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1.
BMC Med ; 21(1): 320, 2023 08 24.
Article in English | MEDLINE | ID: mdl-37620809

ABSTRACT

BACKGROUND: Severe malaria in pregnancy causes maternal mortality, morbidity, and adverse foetal outcomes. The factors contributing to adverse maternal and foetal outcomes are not well defined. We aimed to identify the factors predicting higher maternal mortality and to describe the foetal mortality and morbidity associated with severe falciparum malaria in pregnancy. METHODS: A retrospective cohort study was conducted of severe falciparum malaria in pregnancy, as defined by the World Health Organization severe malaria criteria. The patients were managed prospectively by the Shoklo Malaria Research Unit (SMRU) on the Thailand-Myanmar border or were included in hospital-based clinical trials in six Southeast Asian countries. Fixed-effects multivariable penalised logistic regression was used for analysing maternal mortality. RESULTS: We included 213 (123 SMRU and 90 hospital-based) episodes of severe falciparum malaria in pregnancy managed between 1980 and 2020. The mean maternal age was 25.7 (SD 6.8) years, and the mean gestational age was 25.6 (SD 8.9) weeks. The overall maternal mortality was 12.2% (26/213). Coma (adjusted odds ratio [aOR], 7.18, 95% CI 2.01-25.57, p = 0.0002), hypotension (aOR 11.21, 95%CI 1.27-98.92, p = 0.03) and respiratory failure (aOR 4.98, 95%CI 1.13-22.01, p = 0.03) were associated with maternal mortality. Pregnant women with one or more of these three criteria had a mortality of 29.1% (25/86) (95%CI 19.5 to 38.7%) whereas there were no deaths in 88 pregnant women with hyperparasitaemia (> 10% parasitised erythrocytes) only or severe anaemia (haematocrit < 20%) only. In the SMRU prospective cohort, in which the pregnant women were followed up until delivery, the risks of foetal loss (23.3% by Kaplan-Meier estimator, 25/117) and small-for-gestational-age (38.3%, 23/60) after severe malaria were high. Maternal death, foetal loss and preterm birth occurred commonly within a week of diagnosis of severe malaria. CONCLUSIONS: Vital organ dysfunction in pregnant women with severe malaria was associated with a very high maternal and foetal mortality whereas severe anaemia or hyperparasitaemia alone were not associated with poor prognosis, which may explain the variation of reported mortality from severe malaria in pregnancy. Access to antenatal care must be promoted to reduce barriers to early diagnosis and treatment of both malaria and anaemia.


Subject(s)
Premature Birth , Infant, Newborn , Pregnancy , Humans , Female , Adult , Infant , Prospective Studies , Retrospective Studies , Myanmar , Fetus
2.
Mol Biol Evol ; 39(1)2022 01 07.
Article in English | MEDLINE | ID: mdl-34662416

ABSTRACT

The soil bacterium Burkholderia pseudomallei is the causative agent of melioidosis and a significant cause of human morbidity and mortality in many tropical and subtropical countries. The species notoriously survives harsh environmental conditions but the genetic architecture for these adaptations remains unclear. Here we employed a powerful combination of genome-wide epistasis and co-selection studies (2,011 genomes), condition-wide transcriptome analyses (82 diverse conditions), and a gene knockout assay to uncover signals of "co-selection"-that is a combination of genetic markers that have been repeatedly selected together through B. pseudomallei evolution. These enabled us to identify 13,061 mutation pairs under co-selection in distinct genes and noncoding RNA. Genes under co-selection displayed marked expression correlation when B. pseudomallei was subjected to physical stress conditions, highlighting the conditions as one of the major evolutionary driving forces for this bacterium. We identified a putative adhesin (BPSL1661) as a hub of co-selection signals, experimentally confirmed a BPSL1661 role under nutrient deprivation, and explored the functional basis of co-selection gene network surrounding BPSL1661 in facilitating the bacterial survival under nutrient depletion. Our findings suggest that nutrient-limited conditions have been the common selection pressure acting on this species, and allelic variation of BPSL1661 may have promoted B. pseudomallei survival during harsh environmental conditions by facilitating bacterial adherence to different surfaces, cells, or living hosts.


