Stephen Baker

Summary

Affiliation: Ho Chi Minh City
Country: Vietnam

Publications

  1. pmc Searching for the elusive typhoid diagnostic
    Stephen Baker
    Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
    BMC Infect Dis 10:45. 2010
  2. pmc High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi
    Kathryn E Holt
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nat Genet 40:987-93. 2008
  3. pmc Epidemiological features and risk factors of Salmonella gastroenteritis in children resident in Ho Chi Minh City, Vietnam
    C N Thompson
    Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
    Epidemiol Infect 141:1604-13. 2013
  4. pmc The burden and characteristics of enteric fever at a healthcare facility in a densely populated area of Kathmandu
    Abhilasha Karkey
    Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Lagankhel, Kathmandu, Nepal
    PLoS ONE 5:e13988. 2010
  5. pmc Differential epidemiology of Salmonella Typhi and Paratyphi A in Kathmandu, Nepal: a matched case control investigation in a highly endemic enteric fever setting
    Abhilasha Karkey
    Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
    PLoS Negl Trop Dis 7:e2391. 2013
  6. pmc The policy of free healthcare for children under the age of 6 years in Vietnam: assessment of the uptake for children hospitalised with acute diarrhoea in Ho Chi Minh City
    Mae Shieh
    Novartis Vaccines Institute for Global Health, Siena, Italy
    Trop Med Int Health 18:1444-51. 2013
  7. pmc The microbiological and clinical characteristics of invasive salmonella in gallbladders from cholecystectomy patients in kathmandu, Nepal
    Sabina Dongol
    Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
    PLoS ONE 7:e47342. 2012
  8. pmc Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission
    Stephen Baker
    The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 190 Ben Ham Tu, Quan 5, Ho Chi Minh City, Vietnam
    Open Biol 1:110008. 2011
  9. pmc High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and pathotypes within an urban District of Jakarta, Indonesia
    Stephen Baker
    The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
    J Clin Microbiol 46:1741-6. 2008
  10. pmc Fatal wound infection caused by Chromobacterium violaceum in Ho Chi Minh City, Vietnam
    Stephen Baker
    Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 190 Ben Ham Tu, Quan 5, Ho Chi Minh City, Vietnam
    J Clin Microbiol 46:3853-5. 2008

Detail Information

Publications61

  1. pmc Searching for the elusive typhoid diagnostic
    Stephen Baker
    Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
    BMC Infect Dis 10:45. 2010
    ..Here we discuss the current position of typhoid diagnostics, highlight the need for technological improvements and suggest potential ways of advancing this area...
  2. pmc High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi
    Kathryn E Holt
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nat Genet 40:987-93. 2008
    ..The observed patterns of genetic isolation and drift are consistent with the proposed key role of asymptomatic carriers of Typhi as the main reservoir of this pathogen, highlighting the need for identification and treatment of carriers...
  3. pmc Epidemiological features and risk factors of Salmonella gastroenteritis in children resident in Ho Chi Minh City, Vietnam
    C N Thompson
    Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
    Epidemiol Infect 141:1604-13. 2013
    ..Our findings indicate that Salmonella are an important cause of paediatric gastroenteritis in this setting and we suggest that transmission may occur through direct human contact in the home...
  4. pmc The burden and characteristics of enteric fever at a healthcare facility in a densely populated area of Kathmandu
    Abhilasha Karkey
    Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Lagankhel, Kathmandu, Nepal
    PLoS ONE 5:e13988. 2010
    ..These findings are important for initiating a vaccination scheme and improvements in sanitation. We suggest any such intervention should be implemented throughout the LSMC area...
  5. pmc Differential epidemiology of Salmonella Typhi and Paratyphi A in Kathmandu, Nepal: a matched case control investigation in a highly endemic enteric fever setting
    Abhilasha Karkey
    Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
    PLoS Negl Trop Dis 7:e2391. 2013
    ..Here, we sought to examine individual-level risk factors related to hygiene and sanitation to improve our understanding of the epidemiology of enteric fever in this setting...
