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1. Full Text Ribosomal RNA Gene Restriction Patterns Provide Increased Sensitivity for Typing Salmonella typhi Strains
by M. Altwegg and F. W. Hickman-Brenner and J. J. Farmer
The Journal of Infectious Diseases, ISSN 0022-1899, 7/1989, Volume 160, Issue 1, pp. 145 - 149
To date, epidemiologic associations among strains of Salmonella typhi are based exclusively on phage typing, which may be of limited value if a common phage... 
Bacteriophages | Enzymes | Bacteriophage typing | RNA | Plasmids | Ribosomal RNA | DNA | rRNA genes | Concise Communications | Salmonella typhi | Bile | INFECTIOUS DISEASES | Nucleic Acid Hybridization | DNA, Bacterial - genetics | DNA, Ribosomal - analysis | Bacteriophage Typing | Humans | Salmonella typhi - classification | RNA, Bacterial - genetics | DNA, Bacterial - analysis | RNA, Ribosomal - genetics | Restriction Mapping | Salmonella typhi - genetics | DNA, Ribosomal - genetics
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2. Full Text Evolutionary History of Salmonella Typhi
by Philippe Roumagnac and François-Xavier Weill and Christiane Dolecek and Stephen Baker and Sylvain Brisse and Nguyen Tran Chinh and Thi Anh Hong Le and Camilo J. Acosta and Jeremy Farrar and Gordon Dougan and Mark Achtman
Science, ISSN 0036-8075, 11/2006, Volume 314, Issue 5803, pp. 1301 - 1304
For microbial pathogens, phylogeographic differentiation seems to be relatively common. However, the neutral population structure of Salmonella enterica... 
Haplotypes | Pathogens | Clock rate | Medical genetics | Evolution | Evolutionary genetics | Population structure | Reports | Genetic mutation | Epidemiology | Human genetics | STRAINS | POLYMORPHISMS | MULTIDISCIPLINARY SCIENCES | ESCHERICHIA-COLI | RESISTANCE | DYNAMICS | BACILLUS | FEVER | Adaptation, Physiological | Humans | Carrier State - microbiology | Drug Resistance, Bacterial | Molecular Sequence Data | Genetic Variation | Anti-Bacterial Agents - therapeutic use | Salmonella typhi - drug effects | Drug Resistance, Multiple, Bacterial | Salmonella typhi - genetics | Genes, Bacterial | Africa | Selection, Genetic | Fluoroquinolones - therapeutic use | Typhoid Fever - drug therapy | Polymorphism, Genetic | Biological Evolution | Typhoid Fever - microbiology | DNA Gyrase - genetics | Asia | Fluoroquinolones - pharmacology | Alleles | Anti-Bacterial Agents - pharmacology | Polymorphism, Single Nucleotide | Mutation | Salmonella typhosa | Research | History | Population genetics | Analysis
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3. Full Text Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter-and intracontinental transmission events
by Wong, Vanessa K and Baker, Stephen and Pickard, Derek J and Parkhill, Julian and Page, Andrew J and Feasey, Nicholas A and Kingsley, Robert A and Thomson, Nicholas R and Keane, Jacqueline A and Weill, François-Xavier and Edwards, David J and Hawkey, Jane and Harris, Simon R and Mather, Alison E and Cain, Amy K and Hadfield, James and Hart, Peter J and Thieu, Nga Tran Vu and Klemm, Elizabeth J and Glinos, Dafni A and Breiman, Robert F and Watson, Conall H and Kariuki, Samuel and Gordon, Melita A and Heyderman, Robert S and Okoro, Chinyere and Jacobs, Jan and Lunguya, Octavie and Edmunds, W John and Msefula, Chisomo and Chabalgoity, Jose A and Kama, Mike and Jenkins, Kylie and Dutta, Shanta and Marks, Florian and Campos, Josefina and Thompson, Corinne and Obaro, Stephen and Maclennan, Calman A and Dolecek, Christiane and Keddy, Karen H and Smith, Anthony M and Parry, Christopher M and Karkey, Abhilasha and Mulholland, E. Kim and Campbell, James I and Dongol, Sabina and Basnyat, Buddha and Dufour, Muriel and Bandaranayake, Don and Naseri, Take Toleafoa and Singh, Shalini Pravin and Hatta, Mochammad and Newton, Paul and Onsare, Robert S and Isaia, Lupeoletalalei and Dance, David and Davong, Viengmon and Thwaites, Guy and Wijedoru, Lalith and Crump, John A and De Pinna, Elizabeth and Nair, Satheesh and Nilles, Eric J and Thanh, Duy Pham and Turner, Paul and Soeng, Sona and Valcanis, Mary and Powling, Joan and Dimovski, Karolina and Hogg, Geoff and Farrar, Jeremy and Holt, Kathryn E and Dougan, Gordon
Nature Genetics, ISSN 1061-4036, 05/2015, Volume 47, Issue 6, pp. 632 - 639
The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome... 
POPULATION | EVOLUTION | INCHI1 PLASMIDS | ANNOTATION | GENETICS & HEREDITY | ANTIBIOTIC-RESISTANCE | INTERACTIVE TREE | ENTERICA SEROVAR TYPHI | MUTATIONS | PARATYPHI | FEVER | Genome, Bacterial | Humans | Phylogeography | Molecular Sequence Data | Typhoid Fever - transmission | Typhoid Fever - drug therapy | Phylogeny | Sequence Analysis, DNA | Quinolines - pharmacology | Anti-Bacterial Agents - therapeutic use | Typhoid Fever - microbiology | Drug Resistance, Multiple, Bacterial | Anti-Bacterial Agents - pharmacology | Quinolines - therapeutic use | Salmonella typhi - genetics | Drug resistance in microorganisms | Salmonella typhosa | Genetic aspects | Virulence (Microbiology) | Identification and classification | Haplotypes | Medical research | Salmonella | Genomes | Typhoid | Infectious diseases | Antibiotics | Councils | Plasmids | Data collection | Phylogenetics | Population | Mutation | Acquisitions & mergers | Life Sciences | Microbiology and Parasitology | Bacteriology
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4. Full Text Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants
by Langridge, Gemma C and Phan, Minh-Duy and Turner, Daniel J and Perkins, Timothy T and Parts, Leopold and Haase, Jana and Charles, Ian and Maskell, Duncan J and Peters, Sarah E and Dougan, Gordon and Wain, John and Parkhill, Julian and Turner, A. Keith
Genome Research, ISSN 1088-9051, 12/2009, Volume 19, Issue 12, pp. 2308 - 2316
Very high-throughput sequencing technologies need to be matched by high-throughput functional studies if we are to make full use of the current explosion in... 
BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | LIBRARY | SEQUENCING TECHNOLOGIES | TYPHIMURIUM | COLONIZATION | IDENTIFICATION | VIRULENCE | MOUSE INTESTINE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BILE RESISTANCE | GENETICS & HEREDITY | LIPOPOLYSACCHARIDE | Computational Biology - methods | Chromosomes, Bacterial - genetics | Bacterial Proteins - genetics | Bile - physiology | Chromosome Mapping | Genes, Essential | Sequence Analysis, DNA | Salmonella typhi - growth & development | Salmonella typhi - drug effects | DNA Transposable Elements - genetics | Mutagenesis, Insertional | Mutation | Salmonella typhi - genetics | Salmonella enteritidis | Usage | Transposons | Gene mutations | Analysis | Genetic aspects | Nucleotide sequencing | Research | Methods
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5. Full Text High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi
by Holt, Kathryn E and Parkhill, Julian and Mazzoni, Camila J and Roumagnac, Philippe and Weill, François-Xavier and Goodhead, Ian and Rance, Richard and Baker, Stephen and Maskell, Duncan J and Wain, John and Dolecek, Christiane and Achtman, Mark and Dougan, Gordon
Nature Genetics, ISSN 1061-4036, 08/2008, Volume 40, Issue 8, pp. 987 - 993
Isolates of Salmonella enterica serovar Typhi (Typhi), a human-restricted bacterial pathogen that causes typhoid, show limited genetic variation. We generated... 
STRAINS | RECOMBINATION | SANTIAGO | ACQUISITION | GENETICS & HEREDITY | RESISTANCE | DIVERSITY | ENTERICA SEROVAR TYPHI | PATHOGENICITY ISLAND | BACILLUS | VI EXOPOLYSACCHARIDE | Genome, Bacterial | Humans | Genomic Islands | Molecular Sequence Data | Phylogeny | Typhoid Fever - microbiology | Recombination, Genetic | Salmonella typhi - classification | Plasmids - genetics | Bacteriophages - genetics | Polymorphism, Single Nucleotide | Sequence Analysis, DNA - methods | Salmonella typhi - genetics | Evolution, Molecular | Genetic variation | Analysis | Salmonella typhosa | Genetic aspects | Research | Gene expression | Antigenic determinants | Salmonella | Bacteria | Genetics | E coli | Tropical diseases | Data bases
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6. Full Text A strand-specific RNA-seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi
by Perkins, Timothy T and Kingsley, Robert A and Fookes, Maria C and Gardner, Paul P and James, Keith D and Yu, Lu and Assefa, Samuel A and He, Miao and Croucher, Nicholas J and Pickard, Derek J and Maskell, Duncan J and Parkhill, Julian and Choudhary, Jyoti and Thomson, Nicholas R and Dougan, Gordon
PLoS Genetics, ISSN 1553-7390, 07/2009, Volume 5, Issue 7, p. e1000569
High-density, strand-specific cDNA sequencing (ssRNA-seq) was used to analyze the transcriptome of Salmonella enterica serovar Typhi (S. Typhi). By mapping... 
IRON TRANSPORT | TRANSPORT-SYSTEM | OMPR MUTANTS | COMPLETE GENOME SEQUENCE | NONCODING RNAS | ENTERICA SEROVAR TYPHIMURIUM | ESCHERICHIA-COLI K-12 | SECRETION SYSTEM | GENETICS & HEREDITY | PORIN GENE | PATHOGENICITY ISLAND | Sequence Analysis, RNA | Proteomics | RNA, Bacterial - genetics | Gene Expression Profiling | Bacterial Proteins - analysis | Salmonella typhi - genetics | DNA, Complementary | RNA, Bacterial - analysis | Physiological aspects | Salmonella | Genetic aspects | Research | Nucleotide sequence | Bacillus subtilis | Mascots | Peptides | Genomics | Genomes | Typhoid | Experiments | Data bases
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7. Full Text Salmonella enterica serovar typhi and the pathogenesis of typhoid fever
by Dougan, Gordon and Baker, Stephen
Annual Review of Microbiology, ISSN 0066-4227, 09/2014, Volume 68, pp. 317 - 336
Salmonella enterica serovar Typhi, the cause of typhoid, is host restricted to humans. S. Typhi has a monophyletic population structure, indicating that... 
Enteric fever | Typhoid | Salmonella Typhi | Salmonella Paratyphi A | REDUCED SUSCEPTIBILITY | SEROTYPE TYPHIMURIUM | typhoid | PARATYPHI-A | MICROBIOLOGY | CLINICAL-FEATURES | TRANSMEMBRANE CONDUCTANCE REGULATOR | INTESTINAL INFLAMMATION | enteric fever | TRANSCRIBED SEQUENCES | COMPLETE GENOME SEQUENCE | SELECTIVE CAPTURE | CULTURED EPITHELIAL-CELLS | Anti-Bacterial Agents - therapeutic use | Salmonella typhi - pathogenicity | Animals | Typhoid Fever - microbiology | Salmonella typhi - isolation & purification | Humans | Salmonella typhi - classification | Serogroup | Typhoid Fever - drug therapy | Salmonella typhi - genetics | Salmonella | Microbiological research | Physiological aspects | Host-parasite relationships | Typhoid fever | Research | Health aspects
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8. Full Text MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island
by Ashton, Philip M and Nair, Satheesh and Dallman, Tim and Rubino, Salvatore and Rabsch, Wolfgang and Mwaigwisya, Solomon and Wain, John and O'Grady, Justin
Nature Biotechnology, ISSN 1087-0156, 2015, Volume 33, Issue 3, pp. 296 - 302
Short-read, high-throughput sequencing technology cannot identify the chromosomal position of repetitive insertion sequences that typically flank horizontally... 
TYPHI | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | Chromosomes, Bacterial - genetics | Plasmids - genetics | CpG Islands - genetics | Base Composition - genetics | High-Throughput Nucleotide Sequencing - instrumentation | Drug Resistance, Bacterial - genetics | High-Throughput Nucleotide Sequencing - methods | Nanopores | Salmonella typhi - genetics | Salmonella | Microbiological research | Genetic research | Genetic aspects | Research | Nucleotide sequencing | Virulence (Microbiology) | Health aspects | DNA sequencing
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9. Full Text Emergence of an extensively drug-resistant Salmonella enterica serovar typhi clone harboring a promiscuous plasmid encoding resistance to fluoroquinolones and third-generation cephalosporins
by Klemm, Elizabeth J and Shakoor, Sadia and Page, Andrew J and Qamar, Farah Naz and Judge, Kim and Saeed, Dania K and Wong, Vanessa K and Dallman, Timothy J and Nair, Satheesh and Baker, Stephen and Shaheen, Ghazala and Qureshi, Shahida and Yousafzai, Mohammad Tahir and Saleem, Muhammad Khalid and Hasan, Zahra and Dougan, Gordon and Hasan, Rumina
mBio, ISSN 2161-2129, 01/2018, Volume 9, Issue 1, p. e00105-18
Antibiotic resistance is a major problem in Salmonella enterica serovar Typhi, the causative agent of typhoid. Multidrug-resistant (MDR) isolates are prevalent... 
Salmonella | Typhi | Typhoid | Antibiotic resistance | VISUALIZATION | antibiotic resistance | typhoid | BETA-LACTAMASE | PAKISTAN | MICROBIOLOGY | ANTIMICROBIAL RESISTANCE | Haplotypes | Pakistan | Salmonella typhi - drug effects | Typhoid Fever - microbiology | Salmonella typhi - isolation & purification | Drug Resistance, Multiple, Bacterial | Fluoroquinolones - pharmacology | Anti-Bacterial Agents - pharmacology | Plasmids - analysis | Cephalosporins - pharmacology | Salmonella typhi - genetics | Whole Genome Sequencing
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10. Full Text Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18
by Parkhill, J and Dougan, G and James, K.D and Thomson, N.R and Pickard, D and Wain, J and Churcher, C and Mungall, K.L and Bentley, S.D and Holden, M.T.G and Sebaihia, M and Baker, S and Basham, D and Brooks, K and Chillingworth, T and Connerton, P and Cronin, A and Davis, P and Davies, R.M and Dowd, L and White, N and Farrar, J and Feltwell, T and Hamlin, N and Haque, A and Hien, T.T and Holroyd, S and Jagels, K and Krogh, A and Larsen, T.S and Leather, S and Moule, S and Ó'Gaora, P and Parry, C and Quail, M and Rutherford, K and Simmonds, M and Skelton, J and Stevens, K and Whitehead, S and Barrell, B.G
Nature, ISSN 0028-0836, 10/2001, Volume 413, Issue 6858, pp. 848 - 852
Salmonella enterica serovar Typhi (S. typhi) is the aetiological agent of typhoid fever, a serious invasive bacterial disease of humans with an annual global... 
BACTERIA | PROTEIN | EPITHELIAL-CELLS | YERSINIA-PESTIS | MULTIDISCIPLINARY SCIENCES | PLASMID | COMPLETE DNA-SEQUENCE | TYPHIMURIUM | IDENTIFICATION | VIRULENCE | STRAIN | Genome, Bacterial | Salmonella typhimurium - genetics | Humans | Molecular Sequence Data | Chromosome Mapping | Chromosomes, Bacterial | Sequence Analysis, DNA | DNA, Bacterial | Escherichia coli - genetics | Recombination, Genetic | Gene Deletion | Plasmids - genetics | Mutagenesis, Insertional | Drug Resistance, Multiple, Bacterial - genetics | Salmonella typhi - genetics | Serotyping | Bacteria | Drug resistance | Genomics | Genes
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11. Full Text A Rab32-Dependent Pathway Contributes to Salmonella Typhi Host Restriction
by Stefania Spanò and Jorge E. Galán
Science, ISSN 0036-8075, 11/2012, Volume 338, Issue 6109, pp. 960 - 963
Unlike other Salmonellae, the intracellular bacterial human pathogen Salmonella Typhi exhibits strict host specificity. The molecular bases for this... 
T lymphocytes | Pathogens | Humans | REPORTS | Colony forming units assay | Salmonella typhi | Bacteria | Infections | Mice | Macrophages | Vacuoles | PATHOGENESIS | MULTIDISCIPLINARY SCIENCES | PUDIAK-SYNDROME | SYNDROME GENES | TYPHIMURIUM | BACTERIAL SURVIVAL | LYSOSOME-RELATED ORGANELLES | III SECRETION | HERMANSKY-PUDLAK-SYNDROME | SECRETORY LYSOSOMES | MURINE | Amino Acid Sequence | Bacterial Secretion Systems - genetics | Mice, Inbred C57BL | Cercopithecus aethiops | Molecular Sequence Data | rab GTP-Binding Proteins - genetics | Phylogeny | Bacterial Secretion Systems - physiology | Host-Pathogen Interactions | rab GTP-Binding Proteins - physiology | Animals | Lysosomes - metabolism | RNA Interference | Salmonella typhi - physiology | rab GTP-Binding Proteins - classification | COS Cells | Salmonella typhi - genetics | Salmonella typhosa | Genetic aspects | Cell organelles | Properties | Formation | Salmonella | Human | Effectors | Constrictions | Typhoid | macrophages | Rab32 | innate immunity | Rab GTPases | typhoid fever | lysosome-related organelles | lysosomes | bacterial pathogenesis | membrane traffic | type III secretion
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12. Full Text A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium
by Barquist, Lars and Langridge, Gemma C and Turner, Daniel J and Phan, Minh-Duy and Turner, A. Keith and Bateman, Alex and Parkhill, Julian and Wain, John and Gardner, Paul P
Nucleic Acids Research, ISSN 0305-1048, 04/2013, Volume 41, Issue 8, pp. 4549 - 4564
Salmonella Typhi and Typhimurium diverged only similar to 50 000 years ago, yet have very different host ranges and pathogenicity. Despite the availability of... 
TRANSFER-RNA GENES | COMPLETE GENOME SEQUENCE | INCHI1 PLASMIDS | BIOCHEMISTRY & MOLECULAR BIOLOGY | IN-VIVO | ANTIBIOTIC-RESISTANCE | H-NS | PATHOGENICITY ISLAND | SCALE IDENTIFICATION | ESCHERICHIA-COLI GENOME | III SECRETION SYSTEM | Genes, Bacterial | Gene Library | Salmonella typhimurium - genetics | Salmonella typhimurium - growth & development | Bacterial Proteins - genetics | RNA, Small Untranslated - genetics | Mutagenesis, Insertional | RNA, Untranslated - genetics | DNA Transposable Elements | Salmonella typhi - genetics | Salmonella typhi - growth & development | Genomics
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