Subject(s)
Biological Evolution , Burkholderia pseudomallei , Adhesins, Bacterial , Alleles , Burkholderia pseudomallei/genetics , Burkholderia pseudomallei/physiology , Selection, Genetic , Stress, Physiological
3.
Article in English | MEDLINE | ID: mdl-33526485

ABSTRACT

When severe malaria is suspected in children, the WHO recommends pretreatment with a single rectal dose of artesunate before referral to an appropriate facility. This was an individually randomized, open-label, 2-arm, crossover clinical trial in 82 Congolese children with severe falciparum malaria to characterize the pharmacokinetics of rectal artesunate. At admission, children received a single dose of rectal artesunate (10 mg/kg of body weight) followed 12 h later by intravenous artesunate (2.4 mg/kg) or the reverse order. All children also received standard doses of intravenous quinine. Artesunate and dihydroartemisinin were measured at 11 fixed intervals, following 0- and 12-h drug administrations. Clinical, laboratory, and parasitological parameters were measured. After rectal artesunate, artesunate and dihydroartemisinin showed large interindividual variability (peak concentrations of dihydroartemisinin ranged from 5.63 to 8,090 nM). The majority of patients, however, reached previously suggested in vivo IC50 and IC90 values (98.7% and 92.5%, respectively) of combined concentrations of artesunate and dihydroartemisinin between 15 and 30 min after drug administration. The median (interquartile range [IQR]) time above IC50 and IC90 was 5.68 h (2.90 to 6.08) and 2.74 h (1.52 to 3.75), respectively. The absolute rectal bioavailability (IQR) was 25.6% (11.7 to 54.5) for artesunate and 19.8% (10.3 to 35.3) for dihydroartemisinin. The initial 12-h parasite reduction ratio was comparable between rectal and intravenous artesunate: median (IQR), 84.3% (50.0 to 95.4) versus 69.2% (45.7 to 93.6), respectively (P = 0.49). Despite large interindividual variability, rectal artesunate can initiate and sustain rapid parasiticidal activity in most children with severe falciparum malaria while they are transferred to a facility where parenteral artesunate is available. (This study has been registered at ClinicalTrials.gov under identifier NCT02492178.).


Subject(s)
Antimalarials , Malaria, Falciparum , Malaria , Africa , Antimalarials/therapeutic use , Artesunate/therapeutic use , Child , Humans , Malaria/drug therapy , Malaria, Falciparum/drug therapy , Quinine
4.
Am J Trop Med Hyg ; 104(3): 1022-1033, 2021 01 11.
Article in English | MEDLINE | ID: mdl-33432906

ABSTRACT

Epidemiology, ventilator management, and outcome in patients receiving invasive ventilation in intensive care units (ICUs) in middle-income countries are largely unknown. PRactice of VENTilation in Middle-income Countries is an international multicenter 4-week observational study of invasively ventilated adult patients in 54 ICUs from 10 Asian countries conducted in 2017/18. Study outcomes included major ventilator settings (including tidal volume [V T ] and positive end-expiratory pressure [PEEP]); the proportion of patients at risk for acute respiratory distress syndrome (ARDS), according to the lung injury prediction score (LIPS), or with ARDS; the incidence of pulmonary complications; and ICU mortality. In 1,315 patients included, median V T was similar in patients with LIPS < 4 and patients with LIPS ≥ 4, but lower in patients with ARDS (7.90 [6.8-8.9], 8.0 [6.8-9.2], and 7.0 [5.8-8.4] mL/kg Predicted body weight; P = 0.0001). Median PEEP was similar in patients with LIPS < 4 and LIPS ≥ 4, but higher in patients with ARDS (five [5-7], five [5-8], and 10 [5-12] cmH2O; P < 0.0001). The proportions of patients with LIPS ≥ 4 or with ARDS were 68% (95% CI: 66-71) and 7% (95% CI: 6-8), respectively. Pulmonary complications increased stepwise from patients with LIPS < 4 to patients with LIPS ≥ 4 and patients with ARDS (19%, 21%, and 38% respectively; P = 0.0002), with a similar trend in ICU mortality (17%, 34%, and 45% respectively; P < 0.0001). The capacity of the LIPS to predict development of ARDS was poor (receiver operating characteristic [ROC] area under the curve [AUC] of 0.62, 95% CI: 0.54-0.70). In Asian middle-income countries, where two-thirds of ventilated patients are at risk for ARDS according to the LIPS and pulmonary complications are frequent, setting of V T is globally in line with current recommendations.