  6. pmc The policy of free healthcare for children under the age of 6 years in Vietnam: assessment of the uptake for children hospitalised with acute diarrhoea in Ho Chi Minh City
    Mae Shieh
    Novartis Vaccines Institute for Global Health, Siena, Italy
    Trop Med Int Health 18:1444-51. 2013
    ....
  7. pmc The microbiological and clinical characteristics of invasive salmonella in gallbladders from cholecystectomy patients in kathmandu, Nepal
    Sabina Dongol
    Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
    PLoS ONE 7:e47342. 2012
    ..We predict that such individuals will become increasingly important if current transmission mechanisms are disturbed; prospectively identifying these individuals is, therefore, paramount for rapid local and regional elimination...
  8. pmc Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission
    Stephen Baker
    The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 190 Ben Ham Tu, Quan 5, Ho Chi Minh City, Vietnam
    Open Biol 1:110008. 2011
    ..These findings have implications for typhoid-control strategies, and our innovative approach may be applied to other diseases caused by other monophyletic or emerging pathogens...
  9. pmc High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and pathotypes within an urban District of Jakarta, Indonesia
    Stephen Baker
    The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
    J Clin Microbiol 46:1741-6. 2008
    ..The study also provides insight into the evolution of serovar Typhi and demonstrates the value of a molecular epidemiological technique that is exchangeable, that is internet friendly, and that has global utility...
  10. pmc Fatal wound infection caused by Chromobacterium violaceum in Ho Chi Minh City, Vietnam
    Stephen Baker
    Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 190 Ben Ham Tu, Quan 5, Ho Chi Minh City, Vietnam
    J Clin Microbiol 46:3853-5. 2008
    ..Here, we report a fatal bacteremia caused by Chromobacterium violaceum in Vietnam. We describe a number of clinical, microbiological, and molecular aspects associated with this bacterial infection...
  11. pmc Navigating the future of bacterial molecular epidemiology
    Stephen Baker
    Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Diseases, 190 Ben Ham Tu, Quan 5, Ho Chi Minh City, Viet Nam
    Curr Opin Microbiol 13:640-5. 2010
    ..As genome sequencing, SNP detection and geospatial information become more accessible these methods will continue to transform the way molecular epidemiology is used to study populations of bacterial pathogens...
  12. pmc Mobilization of the incQ plasmid R300B with a chromosomal conjugation system in Salmonella enterica serovar typhi
    Stephen Baker
    The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
    J Bacteriol 190:4084-7. 2008
    ..Evidence suggests that SPI-7 is susceptible to spontaneous circularization, loss, and transposition. Here, we demonstrate that a region within SPI-7 has the ability to mobilize the small incQ plasmid R300B...
  13. pmc High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children
    Kathryn E Holt
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    BMC Infect Dis 10:144. 2010
    ..Kathmandu, the capital of Nepal, is an area of high incidence and the pediatric population appears to be at high risk of exposure and infection...
  14. pmc Endemic norovirus infections in children, Ho Chi Minh City, Vietnam, 2009-2010
    Phan Vu Tra My
    Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
    Emerg Infect Dis 19:977-80. 2013
    ..6% and 2.8%, respectively, were norovirus positive. Risk factors included residential crowding and symptomatic contacts, indicating person-to-person transmission of norovirus...
  15. pmc Highly resistant Salmonella enterica serovar Typhi with a novel gyrA mutation raises questions about the long-term efficacy of older fluoroquinolones for treating typhoid fever
    Kanika Deshpande Koirala
    Oxford University Clinical Research Unit Patan Academy of Health Sciences, Kathmandu, Nepal
    Antimicrob Agents Chemother 56:2761-2. 2012
    ..The isolation of this organism has serious implications for the long-term efficacy of ciprofloxacin and ofloxacin for typhoid treatment...
  16. pmc A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi
    Stephen Baker
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Mol Microbiol 66:1207-18. 2007
    ..These data demonstrate that, like some Streptomyces linear elements, at least one of the terminal inverted repeats of pBSSB1 is non-essential, but that a palindromic repeat sequence may be necessary for replication...
  17. pmc The co-selection of fluoroquinolone resistance genes in the gut flora of Vietnamese children
    Le Thi Minh Vien
    Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
    PLoS ONE 7:e42919. 2012
    ....
