20 results on '"Baker, Stephen"'
Search Results
2. Detection of Salmonella Typhi nucleic acid by RT-PCR and anti-HlyE, -CdtB, -PilL, and -Vi IgM by ELISA at sites in Ghana, Madagascar and Ethiopia
- Author
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Panzner, Ursula, Mogeni, Ondari Daniel, Adu-Sarkodie, Yaw, Toy, Trevor, Jeon, Hyon Jin, Pak, Gi Deok, Park, Se Eun, Enuameh, Yeetey, Owusu-Dabo, Ellis, Van Tan, Trinh, Aseffa, Abraham, Teferi, Mekonnen, Yeshitela, Biruk, Baker, Stephen, Rakotozandrindrainy, Raphael, and Marks, Florian
- Published
- 2022
- Full Text
- View/download PDF
3. Risk factors for the development of neonatal sepsis in a neonatal intensive care unit of a tertiary care hospital of Nepal
- Author
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Manandhar, Sulochana, Amatya, Puja, Ansari, Imran, Joshi, Niva, Maharjan, Nhukesh, Dongol, Sabina, Basnyat, Buddha, Dixit, Sameer M., Baker, Stephen, and Karkey, Abhilasha
- Published
- 2021
- Full Text
- View/download PDF
4. Biphasic pattern in the effect of severe measles infection; the difference between additive and multiplicative scale
- Author
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Le, Nhat Thanh Hoang, Ho, Nhan Thi, Grenfell, Bryan, Baker, Stephen, and Geskus, Ronald B.
- Published
- 2021
- Full Text
- View/download PDF
5. A successful antimicrobial regime for Chromobacterium violaceum induced bacteremia
- Author
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Campbell James I, Lan Nguyen Phu, Qui Phan, Dung Le, Farrar Jeremy J, and Baker Stephen
- Subjects
Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background 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. Case presentation We recently identified a case of severe bacteremia caused by Chromobacterium violaceum at the Hospital for Tropical Diseases (HTD) in Ho Chi Minh City, Vietnam. Here, we describe how rapid microbiological identification and a combination of antimicrobials was used to successfully treat this life threatening infection in a four-year-old child. Conclusions This case shows the need for rapid diagnosis when there is the suspicion of a puncture wound contaminated with water and soil in tropical regions. We suggest that the aggressive antimicrobial combination used here is considered when this infection is suspected.
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- 2013
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- View/download PDF
6. The antimicrobial resistance patterns and associated determinants in Streptococcus suis isolated from humans in southern Vietnam, 1997-2008
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Chau Nguyen VV, Campbell James I, Baker Stephen, Wolbers Marcel, Anh Pham H, Mai Nguyen TH, Nghia Ho DT, Chieu Tran TB, Hoa Ngo T, Hien Tran T, Farrar Jeremy, and Schultsz Constance
- Subjects
Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Streptococcus suis is an emerging zoonotic pathogen and is the leading cause of bacterial meningitis in adults in Vietnam. Systematic data on the antimicrobial susceptibility profiles of S. 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. Methods S. suis strains isolated between 1997 and 2008 were investigated for their susceptibility to six antimicrobial agents. Strains were screened for the presence and expression of tetracycline and erythromycin resistance determinants and the association of tet(M) genes with Tn916- like transposons. The localization of tetracycline resistance gene tet(L) was determined by pulse field gel electrophoresis and Southern blotting. Results We observed a significant increase in resistance to tetracycline and chloramphenicol, which was concurrent with an increase in multi-drug resistance. In tetracycline resistance strains, we identified tet(M), tet(O), tet(W) and tet(L) and confirmed their expression. All tet(M) genes were associated with a Tn916-like transposon. The co-expression of tet(L) and other tetracycline resistance gene(s) encoding for ribosomal protection protein(s) was only detected in strains with a minimum inhibitory concentration (MIC) of tetracycline of ≥ 64 mg/L Conclusions We demonstrated that multi-drug resistance in S. suis causing disease in humans in southern Vietnam has increased over the 11-year period studied. We report the presence and expression of tet(L) in S. suis strains and our data suggest that co-expression of multiple genes encoding distinct mechanism is required for an MIC ≥ 64 mg/L to tetracycline.
- Published
- 2011
- Full Text
- View/download PDF
7. 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
- Author
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Baker Stephen, Campbell James I, Diep Pham T, Duong Van A, Sinh Dinh X, Chuong Ly V, Nghia Ho D, Phu Nguyen H, Mai Nguyen H, Chau Tran TH, Hien Tran T, Lalloo David G, Farrar Jeremy J, and Day Jeremy N
- Subjects
Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Most cases of cryptococcal meningitis occur in patients with HIV infection: the course and outcome of disease in the apparently immunocompetent is much more poorly understood. 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. Methods A prospective descriptive study of HIV negative patients with cryptococcal meningitis based at the Hospital for Tropical Diseases, Ho Chi Minh City. All patients had comprehensive clinical assessment at baseline, were cared for by a dedicated study team, and were followed up for 2 years. Clinical presentation was compared by infecting isolate and outcome. Results 57 patients were studied. Cryptococcus neoformans var grubii molecular type VN1 caused 70% of infections; C. gattii accounted for the rest. Most patients did not have underlying disease (81%), and the rate of underlying disease did not differ by infecting species. 11 patients died while in-patients (19.3%). Independent predictors of death were age ≥ 60 years and a history of convulsions (odds ratios and 95% confidence intervals 8.7 (1 - 76), and 16.1 (1.6 - 161) respectively). Residual visual impairment was common, affecting 25 of 46 survivors (54.3%). Infecting species did not influence clinical phenotype or outcome. The minimum inhibitory concentrations of flucytosine and amphotericin B were significantly higher for C. neoformans var grubii compared with C. gattii (p < 0.001 and p = 0.01 respectively). Conclusion In HIV uninfected individuals in Vietnam, cryptococcal meningitis occurs predominantly in people with no clear predisposing factor and is most commonly due to C. neoformans var grubii. The rates of mortality and visual loss are high and independent of infecting species. There are detectable differences in susceptibility to commonly used antifungal drugs between species, but the clinical significance of this is not clear.
- Published
- 2010
- Full Text
- View/download PDF
8. The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens
- Author
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Chau Tran, Campbell James I, Tu Le, Holt Kathryn, Dunstan Sarah, Thuy Hang, Dongol Sabina, Karkey Abhilasha, Nga Tran, Chau Nguyen, Arjyal Amit, Koirala Samir, Basnyat Buddha, Dolecek Christiane, Farrar Jeremy, and Baker Stephen
- Subjects
Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background PCR amplification for the detection of pathogens in biological material is generally considered a rapid and informative diagnostic technique. 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. Methods We developed and optimised a novel multiplex three colour real-time PCR assay to detect specific target sequences in the genomes of Salmonella serovars Typhi and Paratyphi A. We performed the assay on DNA extracted from blood and bone marrow samples from culture positive and negative enteric fever patients. Results The assay was validated and demonstrated a high level of specificity and reproducibility under experimental conditions. All bone marrow samples tested positive for Salmonella, however, the sensitivity on blood samples was limited. The assay demonstrated an overall specificity of 100% (75/75) and sensitivity of 53.9% (69/128) on all biological samples. We then tested the PCR detection limit by performing bacterial counts after inoculation into blood culture bottles. Conclusions Our findings corroborate previous clinical findings, whereby the bacterial load of S. Typhi in peripheral blood is low, often below detection by culture and, consequently, below detection by PCR. Whilst the assay may be utilised for environmental sampling or on differing biological samples, our data suggest that PCR performed directly on blood samples may be an unsuitable methodology and a potentially unachievable target for the routine diagnosis of enteric fever.
- Published
- 2010
- Full Text
- View/download PDF
9. High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children
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Parkhill Julian, Song Yajun, Pulickal Anoop S, Thorson Stephen, Adhikari Neelam, Basnyat Buddha, Dongol Sabina, Baker Stephen, Holt Kathryn E, Farrar Jeremy J, Murdoch David R, Kelly Dominic F, Pollard Andrew J, and Dougan Gordon
- Subjects
Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Salmonella Typhi (S. Typhi) causes typhoid fever, which remains an important public health issue in many developing countries. 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. Methods We recently defined the population structure of S. Typhi, using new sequencing technologies to identify nearly 2,000 single nucleotide polymorphisms (SNPs) that can be used as unequivocal phylogenetic markers. Here we have used the GoldenGate (Illumina) platform to simultaneously type 1,500 of these SNPs in 62 S. Typhi isolates causing severe typhoid in children admitted to Patan Hospital in Kathmandu. Results Eight distinct S. Typhi haplotypes were identified during the 20-month study period, with 68% of isolates belonging to a subclone of the previously defined H58 S. Typhi. This subclone was closely associated with resistance to nalidixic acid, with all isolates from this group demonstrating a resistant phenotype and harbouring the same resistance-associated SNP in GyrA (Phe83). A secondary clone, comprising 19% of isolates, was observed only during the second half of the study. Conclusions Our data demonstrate the utility of SNP typing for monitoring bacterial populations over a defined period in a single endemic setting. We provide evidence for genotype introduction and define a nalidixic acid resistant subclone of S. Typhi, which appears to be the dominant cause of severe pediatric typhoid in Kathmandu during the study period.
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- 2010
- Full Text
- View/download PDF
10. Searching for the elusive typhoid diagnostic
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Baker Stephen, Favorov Michael, and Dougan Gordon
- Subjects
Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Typhoid (enteric) fever is still a common disease in many developing countries but current diagnostic tests are inadequate. Studies on pathogenesis and genomics have provided new insight into the organisms that cause enteric fever. Better understanding of the microorganisms explains, in part, why our current typhoid methodologies are limited in their diagnostic information and why developing new strategies may be a considerable challenge. Here we discuss the current position of typhoid diagnostics, highlight the need for technological improvements and suggest potential ways of advancing this area.
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- 2010
- Full Text
- View/download PDF
11. A changing picture of shigellosis in southern Vietnam: shifting species dominance, antimicrobial susceptibility and clinical presentation
- Author
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Parry Christopher, My Phan, Boni Maciej F, Hoang Nguyen, Campbell James I, Duy Pham, Nga Tran, Nhu Nguyen, Vinh Ha, Van Minh Pham, Thuy Cao, Diep To, Phuong Le, Chinh Mai, Loan Ha, Tham Nguyen, Lanh Mai, Mong Bui, Anh Vo, Bay Phan, Chau Nguyen, Farrar Jeremy, and Baker Stephen
- Subjects
Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Shigellosis remains considerable public health problem in some developing countries. The nature of Shigellae suggests that they are highly adaptable when placed under selective pressure in a human population. This is demonstrated by variation and fluctuations in serotypes and antimicrobial resistance profile of organisms circulating in differing setting in endemic locations. 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. Methods Here we compare microbiological, clinical and epidemiological data from patients with shigellosis over three different periods in southern Vietnam spanning14 years. Results Our data demonstrates a shift in dominant infecting species (S. flexneri to S. sonnei) and resistance profile of the organisms circulating in southern Vietnam. We find that there was no significant variation in the syndromes associated with either S. sonnei or S. flexneri, yet the clinical features of the disease are more severe in later observations. Conclusions Our findings show a change in clinical presentation of shigellosis in this setting, as the disease may be now more pronounced, this is concurrent with a change in antimicrobial resistance profile. These data highlight the socio-economic development of southern Vietnam and should guide future vaccine development and deployment strategies. Trial Registration Current Controlled Trials ISRCTN55945881
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- 2009
- Full Text
- View/download PDF
12. Current challenges and possible solutions to improve access to care and treatment for hepatitis C infection in Vietnam: a systematic review.
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Berto, Alessandra, Day, Jeremy, Nguyen Van Vinh Chau, Thwaites, Guy E., Ngoc Nghiem My, Baker, Stephen, Darton, Thomas C., Van Vinh Chau, Nguyen, and My, Ngoc Nghiem
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HEPATITIS C ,FLAVIVIRAL diseases ,MEDICAL microbiology ,COMMUNICABLE diseases ,LIVER diseases ,HEPATITIS C treatment ,HEALTH services accessibility ,HEPATITIS viruses ,SYSTEMATIC reviews ,DISEASE incidence ,DISEASE prevalence - Abstract
Background: Hepatitis C infection is a major public health concern in low- and middle-income countries where an estimated 71.1 million individuals are living with chronic infection. The World Health Organization (WHO) has recently released new guidance for hepatitis C virus (HCV) treatment programs, which include improving the access to new direct-acting antiviral agents. In Vietnam, a highly populated middle-income country, the seroprevalence of HCV infection is approximately 4% and multiple genotypes co-circulate in the general population. Here we review what is currently known regarding the epidemiology of HCV in Vietnam and outline options for reducing the significant burden of morbidity and mortality in our setting.Methods: We performed a systematic review of the currently available literature to evaluate what has been achieved to date with efforts to control HCV infection in Vietnam.Results: This search retrieved few publications specific to Vietnam indicating a significant gap in baseline epidemiological and public health data. Key knowledge gaps identified included an understanding of the prevalence in specific high-risk groups, characterization of circulating HCV genotypes in the population and likely response to treatment, and the extent to which HCV treatment is available, accessed and utilized.Conclusions: We conclude that there is an urgent need to perform up to date assessments of HCV disease burden in Vietnam, especially in high-risk groups, in whom incidence is high and cross infection with multiple genotypes is likely to be frequent. Coordinating renewed surveillance measures with forthcoming HCV treatment studies should initiate the traction required to achieve the WHO goal of eliminating HCV as a public health threat by 2030, at least in this region. [ABSTRACT FROM AUTHOR]- Published
- 2017
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- View/download PDF
13. Risk factors for the development of severe typhoid fever in Vietnam.
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Parry, Christopher M., Thompson, Corinne, Ha Vinh, Nguyen Tran Chinh, Le Thi Phuong, Vo Anh Ho, Tran Tinh Hien, John Wain, Farrar, Jeremy J., and Baker, Stephen
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SALMONELLA enterica serovar Typhi ,TYPHOID fever ,DRUG resistance in bacteria ,ANTI-infective agents ,DISEASE risk factors - Abstract
Background Typhoid fever is a systemic infection caused by the bacterium Salmonella enterica serovar Typhi. 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. Methods We analysed clinical data from 581 patients consecutively admitted with culture confirmed typhoid fever to two hospitals in Vietnam during two periods in 1993-1995 and 1997-1999. These periods spanned a change in the antimicrobial resistance phenotypes of the infecting organisms i.e. fully susceptible to standard antimicrobials, resistance to chloramphenicol, ampicillin and trimethoprim-sulphamethoxazole (multidrug resistant, MDR), and intermediate susceptibility to ciprofloxacin (nalidixic acid resistant). Age, sex, duration of illness prior to admission, hospital location and the presence of MDR or intermediate ciprofloxacin susceptibility in the infecting organism were examined by logistic regression analysis to identify factors independently associated with severe typhoid at the time of hospital admission. Results The prevalence of severe typhoid was 15.5% (90/581) and included: gastrointestinal bleeding (43; 7.4%); hepatitis (29; 5.0%); encephalopathy (16; 2.8%); myocarditis (12; 2.1%); intestinal perforation (6; 1.0%); haemodynamic shock (5; 0.9%), and death (3; 0.5%). Severe disease was more common with increasing age, in those with a longer duration of illness and in patients infected with an organism exhibiting intermediate susceptibility to ciprofloxacin. Notably an MDR phenotype was not associated with severe disease. Severe disease was independently associated with infection with an organism with an intermediate susceptibility to ciprofloxacin (AOR 1.90; 95% CI 1.18-3.07; p = 0.009) and male sex (AOR 1.61 (1.00- 2.57; p = 0.035). Conclusions In this group of patients hospitalised with typhoid fever infection with an organism with intermediate susceptibility to ciprofloxacin was independently associated with disease severity. During this period many patients were being treated with fluoroquinolones prior to hospital admission. Ciprofloxacin and ofloxacin should be used with caution in patients infected with S. Typhi that have intermediate susceptibility to ciprofloxacin. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
14. The antimicrobial resistance patterns and associated determinants in Streptococcus suis isolated from humans in southern Vietnam, 1997-2008.
- Author
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Hoa, Ngo T., Chieu, Tran T. B., Nghia, Ho D. T., Mai, Nguyen T. H., Anh, Pham H., Wolbers, Marcel, Baker, Stephen, Campbell, James I., Chau, Nguyen W., Hien, Tran T., Farrar, Jeremy, and Schultsz, Constance
- Subjects
STREPTOCOCCUS ,MENINGITIS ,ZOONOSES ,TETRACYCLINE ,ERYTHROMYCIN - Abstract
Background: Streptococcus suis is an emerging zoonotic pathogen and is the leading cause of bacterial meningitis in adults in Vietnam. Systematic data on the antimicrobial susceptibility profiles of S. 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. Methods: S. suis strains isolated between 1997 and 2008 were investigated for their susceptibility to six antimicrobial agents. Strains were screened for the presence and expression of tetracycline and erythromycin resistance determinants and the association of tet(M) genes with Tn916- like transposons. The localization of tetracycline resistance gene tet(L) was determined by pulse field gel electrophoresis and Southern blotting. Results: We observed a significant increase in resistance to tetracycline and chloramphenicol, which was concurrent with an increase in multi-drug resistance. In tetracycline resistance strains, we identified tet(M), tet(O), tet (W) and tet(L) and confirmed their expression. All tet(M) genes were associated with a Tn916-like transposon. The co-expression of tet(L) and other tetracycline resistance gene(s) encoding for ribosomal protection protein(s) was only detected in strains with a minimum inhibitory concentration (MIC) of tetracycline of ≥ 64 mg/L Conclusions: We demonstrated that multi-drug resistance in S. suis causing disease in humans in southern Vietnam has increased over the 11-year period studied. We report the presence and expression of tet(L) in S. suis strains and our data suggest that co-expression of multiple genes encoding distinct mechanism is required for an MIC ≥ 64 mg/L to tetracycline. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
15. High-throughput bacterial SNP typing identifiesdistinct clusters of Salmonella Typhi causingtyphoid in Nepalese children.
- Author
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Holt, Kathryn E., Baker, Stephen, Dongol, Sabina, Basnyat, Buddha, Adhikari, Neelam, Thorson, Stephen, Pulickal, Anoop S., Yajun Song, Parkhill, Julian, Farrar, Jeremy J., Murdoch, David R., Kelly, Dominic F., Pollard, Andrew J., and Dougan, Gordon
- Subjects
- *
SALMONELLA typhi , *TYPHOID fever , *PUBLIC health , *BIOMARKERS - Abstract
Background: Salmonella Typhi (S. Typhi) causes typhoid fever, which remains an important public health issue in many developing countries. 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. Methods: We recently defined the population structure of S. Typhi, using new sequencing technologies to identify nearly 2,000 single nucleotide polymorphisms (SNPs) that can be used as unequivocal phylogenetic markers. Here we have used the GoldenGate (Illumina) platform to simultaneously type 1,500 of these SNPs in 62 S. Typhi isolates causing severe typhoid in children admitted to Patan Hospital in Kathmandu. Results: Eight distinct S. Typhi haplotypes were identified during the 20-month study period, with 68% of isolates belonging to a subclone of the previously defined H58 S. Typhi. This subclone was closely associated with resistance to nalidixic acid, with all isolates from this group demonstrating a resistant phenotype and harbouring the same resistance-associated SNP in GyrA (Phe83). A secondary clone, comprising 19% of isolates, was observed only during the second half of the study. Conclusions: Our data demonstrate the utility of SNP typing for monitoring bacterial populations over a defined period in a single endemic setting. We provide evidence for genotype introduction and define a nalidixic acid resistant subclone of S. Typhi, which appears to be the dominant cause of severe pediatric typhoid in Kathmandu during the study period. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
16. A prospective descriptive study of cryptococcalmeningitis in HIV uninfected patients in Vietnam -high prevalence of Cryptococcus neoformans vargrubii in the absence of underlying disease.
- Author
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Chau, Tran T. H., Mai, Nguyen H., Phu, Nguyen H., Nghia, Ho D., Chuong, Ly V., Sinh, Dinh X., Duong, Van A., Diep, Pham T., Campbell, James I., Baker, Stephen, Hien, Tran T., Lalloo, David G., Farrar, Jeremy J., and Day, Jeremy N.
- Subjects
MENINGITIS ,CRYPTOCOCCALES ,HIV infections ,HIV-positive persons ,CRYPTOCOCCUS neoformans - Abstract
Background: Most cases of cryptococcal meningitis occur in patients with HIV infection: the course and outcome of disease in the apparently immunocompetent is much more poorly understood. 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. Methods: A prospective descriptive study of HIV negative patients with cryptococcal meningitis based at the Hospital for Tropical Diseases, Ho Chi Minh City. All patients had comprehensive clinical assessment at baseline, were cared for by a dedicated study team, and were followed up for 2 years. Clinical presentation was compared by infecting isolate and outcome. Results: 57 patients were studied. Cryptococcus neoformans var grubii molecular type VN1 caused 70% of infections; C. gattii accounted for the rest. Most patients did not have underlying disease (81%), and the rate of underlying disease did not differ by infecting species. 11 patients died while in-patients (19.3%). Independent predictors of death were age ≥ 60 years and a history of convulsions (odds ratios and 95% confidence intervals 8.7 (1 - 76), and 16.1 (1.6 - 161) respectively). Residual visual impairment was common, affecting 25 of 46 survivors (54.3%). Infecting species did not influence clinical phenotype or outcome. The minimum inhibitory concentrations of flucytosine and amphotericin B were significantly higher for C. neoformans var grubii compared with C. gattii (p < 0.001 and p = 0.01 respectively). Conclusion: In HIV uninfected individuals in Vietnam, cryptococcal meningitis occurs predominantly in people with no clear predisposing factor and is most commonly due to C. neoformans var grubii. The rates of mortality and visual loss are high and independent of infecting species. There are detectable differences in susceptibility to commonly used antifungal drugs between species, but the clinical significance of this is not clear. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
17. The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens.
- Author
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Nga, Tran Vu Thieu, Karkey, Abhilasha, Dongol, Sabina, Thuy, Hang Nguyen, Dunstan, Sarah, Holt, Kathryn, Tu, Le Thi Phuong, Campbell, James I., Chau, Tran Thuy, Chau, Nguyen Van Vinh, Arjyal, Amit, Koirala, Samir, Basnyat, Buddha, Dolecek, Christiane, Farrar, Jeremy, and Baker, Stephen
- Subjects
TYPHOID fever ,SALMONELLA diseases ,POLYMERASE chain reaction ,PATHOGENIC microorganisms ,BIOMEDICAL materials - Abstract
Background: PCR amplification for the detection of pathogens in biological material is generally considered a rapid and informative diagnostic technique. 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. Methods: We developed and optimised a novel multiplex three colour real-time PCR assay to detect specific target sequences in the genomes of Salmonella serovars Typhi and Paratyphi A. We performed the assay on DNA extracted from blood and bone marrow samples from culture positive and negative enteric fever patients. Results: The assay was validated and demonstrated a high level of specificity and reproducibility under experimental conditions. All bone marrow samples tested positive for Salmonella, however, the sensitivity on blood samples was limited. The assay demonstrated an overall specificity of 100% (75/75) and sensitivity of 53.9% (69/128) on all biological samples. We then tested the PCR detection limit by performing bacterial counts after inoculation into blood culture bottles. Conclusions: Our findings corroborate previous clinical findings, whereby the bacterial load of S. Typhi in peripheral blood is low, often below detection by culture and, consequently, below detection by PCR. Whilst the assay may be utilised for environmental sampling or on differing biological samples, our data suggest that PCR performed directly on blood samples may be an unsuitable methodology and a potentially unachievable target for the routine diagnosis of enteric fever. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
18. A prospective study of the importance of enteric fever as a cause of non-malarial febrile illness in patients admitted to Chittagong Medical College Hospital, Bangladesh.
- Author
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Maude RR, Ghose A, Samad R, de Jong HK, Fukushima M, Wijedoru L, Hassan MU, Hossain MA, Karim MR, Sayeed AA, van den Ende S, Pal S, Zahed AS, Rahman W, Karnain R, Islam R, Tran DT, Ha TT, Pham AH, Campbell JI, van Doorn HR, Maude RJ, van der Poll T, Wiersinga WJ, Day NP, Baker S, Dondorp AM, Parry CM, and Faiz MA
- Subjects
- Adolescent, Adult, Aged, Bangladesh epidemiology, Child, Child, Preschool, Female, Fever microbiology, Hospitalization statistics & numerical data, Hospitals, University, Humans, Infant, Malaria complications, Malaria epidemiology, Malaria microbiology, Malaria virology, Male, Middle Aged, Typhoid Fever epidemiology, Typhoid Fever microbiology, Young Adult, Fever etiology, Salmonella typhi isolation & purification, Salmonella typhi physiology, Typhoid Fever complications
- Abstract
Background: Fever is a common cause of hospital admission in Bangladesh but causative agents, other than malaria, are not routinely investigated. Enteric fever is thought to be common., Methods: Adults and children admitted to Chittagong Medical College Hospital with a temperature of ≥38.0 °C were investigated using a blood smear for malaria, a blood culture, real-time PCR to detect Salmonella Typhi, S. Paratyphi A and other pathogens in blood and CSF and an NS1 antigen dengue ELISA., Results: We enrolled 300 febrile patients with a negative malaria smear between January and June 2012: 156 children (aged ≤15 years) and 144 adults with a median (interquartile range) age of 13 (5-31) years and median (IQR) illness duration before admission of five (2-8) days. Clinical enteric fever was diagnosed in 52 patients (17.3 %), lower respiratory tract infection in 48 (16.0 %), non-specific febrile illness in 48 (16.0 %), a CNS infection in 37 patients (12.3 %), urinary sepsis in 23 patients (7.7 %), an upper respiratory tract infection in 21 patients (7.0 %), and diarrhea or dysentery in 21 patients (7.0 %). Malaria was still suspected in seven patients despite a negative microscopy test. S. Typhi was detected in blood by culture or PCR in 34 (11.3 %) of patients. Of note Rickettsia typhi and Orientia tsutsugamushi were detected by PCR in two and one patient respectively. Twenty-nine (9 %) patients died during their hospital admission (15/160 (9.4 %) of children and 14/144 (9.7 %) adults). Two of 52 (3.8 %) patients with enteric fever, 5/48 (10.4 %) patients with lower respiratory tract infections, and 12/37 (32.4 %) patients with CNS infection died., Conclusion: Enteric fever was confirmed in 11.3 % of patients admitted to this hospital in Bangladesh with non-malaria fever. Lower respiratory tract and CNS infections were also common. CNS infections in this location merit more detailed study due to the high mortality.
- Published
- 2016
- Full Text
- View/download PDF
19. 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.
- Author
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Chau TT, Mai NH, Phu NH, Nghia HD, Chuong LV, Sinh DX, Duong VA, Diep PT, Campbell JI, Baker S, Hien TT, Lalloo DG, Farrar JJ, and Day JN
- Subjects
- Adolescent, Adult, Aged, Amphotericin B pharmacology, Antifungal Agents pharmacology, Antifungal Agents therapeutic use, Cryptococcus gattii isolation & purification, Cryptococcus neoformans isolation & purification, Female, Flucytosine pharmacology, Humans, Male, Meningitis, Cryptococcal mortality, Meningitis, Cryptococcal pathology, Microbial Sensitivity Tests, Middle Aged, Prevalence, Prospective Studies, Treatment Outcome, Vietnam epidemiology, Young Adult, HIV Infections complications, Meningitis, Cryptococcal epidemiology, Meningitis, Cryptococcal microbiology
- Abstract
Background: Most cases of cryptococcal meningitis occur in patients with HIV infection: the course and outcome of disease in the apparently immunocompetent is much more poorly understood. 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., Methods: A prospective descriptive study of HIV negative patients with cryptococcal meningitis based at the Hospital for Tropical Diseases, Ho Chi Minh City. All patients had comprehensive clinical assessment at baseline, were cared for by a dedicated study team, and were followed up for 2 years. Clinical presentation was compared by infecting isolate and outcome., Results: 57 patients were studied. Cryptococcus neoformans var grubii molecular type VN1 caused 70% of infections; C. gattii accounted for the rest. Most patients did not have underlying disease (81%), and the rate of underlying disease did not differ by infecting species. 11 patients died while in-patients (19.3%). Independent predictors of death were age > or = 60 years and a history of convulsions (odds ratios and 95% confidence intervals 8.7 (1 - 76), and 16.1 (1.6 - 161) respectively). Residual visual impairment was common, affecting 25 of 46 survivors (54.3%). Infecting species did not influence clinical phenotype or outcome. The minimum inhibitory concentrations of flucytosine and amphotericin B were significantly higher for C. neoformans var grubii compared with C. gattii (p < 0.001 and p = 0.01 respectively)., Conclusion: In HIV uninfected individuals in Vietnam, cryptococcal meningitis occurs predominantly in people with no clear predisposing factor and is most commonly due to C. neoformans var grubii. The rates of mortality and visual loss are high and independent of infecting species. There are detectable differences in susceptibility to commonly used antifungal drugs between species, but the clinical significance of this is not clear.
- Published
- 2010
- Full Text
- View/download PDF
20. A changing picture of shigellosis in southern Vietnam: shifting species dominance, antimicrobial susceptibility and clinical presentation.
- Author
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Vinh H, Nhu NT, Nga TV, Duy PT, Campbell JI, Hoang NV, Boni MF, My PV, Parry C, Nga TT, Van Minh P, Thuy CT, Diep TS, Phuong le T, Chinh MT, Loan HT, Tham NT, Lanh MN, Mong BL, Anh VT, Bay PV, Chau NV, Farrar J, and Baker S
- Subjects
- Child, Preschool, Drug Resistance, Multiple, Bacterial, Female, Humans, Infant, Male, Microbial Sensitivity Tests, Seasons, Serotyping, Shigella flexneri classification, Shigella flexneri drug effects, Shigella flexneri pathogenicity, Shigella sonnei classification, Shigella sonnei drug effects, Shigella sonnei pathogenicity, Vietnam epidemiology, Dysentery, Bacillary epidemiology, Dysentery, Bacillary microbiology
- Abstract
Background: Shigellosis remains considerable public health problem in some developing countries. The nature of Shigellae suggests that they are highly adaptable when placed under selective pressure in a human population. This is demonstrated by variation and fluctuations in serotypes and antimicrobial resistance profile of organisms circulating in differing setting in endemic locations. 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., Methods: Here we compare microbiological, clinical and epidemiological data from patients with shigellosis over three different periods in southern Vietnam spanning 14 years., Results: Our data demonstrates a shift in dominant infecting species (S. flexneri to S. sonnei) and resistance profile of the organisms circulating in southern Vietnam. We find that there was no significant variation in the syndromes associated with either S. sonnei or S. flexneri, yet the clinical features of the disease are more severe in later observations., Conclusions: Our findings show a change in clinical presentation of shigellosis in this setting, as the disease may be now more pronounced, this is concurrent with a change in antimicrobial resistance profile. These data highlight the socio-economic development of southern Vietnam and should guide future vaccine development and deployment strategies., Trial Registration: Current Controlled Trials ISRCTN55945881.
- Published
- 2009
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