Subject(s)
Developing Countries/statistics & numerical data , Epidemiological Monitoring , Intensive Care Units/statistics & numerical data , Respiration, Artificial/methods , Respiration, Artificial/statistics & numerical data , Respiratory Distress Syndrome/therapy , Adult , Aged , Asia/epidemiology , Female , Humans , Male , Middle Aged , Prospective Studies , Respiratory Distress Syndrome/epidemiology , Treatment Outcome
6.
Tuberculosis (Edinb) ; 95(5): 575-80, 2015 Sep.
Article in English | MEDLINE | ID: mdl-26156785

ABSTRACT

Tuberculosis (TB) is an important cause of morbidity and mortality worldwide. Granzymes (gzms) are proteases mainly found in cytotoxic lymphocytes, but also extracellularly. While the role of gzms in target cell death has been widely characterized, considerable evidence points towards broader roles related to infectious and inflammatory responses. To investigate the expression of the gzms in TB, intracellular gzms A, B and K were measured by flow cytometry in lymphocyte populations from peripheral blood mononuclear cells from 18 TB patients and 12 healthy donors from Bangladesh, and extracellular levels of gzmA and B were measured in serum from 58 TB patients and 31 healthy controls. TB patients showed increased expression of gzmA in CD8(+) T, CD4(+) T and CD56(+) T, but not NK, cells, and of gzmB in CD8(+) T cells, when compared to controls. GzmK expression was not altered in TB patients in any lymphocyte subset. The extracellular levels of gzmA and, to a lesser extent, of gzmB, were increased in TB patients, but did not correlate with intracellular gzm expression in lymphocyte subsets. Our results reveal enhanced intra- and extracellular expression of gzmA and B in patients with pulmonary TB, suggesting that gzms are part of the host response to tuberculosis.


Subject(s)
Granzymes/blood , T-Lymphocytes/enzymology , Tuberculosis/blood , Tuberculosis/enzymology , Adult , Bangladesh , Biomarkers/blood , Case-Control Studies , Female , Flow Cytometry , Host-Pathogen Interactions , Humans , Male , Mycobacterium tuberculosis/immunology , Mycobacterium tuberculosis/pathogenicity , T-Lymphocytes/immunology , T-Lymphocytes/microbiology , Tuberculosis/diagnosis , Tuberculosis/immunology , Tuberculosis/microbiology , Up-Regulation , Young Adult
7.
BMC Infect Dis ; 15: 98, 2015 Feb 26.
Article in English | MEDLINE | ID: mdl-25887604