  18. pmc The dynamics of GII.4 Norovirus in Ho Chi Minh City, Vietnam
    Phan Vu Tra My
    Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
    Infect Genet Evol 18:335-43. 2013
    ..4-2010 variant was detected. These data show that NoV GII.4 variants are highly endemic in HCMC and describe a scenario of rapid NoV strain replacement occurring in HCMC in early 2010. ..
  19. pmc Gatifloxacin versus ofloxacin for the treatment of uncomplicated enteric fever in Nepal: an open-label, randomized, controlled trial
    Samir Koirala
    Oxford University Clinical Research Unit Nepal, Patan Academy of Health Sciences, Patan Hospital, Patan, Nepal
    PLoS Negl Trop Dis 7:e2523. 2013
    ....
  20. pmc The influence of reduced susceptibility to fluoroquinolones in Salmonella enterica serovar Typhi on the clinical response to ofloxacin therapy
    Christopher M Parry
    Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
    PLoS Negl Trop Dis 5:e1163. 2011
    ..Data from 540 patients randomised to ofloxacin treatment was analysed to identify an MIC of the infecting organism associated with treatment failure...
  21. pmc The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens
    Tran Vu Thieu Nga
    Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
    BMC Infect Dis 10:125. 2010
    ..Invasive Salmonella serovars, which cause enteric fever, can be commonly cultured from the blood of infected patients. Yet, the isolation of invasive Salmonella serovars from blood is protracted and potentially insensitive...
  22. pmc Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam
    Kathryn E Holt
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Negl Trop Dis 5:e929. 2011
    ..Typhi isolated from 267 typhoid fever patients in the Mekong delta region participating in a randomized trial conducted between 2004 and 2005...
  23. pmc The validation and utility of a quantitative one-step multiplex RT real-time PCR targeting rotavirus A and norovirus
    Tran Thi Ngoc Dung
    The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
    J Virol Methods 187:138-43. 2013
    ..This internally controlled real-time PCR method is robust, exhibits a high degree of reproducibility, and may have a greater utility and sensitivity than commercial EIA kits...
  24. pmc Differential phenotypic and genotypic characteristics of qnrS1-harboring plasmids carried by hospital and community commensal enterobacteria
    Le Thi Minh Vien
    The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
    Antimicrob Agents Chemother 55:1798-802. 2011
    ..Our data imply that the characteristics of the two plasmid groups are indicative of distinct selective pressures in the differing environments...
  25. pmc Gatifloxacin versus chloramphenicol for uncomplicated enteric fever: an open-label, randomised, controlled trial
    Amit Arjyal
    Oxford University Clinical Research Unit Patan Academy of Health Sciences, Kathmandu, Nepal
    Lancet Infect Dis 11:445-54. 2011
    ..We aimed to investigate whether gatifloxacin, a new generation and affordable fluoroquinolone, is better than chloramphenicol for the treatment of uncomplicated enteric fever in children and adults...
  26. pmc A multi-center randomized trial to assess the efficacy of gatifloxacin versus ciprofloxacin for the treatment of shigellosis in Vietnamese children
    Ha Vinh
    The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
    PLoS Negl Trop Dis 5:e1264. 2011
    ..We aimed to assess the efficacy of gatifloxacin versus ciprofloxacin in the treatment of uncomplicated shigellosis in children...
  27. ncbi The genome of Salmonella enterica serovar Typhi
    Stephen Baker
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
    Clin Infect Dis 45:S29-33. 2007
    ..Evidence suggests that, as well as undergoing gene degradation, S. Typhi has also recently acquired genes, such as those encoding the Vi antigen, by horizontal transfer events...
  28. ncbi The characterization of ESBL genes in Escherichia coli and Klebsiella pneumoniae causing nosocomial infections in Vietnam
    Nguyen Hoang Thu Trang
    Faculty of Pharmacy, University of Medicine and Pharmacy, Ho Chi Minh City, Viet Nam
    J Infect Dev Ctries 7:922-8. 2013
    ..We aimed to investigate the complement of ESBL genes in E. coli and Klebsiella pneumoniae causing nosocomial infections in hospitals in Ho Chi Minh City, Vietnam...
