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Stephen Baker

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Vietnam

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Publications

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Helena M B Seth-Smith; Elena Shipitsyna; Rachel J Skilton; Magnus Unemo; Stephen Baker; Ian N Clarke; Lesley T Cutcliffe; Pham Thanh Duy; Daniel Golparian; Simon R Harris; Catherine A Ison; Hamid Jalal; David A Lewis; Peter Marsh; Colette O'Neill; Julian Parkhill; Surendra Parmar; Rachel Pitt; Frans M Radebe; Paul Scott; Nicholas R Thomson
Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture.
Nguyen Hoan Phu; Tran My Phuong; Le Hong Thai; Cao Quang Thai; Nguyen Van Vinh Chau; Stephen Baker; James Campbell; Tran Thi Hong Chau; Nguyen Thi Hoang Mai; Pham Phu Loc; Dinh Nguyen Huy Man; Tran Vu Thieu Nga; Ho Dang Trung Nghia; James Whitehorn
Fatal consequences of freshwater pearl diving.
Marion-Eliëtte Kolader; Ha Manh Tuan; Laura Merson; Tran Thi Ngoc Dung; Pham Thi Ngoc Tuyet; Corinne Thompson; H Rogier van Doorn; Nguyen Van Vinh Chau; Ha Vinh; Marcel Wolbers; James I Campbell; Jeremy Farrar; Stephen Baker
An oral preparation of Lactobacillus acidophilus for the treatment of uncomplicated acute watery diarrhoea in Vietnamese children: study protocol for a multicentre, randomised, placebo-controlled trial.

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All Publications

2013: Helena M B Seth-Smith; Elena Shipitsyna; Rachel J Skilton; Magnus Unemo; Stephen Baker; Ian N Clarke; Lesley T Cutcliffe; Pham Thanh Duy; Daniel Golparian; Simon R Harris; Catherine A Ison; Hamid Jalal; David A Lewis; Peter Marsh; Colette O'Neill; Julian Parkhill; Surendra Parmar; Rachel Pitt; Frans M Radebe; Paul Scott; Nicholas R Thomson
Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture.
Genome research 2013;23(5):855-66.
2013: Nguyen Hoan Phu; Tran My Phuong; Le Hong Thai; Cao Quang Thai; Nguyen Van Vinh Chau; Stephen Baker; James Campbell; Tran Thi Hong Chau; Nguyen Thi Hoang Mai; Pham Phu Loc; Dinh Nguyen Huy Man; Tran Vu Thieu Nga; Ho Dang Trung Nghia; James Whitehorn
Fatal consequences of freshwater pearl diving.
Lancet 2013;381(9861):176.
2013: Marion-Eliëtte Kolader; Ha Manh Tuan; Laura Merson; Tran Thi Ngoc Dung; Pham Thi Ngoc Tuyet; Corinne Thompson; H Rogier van Doorn; Nguyen Van Vinh Chau; Ha Vinh; Marcel Wolbers; James I Campbell; Jeremy Farrar; Stephen Baker
An oral preparation of Lactobacillus acidophilus for the treatment of uncomplicated acute watery diarrhoea in Vietnamese children: study protocol for a multicentre, randomised, placebo-controlled trial.
Trials 2013;14():27.
2013: James I Campbell; Le Thi Dung; Jeremy J Farrar; Nguyen Phu Huong Lan; Phan Tu Qui; Stephen Baker
A successful antimicrobial regime for Chromobacterium violaceum induced bacteremia.
BMC infectious diseases 2013;13():4.
2013: Tran Thi Ngoc Dung; Pham Thanh Duy; Jeremy J Farrar; Nguyen Thi Thu Hau; Nguyen Van Minh Hoang; Huynh Le Anh Huy; Duong Thi Hue Kien; Hoang Le Phuc; Phan Vu Tra My; Tran Thi Thu Nga; Tran Vu Thieu Nga; Voong Vinh Phat; Cameron Simmons; Tang Chi Thuong; Cao Thu Thuy; Ha Manh Tuan; Pham Thi Ngoc Tuyet; Pham Van Minh; Ha Vinh; Nguyen Thanh Vinh; James I Campbell; Nguyen Tran Chinh; Stephen Baker
The validation and utility of a quantitative one-step multiplex RT real-time PCR targeting rotavirus A and norovirus.
Journal of virological methods 2013;187(1):138-43.
2012: Tran Vu Thieu Nga; Christopher M Parry; John Wain; James I Campbell; Nguyen Van Vinh Chau; Jeremy N Day; To Song Diep; Christiane Dolecek; Le Thi Dung; Jeremy J Farrar; Tran Tinh Hien; Nguyen Van Minh Hoang; Nguyen Phu Huong Lan; Thuy Le; Stephen Baker
The decline of typhoid and the rise of non-typhoid salmonellae and fungal infections in a changing HIV landscape: bloodstream infection trends over 15 years in southern Vietnam.
Transactions of the Royal Society of Tropical Medicine and Hygiene 2012;106(1):26-34.
2011: Stephen Baker; Buddha Basnyat; Maciej F Boni; James I Campbell; Archie C A Clements; Christiane Dolecek; Sabina Dongol; Gordon Dougan; Pham Thanh Duy; Naomi Hammond; Kathryn E Holt; Abhilasha Karkey; Samir Koirala; Tran Vu Thieu Nga; Amit Arjyal; Jeremy J Farrar
Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission.
Open biology 2011;1(2):110008.
2011: Phan Vu Tra My; Ha Vinh; Nguyen Thanh Vinh; Phan Van Be Bay; James I Campbell; Jeremy Farrar; Nguyen Van Minh Hoang; Edward C Holmes; Le Thi Phuong; Maia A Rabaa; Nguyen Thi Tham; Stephen Baker
The emergence of rotavirus G12 and the prevalence of enteric viruses in hospitalized pediatric diarrheal patients in southern Vietnam.
The American journal of tropical medicine and hygiene 2011;85(4):768-75.
2011: Ha Vinh; Marcel Wolbers; Nguyen Duc Anh; Vo Thi Cuc Anh; Phan Van Be Bay; James I Campbell; Nguyen Van Vinh Chau; Mai Thu Chinh; Jeremy N Day; To Song Diep; Christiane Dolecek; Pham Thanh Duy; Jeremy J Farrar; Nguyen Van Minh Hoang; Nguyen Phu Huong Lan; Ha Thi Loan; Pham Van Minh; Bui Li Mong; Tran Vu Thieu Nga; Nguyen Thi Khanh Nhu; Le Thi Phuong; Nguyen Thi Hong Tham; Nguyen Thi Thu Thao; Cao Thu Thuy; Stephen Baker
A multi-center randomized trial to assess the efficacy of gatifloxacin versus ciprofloxacin for the treatment of shigellosis in Vietnamese children.
PLoS neglected tropical diseases 2011;5(8):e1264.
2011: Kathryn E Holt; Sam Kariuki; Satheesh Nair; Tran Vu Thieu Nga; Julian Parkhill; Minh Duy Phan; Arthur K Turner; Stephen Baker; Gordon Dougan; Shanta Dutta; Pham Thanh Duy; Séamus Fanning; Sinéad Farrell-Ward; Ciara Walsh; François-Xavier Weill; John Wain
Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid.
PLoS neglected tropical diseases 2011;5(7):e1245.
2011: Christopher M Parry; Lalith Wijedoru; Amit Arjyal; Stephen Baker
The utility of diagnostic tests for enteric fever in endemic locations.
Expert review of anti-infective therapy 2011;9(6):711-25.
2011: Amit Arjyal; Buddha Basnyat; Samir Koirala; Abhilasha Karkey; Sabina Dongol; Krishna Kumar Agrawaal; Nikki Shakya; Kabina Shrestha; Manish Sharma; Sanju Lama; Kasturi Shrestha; Nely Shrestha Khatri; Umesh Shrestha; James I Campbell; Stephen Baker; Jeremy Farrar; Marcel Wolbers; Christiane Dolecek
Gatifloxacin versus chloramphenicol for uncomplicated enteric fever: an open-label, randomised, controlled trial.
The Lancet infectious diseases 2011;11(6):445-54.
2011: Le Thi Minh Vien; manal abu oun; Victoria Morrison; Nicholas Thomson; James I Campbell; Martin J Woodward; Nguyen Van Vinh Chau; Jeremy Farrar; Constance Schultsz; Stephen Baker
Differential phenotypic and genotypic characteristics of qnrS1-harboring plasmids carried by hospital and community commensal enterobacteria.
Antimicrobial agents and chemotherapy 2011;55(4):1798-802.
2011: Nicholas J Croucher; Simon R Harris; Christophe Fraser; Michael A Quail; John Burton; Mark van der Linden; Lesley McGee; Anne Von Gottberg; Jae Hoon Song; Kwan Soo Ko; Bruno Pichon; Stephen Baker; Christopher M Parry; Lotte M Lambertsen; Dea Shahinas; Dylan R Pillai; Tim Mitchell; Gordon Dougan; Alexander Tomasz; keith klugman; Julian Parkhill; William P Hanage; Stephen D Bentley
Rapid pneumococcal evolution in response to clinical interventions.
Science (New York, N.Y.) 2011;331(6016):430-4.
2011: Kathryn E Holt; Christiane Dolecek; Tran Thuy Chau; Pham Thanh Duy; Tran Thi Phi La; Nguyen Van Minh Hoang; Tran Vu Thieu Nga; James I Campbell; Bui Huu Manh; Nguyen Van Vinh Chau; Tran Tinh Hien; Jeremy Farrar; Gordon Dougan; Stephen Baker
Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam.
PLoS neglected tropical diseases 2011;5(1):e929.
2011: Ngo T Hoa; Tran T B Chieu; Ho D T Nghia; Nguyen Thi Hoang Mai; Pham H Anh; Marcel Wolbers; Stephen Baker; James I Campbell; Nguyen Van Vinh Chau; Tran Tinh Hien; Jeremy Farrar; Constance Schultsz
The antimicrobial resistance patterns and associated determinants in Streptococcus suis isolated from humans in southern Vietnam, 1997-2008.
BMC infectious diseases 2011;11():6.
2010: Kathryn E Holt; Stephen Baker; Sabina Dongol; Buddha Basnyat; Neelam Adhikari; Stephen Thorson; Anoop S Pulickal; Yajun Song; Julian Parkhill; Jeremy J Farrar; David R Murdoch; Dominic F Kelly; Andrew J Pollard; Gordon Dougan
High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children.
BMC infectious diseases 2010;10():144.
2008: Kathryn E Holt; Julian Parkhill; Camila J Mazzoni; Philippe Roumagnac; François-Xavier Weill; Ian Goodhead; Richard Rance; Stephen Baker; Duncan J Maskell; John Wain; Christiane Dolecek; Mark Achtman; Gordon Dougan
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.
Nature genetics 2008;40(8):987-93.
2008: Anne Bishop; Deborah House; Timothy Perkins; Stephen Baker; Robert Kingsley; Gordon Dougan
Interaction of Salmonella enterica serovar Typhi with cultured epithelial cells: roles of surface structures in adhesion and invasion.
Microbiology (Reading, England) 2008;154(Pt 7):1914-26.
2008: Stephen Baker; Derek Pickard; Sally Whitehead; Jeremy Farrar; Gordon Dougan
Mobilization of the incQ plasmid R300B with a chromosomal conjugation system in Salmonella enterica serovar typhi.
Journal of bacteriology 2008;190(11):4084-7.
2008: Stephen Baker; Kathryn Holt; Esther van de Vosse; Philippe Roumagnac; Sally Whitehead; Emma King; Philip Ewels; Andrew Keniry; François-Xavier Weill; Diane Lightfoot; Jaap T van Dissel; Kenneth E Sanderson; Jeremy Farrar; Mark Achtman; Panos Deloukas; Gordon Dougan
High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and pathotypes within an urban District of Jakarta, Indonesia.
Journal of clinical microbiology 2008;46(5):1741-6.
2008: Derek Pickard; Nicholas R Thomson; Stephen Baker; John Wain; Mercedes Pardo; David Goulding; Nancy Hamlin; Jyoti Choudhary; John Threfall; Gordon Dougan
Molecular characterization of the Salmonella enterica serovar Typhi Vi-typing bacteriophage E1.
Journal of bacteriology 2008;190(7):2580-7.
2007: Stephen Baker; Kathryn Holt; Sally Whitehead; Ian Goodhead; Tim Perkins; Bruce A D Stocker; Jonathan Hardy; Gordon Dougan
A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi.
Molecular microbiology 2007;66(5):1207-18.
2007: Stephen Baker; Gordon Dougan
The genome of Salmonella enterica serovar Typhi.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2007;45 Suppl 1():S29-33.
2007: Stephen Baker; Jonathan Hardy; Kenneth E Sanderson; Michael A Quail; Ian Goodhead; Robert Kingsley; Julian Parkhill; Bruce A D Stocker; Gordon Dougan
A novel linear plasmid mediates flagellar variation in Salmonella Typhi.
PLoS pathogens 2007;3(5):e59.
2005: Muna F Anjum; Chris Marooney; Maria Fookes; Stephen Baker; Gordon Dougan; Alasdair Ivens; Martin J Woodward
Identification of core and variable components of the Salmonella enterica subspecies I genome by microarray.
Infection and immunity 2005;73(12):7894-905.
2005: Stephen Baker; Yasra Sarwar; Hafsa Aziz; Asma Haque; Aamir Ali; Gordon Dougan; John Wain; Abdul Haque
Detection of Vi-negative Salmonella enterica serovar typhi in the peripheral blood of patients with typhoid fever in the Faisalabad region of Pakistan.
Journal of clinical microbiology 2005;43(9):4418-25.
2005: Anne L Bishop; Stephen Baker; Sara Jenks; Maria Fookes; Peadar Ó Gaora; Derek Pickard; Muna F Anjum; Jeremy Farrar; Tran Tinh Hien; Alasdair Ivens; Gordon Dougan
Analysis of the hypervariable region of the Salmonella enterica genome associated with tRNA(leuX).
Journal of bacteriology 2005;187(7):2469-82.
2005: John Wain; Deborah House; Afia Zafar; Stephen Baker; Satheesh Nair; Claire Kidgell; Zulfiqar A Bhutta; Gordon Dougan; Rumina Hasan
Vi antigen expression in Salmonella enterica serovar Typhi clinical isolates from Pakistan.
Journal of clinical microbiology 2005;43(3):1158-65.
2004: Nicholas Thomson; Stephen Baker; Derek Pickard; Maria Fookes; Muna F Anjum; Nancy Hamlin; John Wain; Deborah House; Zulfiqar A Bhutta; Kaman Chan; Stanley Falkow; Julian Parkhill; Martin Woodward; Alasdair Ivens; Gordon Dougan
The role of prophage-like elements in the diversity of Salmonella enterica serovars.
Journal of molecular biology 2004;339(2):279-300.
2004: Minghsun Liu; Mari Gingery; Sergei R Doulatov; Yichin Liu; Asher Hodes; Stephen Baker; Paul Davis; Mark Simmonds; Carol Churcher; Karen Mungall; Michael A Quail; Andrew Preston; Eric T Harvill; Duncan J Maskell; Frederick A Eiserling; Julian Parkhill; Jeff F Miller
Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes.
Journal of bacteriology 2004;186(5):1503-17.
2003: Derek Pickard; John Wain; Stephen Baker; Alexandra Line; Sonia Chohan; Maria Fookes; Andrew Barron; Peadar Ó Gaora; José A Chabalgoity; Niren Thanky; Christoph Scholes; Nicholas Thomson; Michael A Quail; Julian Parkhill; Gordon Dougan
Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7.
Journal of bacteriology 2003;185(17):5055-65.
2001: SM Townsend; N E Kramer; R Edwards; Stephen Baker; Nancy Hamlin; Mark Simmonds; K Stevens; S Maloy; Julian Parkhill; Gordon Dougan; Andreas J Baumler
Salmonella enterica serovar Typhi possesses a unique repertoire of fimbrial gene sequences.
Infection and immunity 2001;69(5):2894-901.