ABSTRACT

BACKGROUND: Tuberculosis (TB) is an important cause of morbidity and mortality worldwide. Toll-like-receptors (TLRs) are important for the recognition of the causative agent Mycobacterium tuberculosis. Negative regulation of TLRs is necessary to control deleterious inflammatory damage, but could provide a means of immune evasion by M. tuberculosis as well. METHODS: To obtain insight in the extent of expression of inhibitory regulators of immunity in patients with active TB, peripheral-blood-mononuclear-cells (PBMCs) and plasma were obtained from 54 TB patients and 29 healthy blood donors from Chittagong, Bangladesh. Bilateral alveolar macrophages were obtained from an infected versus a contralateral normal lung segment of 9 patients. Statistical analyses were performed using Mann-Whitney U and Wilcoxon matched pairs testing. Correlations were calculated using the Spearman rho test. RESULTS: PBMCs harvested from TB patients demonstrated increased mRNA expression of IL-1-receptor-associated-kinase-M, suppressor-of-cytokine-signalling-3 and Toll-interacting-protein. Flow cytometry revealed enhanced expression of IL-1-receptor-like-1 (ST2) on lymphocytes. Plasma soluble ST2 was elevated in patients with TB and correlated with established TB biomarkers, most strongly with soluble interleukin-2 receptor subunit α and interleukin-8. Alveolar macrophage mRNA expression of negative TLR regulators did not differ between the infected and contralateral lung side. CONCLUSION: These results show enhanced expression of distinct negative regulators of innate immunity in PBMCs of patients with TB and identify plasma soluble ST2 as a potential novel biomarker for TB disease activity.


Subject(s)
Immunity, Innate/immunology , Tuberculosis, Pulmonary/immunology , Adolescent , Adult , Aged , Aged, 80 and over , Bangladesh/epidemiology , Female , Flow Cytometry , Humans , Interleukin-8/immunology , Leukocytes, Mononuclear/immunology , Male , Middle Aged , Mycobacterium tuberculosis/immunology , Toll-Like Receptors/immunology , Tuberculosis, Pulmonary/blood , Tuberculosis, Pulmonary/epidemiology , Young Adult
8.
Am J Trop Med Hyg ; 92(4): 875-878, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25667056

ABSTRACT

Undifferentiated febrile illnesses (UFIs) are common in low- and middle-income countries. We prospectively investigated the causes of UFIs in 627 patients presenting to a tertiary referral hospital in Kathmandu, Nepal. Patients with microbiologically confirmed enteric fever (218 of 627; 34.8%) randomized to gatifloxacin or ofloxacin treatment were previously reported. We randomly selected 125 of 627 (20%) of these UFI patients, consisting of 96 of 409 (23%) cases with sterile blood cultures and 29 of 218 (13%) cases with enteric fever, for additional diagnostic investigations. We found serological evidence of acute murine typhus in 21 of 125 (17%) patients, with 12 of 21 (57%) patients polymerase chain reaction (PCR)-positive for Rickettsia typhi. Three UFI cases were quantitative PCR-positive for Rickettsia spp., two UFI cases were seropositive for Hantavirus, and one UFI case was seropositive for Q fever. Fever clearance time (FCT) for rickettsial infection was 44.5 hours (interquartile range = 26-66 hours), and there was no difference in FCT between ofloxacin or gatifloxacin. Murine typhus represents an important cause of predominantly urban UFIs in Nepal, and fluoroquinolones seem to be an effective empirical treatment.


Subject(s)
Anti-Bacterial Agents/therapeutic use , Q Fever/epidemiology , Rickettsia Infections/epidemiology , Typhoid Fever/epidemiology , Typhus, Endemic Flea-Borne/epidemiology , Fever , Fluoroquinolones/therapeutic use , Gatifloxacin , Humans , Nepal/epidemiology , Ofloxacin/therapeutic use , Prospective Studies , Q Fever/drug therapy , Rickettsia Infections/drug therapy , Typhoid Fever/drug therapy , Typhus, Endemic Flea-Borne/drug therapy
9.
Trials ; 15: 441, 2014 Nov 12.
Article in English | MEDLINE | ID: mdl-25391338

ABSTRACT

BACKGROUND: Cryptococcal meningitis (CM) is a severe AIDS-defining illness with 90-day case mortality as high as 70% in sub-Saharan Africa, despite treatment. It is the leading cause of death in HIV patients in Asia and Africa.No major advance has been made in the treatment of CM since the 1970s. The mainstays of induction therapy are amphotericin B and flucytosine, but these are often poorly available where the disease burden is highest. Adjunctive treatments, such as dexamethasone, have had dramatic effects on mortality in other neurologic infections, but are untested in CM. Given the high death rates in patients receiving current optimal treatment, and the lack of new agents on the horizon, adjuvant treatments, which offer the potential to reduce mortality in CM, should be tested.The principal research question posed by this study is as follows: does adding dexamethasone to standard antifungal therapy for CM reduce mortality? Dexamethasone is a cheap, readily available, and practicable intervention. METHOD: A double-blind placebo-controlled trial with parallel arms in which patients are randomised to receive either dexamethasone or placebo, in addition to local standard of care. The study recruits patients in both Asia and Africa to ensure the relevance of its results to the populations in which the disease burden is highest. The 10-week mortality risk in the control group is expected to be between 30% and 50%, depending on location, and the target hazard ratio of 0.7 corresponds to absolute risk reductions in mortality from 30% to 22%, or from 50% to 38%. Assuming an overall 10-week mortality of at least 30% in our study population, recruitment of 824 patients will be sufficient to observe the expected number of deaths. Allowing for some loss to follow-up, the total sample size for this study is 880 patients. To generate robust evidence across both continents, we aim to recruit roughly similar numbers of patients from each continent. The primary end point is 10-week mortality. Ethical approval has been obtained from Oxford University's Tropical Research Ethics Committee (OxTREC), and as locally mandated at each site. TRIAL REGISTRATION: International Standard Randomised Controlled Trial Number: ISRCTN59144167 26-July-2012.


Subject(s)
AIDS-Related Opportunistic Infections/drug therapy , Anti-Inflammatory Agents/therapeutic use , Antifungal Agents/therapeutic use , Dexamethasone/therapeutic use , HIV Infections/complications , Meningitis, Cryptococcal/drug therapy , Research Design , AIDS-Related Opportunistic Infections/diagnosis , AIDS-Related Opportunistic Infections/microbiology , AIDS-Related Opportunistic Infections/mortality , Anti-Inflammatory Agents/adverse effects , Antifungal Agents/adverse effects , Asia , Clinical Protocols , Dexamethasone/adverse effects , Double-Blind Method , Drug Therapy, Combination , HIV Infections/diagnosis , HIV Infections/mortality , HIV Infections/virology , Humans , Malawi , Meningitis, Cryptococcal/diagnosis , Meningitis, Cryptococcal/microbiology , Meningitis, Cryptococcal/mortality , Time Factors , Treatment Outcome , Uganda
10.
Intensive Care Med Exp ; 2(1): 21, 2014 Dec.
Article in English | MEDLINE | ID: mdl-26215706

ABSTRACT

BACKGROUND: Neutrophil extracellular traps (NETs) are a central player in the host response to bacteria: neutrophils release extracellular DNA (nucleosomes) and neutrophil elastase to entrap and kill bacteria. We studied the role of NETs in Burkholderia pseudomallei infection (melioidosis), an important cause of Gram-negative sepsis in Southeast Asia. METHODS: In a prospective observational study, circulating nucleosomes and neutrophil elastase were assayed in 44 patients with Gram-negative sepsis caused by B. pseudomallei (melioidosis) and 82 controls. Functional assays included human neutrophil stimulation and killing assays and a murine model of B. pseudomallei infection in which NET function was compromised using DNase. Specified pathogen-free 8- to 12-week-old C57BL/6 mice were sacrificed post-infection to assess bacterial loads, inflammation, and pathology. RESULTS: Nucleosome and neutrophil elastase levels were markedly elevated in patients compared to controls. NETs killed B. pseudomallei effectively, and neutrophils stimulated with B. pseudomallei showed increased elastase and DNA release in a time- and dose-dependent matter. In mice, NET disruption with intravenous DNase administration resulted in decreased nucleosome levels. Although DNase treatment of mice resulted in diminished liver inflammation, no differences were observed in bacterial dissemination or systemic inflammation. CONCLUSION: B. pseudomallei is a potent inducer of NETosis which was reflected by greatly increased levels of NET-related components in melioidosis patients. Although NETs exhibited antibacterial activity against B. pseudomallei, NET formation did not protect against bacterial dissemination and inflammation during B. pseudomallei-induced sepsis.

11.
PLoS One ; 6(2): e17439, 2011 Feb 24.
Article in English | MEDLINE | ID: mdl-21390277

ABSTRACT

BACKGROUND: Modelling is widely used to inform decisions about management of malaria and acute febrile illnesses. Most models depend on estimates of the probability that untreated patients with malaria or bacterial illnesses will progress to severe disease or death. However, data on these key parameters are lacking and assumptions are frequently made based on expert opinion. Widely diverse opinions can lead to conflicting outcomes in models they inform. METHODS AND FINDINGS: A Delphi survey was conducted with malaria experts aiming to reach consensus on key parameters for public health and economic models, relating to the outcome of untreated febrile illnesses. Survey questions were stratified by malaria transmission intensity, patient age, and HIV prevalence. The impact of the variability in opinion on decision models is illustrated with a model previously used to assess the cost-effectiveness of malaria rapid diagnostic tests. Some consensus was reached around the probability that patients from higher transmission settings with untreated malaria would progress to severe disease (median 3%, inter-quartile range (IQR) 1-5%), and the probability that a non-malaria illness required antibiotics in areas of low HIV prevalence (median 20%). Children living in low transmission areas were considered to be at higher risk of progressing to severe malaria (median 30%, IQR 10-58%) than those from higher transmission areas (median 13%, IQR 7-30%). Estimates of the probability of dying from severe malaria were high in all settings (medians 60-73%). However, opinions varied widely for most parameters, and did not converge on resurveying. CONCLUSIONS: This study highlights the uncertainty around potential consequences of untreated malaria and bacterial illnesses. The lack of consensus on most parameters, the wide range of estimates, and the impact of variability in estimates on model outputs, demonstrate the importance of sensitivity analysis for decision models employing expert opinion. Results of such models should be interpreted cautiously. The diversity of expert opinion should be recognised when policy options are debated.


Subject(s)
Decision Support Techniques , Fever/diagnosis , Fever/economics , Models, Economic , Tropical Climate , Acute Disease , Adolescent , Adult , Child , Child, Preschool , Critical Illness/economics , Critical Illness/epidemiology , Critical Illness/therapy , Delphi Technique , Disease Progression , Fever/complications , Fever/epidemiology , Health , Humans , Infant , Infant, Newborn , Malaria/diagnosis , Malaria/economics , Malaria/epidemiology , Outcome Assessment, Health Care/methods , Outcome Assessment, Health Care/statistics & numerical data , Probability , Prognosis , Young Adult
12.
J Phys Chem A ; 114(43): 11825-32, 2010 Nov 04.
Article in English | MEDLINE | ID: mdl-20923209

ABSTRACT

This work presents thermochemical data for possible gas phase intermediate species in an industrial rutile chlorinator. An algorithm developed for previous work is employed to ensure that all possible species are considered, reducing the number of important species neglected. Thermochemical data and enthalpies of formation are calculated for 22 new species using density functional theory, post Hartree-Fock coupled cluster calculations, and statistical mechanics. Equilibrium calculations are performed to identify whether any Ti/C intermediates are likely to be important to the high temperature industrial process. These new species are not present at high concentration in the exit stream. It is therefore likely that the two chemical processes do not interact. Rather, the Cl2 rapidly reacts with the solid TiO2 to form TiCl4 and O2. The latter then reacts with the solid C to form CO and CO2 and provide the heat. Data for all the new species is provided as Supporting Information. Finally, a new methodology for data collaboration is investigated in which the data is made openly accessible using the resource description framework. Example scripts are provided to demonstrate how to query and retrieve the data automatically.


Subject(s)
Chlorides/chemistry , Quantum Theory , Thermodynamics , Algorithms , Gases/chemistry , Oxygen/chemistry , Titanium/chemistry
13.
PLoS Negl Trop Dis ; 4(2): e610, 2010 Feb 23.
Article in English | MEDLINE | ID: mdl-20186324

ABSTRACT

BACKGROUND: Symptoms and signs of leptospirosis are non-specific. Several diagnostic tests for leptospirosis are available and in some instances are being used prior to treatment of leptospirosis-suspected patients. There is therefore a need to evaluate the cost-effectiveness of the different treatment strategies in order to avoid misuse of scarce resources and ensure best possible health outcomes for patients. METHODS: The study population was adult patients, presented with uncomplicated acute febrile illness, without an obvious focus of infection or malaria or typical dengue infection. We compared the cost and effectiveness of 5 management strategies: 1) no patients tested or given antibiotic treatment; 2) all patients given empirical doxycycline treatment; patients given doxycycline when a patient is tested positive for leptospirosis using: 3) lateral flow; 4) MCAT; 5) latex test. The framework used is a cost-benefit analysis, accounting for all direct medical costs in diagnosing and treating patients suspected of leptospirosis. Outcomes are measured in length of fever after treatment which is then converted to productivity losses to capture the full economic costs. FINDINGS: Empirical doxycycline treatment was the most efficient strategy, being both the least costly alternative and the one that resulted in the shortest duration of fever. The limited sensitivity of all three diagnostic tests implied that their use to guide treatment was not cost-effective. The most influential parameter driving these results was the cost of treating patients with complications for patients who did not receive adequate treatment as a result of incorrect diagnosis or a strategy of no-antibiotic-treatment. CONCLUSIONS: Clinicians should continue treating suspected cases of leptospirosis on an empirical basis. This conclusion holds true as long as policy makers are not prioritizing the reduction of use of antibiotics, in which case the use of the latex test would be the most efficient strategy.


Subject(s)
Anti-Bacterial Agents/therapeutic use , Case Management/economics , Doxycycline/therapeutic use , Leptospirosis/diagnosis , Leptospirosis/drug therapy , Adolescent , Adult , Aged , Aged, 80 and over , Female , Humans , Leptospirosis/economics , Male , Middle Aged , Time Factors , Treatment Outcome , Young Adult
14.
Science ; 327(5964): 469-74, 2010 Jan 22.
Article in English | MEDLINE | ID: mdl-20093474

ABSTRACT

Current methods for differentiating isolates of predominant lineages of pathogenic bacteria often do not provide sufficient resolution to define precise relationships. Here, we describe a high-throughput genomics approach that provides a high-resolution view of the epidemiology and microevolution of a dominant strain of methicillin-resistant Staphylococcus aureus (MRSA). This approach reveals the global geographic structure within the lineage, its intercontinental transmission through four decades, and the potential to trace person-to-person transmission within a hospital environment. The ability to interrogate and resolve bacterial populations is applicable to a range of infectious diseases, as well as microbial ecology.


Subject(s)
Cross Infection/microbiology , Genome, Bacterial , Methicillin-Resistant Staphylococcus aureus/classification , Methicillin-Resistant Staphylococcus aureus/genetics , Staphylococcal Infections/microbiology , Asia/epidemiology , Bacterial Typing Techniques , Cross Infection/epidemiology , Cross Infection/transmission , Europe/epidemiology , Evolution, Molecular , Genomics/methods , Humans , Likelihood Functions , Methicillin-Resistant Staphylococcus aureus/isolation & purification , Molecular Epidemiology , Molecular Sequence Data , Phylogeny , Polymorphism, