceae counts in pig feed ingredients and compound feed from feed mills in Ireland, Preventive Veterinary Medicine, vol.121, issue.3-4, pp.3-4231, 2015. ,
DOI : 10.1016/j.prevetmed.2015.07.002
Investigation of the genetic diversity among isolates of Salmonella enterica serovar Dublin from animals and humans from England, Wales and Ireland, Journal of Applied Microbiology, vol.135, issue.5, pp.732-776, 2002. ,
DOI : 10.1099/00221287-5-5-919