  29. pmc Risk factors for the development of severe typhoid fever in Vietnam
    Christopher M Parry
    Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Vietnam
    BMC Infect Dis 14:73. 2014
    ..Age, sex, prolonged duration of illness, and infection with an antimicrobial resistant organism have been proposed risk factors for the development of severe disease or fatality in typhoid fever...
  30. pmc Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae
    Helena M B Seth-Smith
    Pathogen Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    J Bacteriol 194:1494-504. 2012
    ..We present a growing family of SPI-7-related ICEs whose mobility, abundance, and cargo variability indicate that these elements may have had a large impact on the evolution of the Enterobacteriaceae...
  31. pmc Most cases of cryptococcal meningitis in HIV-uninfected patients in Vietnam are due to a distinct amplified fragment length polymorphism-defined cluster of Cryptococcus neoformans var. grubii VN1
    Jeremy N Day
    Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
    J Clin Microbiol 49:658-64. 2011
    ..Two clusters of C. neoformans var. grubii VN1 are responsible for the majority of cases of cryptococcal meningitis in Vietnam. The distribution of these clusters differs according to the immune status of the host...
  32. pmc Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid
    Kathryn E Holt
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
    PLoS Negl Trop Dis 5:e1245. 2011
    ..Typhi host. The PST6 plasmid conferred the ability to grow in high salt medium (4.7% NaCl), which we demonstrate is due to the presence in PST6 of the Tn6062 transposon encoding BetU...
  33. doi 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
    Tran Vu Thieu Nga
    The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 190 Ben Ham Tu, Quan 5, Ho Chi Minh City, Vietnam
    Trans R Soc Trop Med Hyg 106:26-34. 2012
    ..We propose such changes are related to increasing economic prosperity and HIV prevalence, and this pattern marks a substantial change in the epidemiology of invasive salmonellosis in Southeast Asia...
  34. pmc The emergence of rotavirus G12 and the prevalence of enteric viruses in hospitalized pediatric diarrheal patients in southern Vietnam
    Phan Vu Tra My
    Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
    Am J Trop Med Hyg 85:768-75. 2011
    ....
  35. pmc The prevalence and genetic diversity of group A rotaviruses on pig farms in the Mekong Delta region of Vietnam
    Pham Hong Anh
    Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam
    Vet Microbiol 170:258-65. 2014
    ..The epidemiological relevance of these findings for veterinary practitioners and to ongoing pediatric ARoV vaccine initiatives in Vietnam merits further study. ..
  36. pmc Suitable disk antimicrobial susceptibility breakpoints defining Salmonella enterica serovar Typhi isolates with reduced susceptibility to fluoroquinolones
    Christopher M Parry
    The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 190 Ben Ham Tu, Quan 5, Ho Chi Minh City, Vietnam
    Antimicrob Agents Chemother 54:5201-8. 2010
    ..Screening for nalidixic acid resistance or ciprofloxacin and ofloxacin disk inhibition zone are suitable for detecting S. Typhi isolates with reduced fluoroquinolone susceptibility...
  37. pmc A successful antimicrobial regime for Chromobacterium violaceum induced bacteremia
    James I Campbell
    The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
    BMC Infect Dis 13:4. 2013
    ..Chromobacterium violaceum is a proteobacterium found in soil and water in tropical regions. The organism rarely causes infection in humans, yet can cause a severe systemic infection by entering the bloodstream via an open wound...
  38. pmc The sudden dominance of blaCTX-M harbouring plasmids in Shigella spp. Circulating in Southern Vietnam
    Nhu Thi Khanh Nguyen
    The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
    PLoS Negl Trop Dis 4:e702. 2010
    ..Vietnam is representative of a typical transitional middle income country where the spectrum of infectious diseases combined with the spread of drug resistance is shifting and bringing new healthcare challenges...
  39. pmc Molecular characterization of the Salmonella enterica serovar Typhi Vi-typing bacteriophage E1
    Derek Pickard
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    J Bacteriol 190:2580-7. 2008
    ..The genome of the Vi phage E1 is significantly related to other bacteriophages belonging to the same serovar Typhi phage-typing set, and we demonstrate a role for phage DNA modification in determining host specificity...
  40. pmc High prevalence of plasmid-mediated quinolone resistance determinants in commensal members of the Enterobacteriaceae in Ho Chi Minh City, Vietnam
    Thi Minh Vien Le
    Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
    J Med Microbiol 58:1585-92. 2009
    ..These data suggest that intestinal commensal organisms are a significant reservoir for the dissemination of plasmid-mediated quinolone resistance in Ho Chi Minh City...
  41. pmc 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
    Marion Eliëtte Kolader
    The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
    Trials 14:27. 2013
    ..We have designed a RCT to test the hypothesis that an oral preparation of Lactobacillus acidophilus is superior to placebo in the treatment of acute watery diarrhoea in Vietnamese children...
  42. ncbi Kathmandu, Nepal: still an enteric fever capital of the world
    Abhilasha Karkey
    Oxford University Clinical Research Unit, Patan Hospital, Lagankhel, Lalitpur, Bagmati, Kathmandu, Nepal
    J Infect Dev Ctries 2:461-5. 2008
    ..Our findings highlight the requirement for better understanding of the disease within the city; in turn, this will aid development of a targeted control strategy...
  43. pmc Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification
    Duy Pham Thanh
    The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
    J Clin Microbiol 51:2950-8. 2013
    ..This MLPA scheme offers a more-sensitive and interpretable alternative to the nonphylogenetic subgrouping methodologies that are currently used in reference and research laboratories in areas where typhoid is endemic. ..
  44. pmc Detection of Vi-negative Salmonella enterica serovar typhi in the peripheral blood of patients with typhoid fever in the Faisalabad region of Pakistan
    Stephen Baker
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    J Clin Microbiol 43:4418-25. 2005
    ..The method described here can be used to monitor the incidence of Vi-negative serovar Typhi in regions where the Vi vaccine is used...
  45. pmc A novel linear plasmid mediates flagellar variation in Salmonella Typhi
    Stephen Baker
    The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
    PLoS Pathog 3:e59. 2007
    ..The DNA sequence of pBSSB1 was determined to be just over 27 kbp, and was predicted to encode 33 coding sequences. To our knowledge, pBSSB1 is the first non-bacteriophage-related linear plasmid to be described in the Enterobacteriaceae...
  46. pmc Identification of a new cyclovirus in cerebrospinal fluid of patients with acute central nervous system infections
    Le Van Tan
    Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, South East Asia Infectious Diseases Clinical Research Network, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
    MBio 4:e00231-13. 2013
    ..Further research is needed to address the epidemiology and pathogenicity of this novel, potentially zoonotic virus...
  47. pmc A changing picture of shigellosis in southern Vietnam: shifting species dominance, antimicrobial susceptibility and clinical presentation
    Ha Vinh
    The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
    BMC Infect Dis 9:204. 2009
    ..Antimicrobial resistance in the genus Shigella is a constant threat, with reports of organisms in Asia being resistant to multiple antimicrobials and new generation therapies...
  48. ncbi The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome
    Mohammed Sebaihia
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Nat Genet 38:779-86. 2006
    ..The extreme genome variability was confirmed by whole-genome microarray analysis; it may reflect the organism's niche in the gut and should provide information on the evolution of virulence in this organism...
  49. pmc The antimicrobial resistance patterns and associated determinants in Streptococcus suis isolated from humans in southern Vietnam, 1997-2008
    Ngo T Hoa
    Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
    BMC Infect Dis 11:6. 2011
    ..suis strains isolated from human cases are lacking. We studied antimicrobial resistance and associated resistance determinants in S. suis isolated from patients with meningitis in southern Vietnam...
  50. pmc Analysis of the hypervariable region of the Salmonella enterica genome associated with tRNA(leuX)
    Anne L Bishop
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    J Bacteriol 187:2469-82. 2005
    ..coli, suggesting that these mobile genetic elements have played a major role in driving the variability of this region...
  51. ncbi Microbiologic characterization and antimicrobial susceptibility of Clostridium tetani isolated from wounds of patients with clinically diagnosed tetanus
    James I Campbell
    Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam
    Am J Trop Med Hyg 80:827-31. 2009
    ..These data show that the intravenous route for penicillin may be inadequate for clearing the infection and emphasizes wound debridement in the treatment of tetanus...
  52. pmc Evaluation of the diagnostic accuracy of a typhoid IgM flow assay for the diagnosis of typhoid fever in Cambodian children using a Bayesian latent class model assuming an imperfect gold standard
    Catrin E Moore
    Mahidol Oxford Tropical Medicine Research Unit MORU, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand Centre for Clinical Vaccinology and Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom Angkor Hospital for Children, Siem Reap, Cambodia Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam Institute of Child Health, University College London, London, United Kingdom London School of Hygiene and Tropical Medicine, London, United Kingdom Liverpool School of Tropical Medicine, Liverpool, United Kingdom
    Am J Trop Med Hyg 90:114-20. 2014
    ..9% (95% credible interval = 58-90), with a specificity of 97.5% (95% credible interval = 95-100). The model estimates of IgMFA sensitivity and specificity were comparable with BCs and better than estimates using conventional analysis...
  53. pmc Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture
    Helena M B Seth-Smith
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
    Genome Res 23:855-66. 2013
    ..This method will prove a useful tool in answering questions relating to the biology of many difficult-to-culture or fastidious bacteria of clinical concern...
  54. pmc A prospective descriptive study of cryptococcal meningitis in HIV uninfected patients in Vietnam - high prevalence of Cryptococcus neoformans var grubii in the absence of underlying disease
    Tran Th Chau
    Hospital for Tropical Diseases, Quan, Ho Chi Minh City, Vietnam
    BMC Infect Dis 10:199. 2010
    ..We describe a cohort of HIV uninfected Vietnamese patients with cryptococcal meningitis in whom underlying disease is uncommon, and relate presenting features of patients and the characteristics of the infecting species to outcome...
  55. pmc Rapid pneumococcal evolution in response to clinical interventions
    Nicholas J Croucher
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Science 331:430-4. 2011
    ..This study details how genomic plasticity within lineages of recombinogenic bacteria can permit adaptation to clinical interventions over remarkably short time scales...
  56. ncbi The role of prophage-like elements in the diversity of Salmonella enterica serovars
    Nicholas Thomson
    The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    J Mol Biol 339:279-300. 2004
    ..Lysogenic bacteriophages therefore play a crucial role in the generation of genetic diversity within S.enterica...
  57. pmc Evolutionary history of Salmonella typhi
    Philippe Roumagnac
    Max Planck Institut für Infektionsbiologie, Department of Molecular Biology, Chariteplatz 1, 10117 Berlin, Germany
    Science 314:1301-4. 2006
    ..Neutral evolution in Typhi appears to reflect the asymptomatic carrier state, and adaptive evolution depends on the rapid transmission of phenotypic changes through acute infections...
  58. pmc Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7
    Derek Pickard
    Centre for Molecular Microbiology and Infection, Department of Biological Sciences, Imperial College of Science, Technology and Medicine, Armstrong Road, London SW7 2AZ, UK
    J Bacteriol 185:5055-65. 2003
    ..citri. This analysis suggested that SPI-7 may be a mobile element, such as a conjugative transposon or an integrated plasmid remnant...
  59. pmc Interaction of Salmonella enterica serovar Typhi with cultured epithelial cells: roles of surface structures in adhesion and invasion
    Anne Bishop
    The Centre for Molecular Microbiology and Infection, Faculty of Life Sciences, Division of Molecular and Cell Biology, Imperial College London, London SW7 2AZ, UK
    Microbiology 154:1914-26. 2008
    ..Mutation of the staA, tcfA or pilS genes did not affect invasion or adhesion in either the presence or the absence of Vi capsule...
  60. pmc Vi antigen expression in Salmonella enterica serovar Typhi clinical isolates from Pakistan
    John Wain
    Investigative Sciences, Centre for Molecular Microbiology and Infection, Imperial College, London, United Kingdom
    J Clin Microbiol 43:1158-65. 2005
    ....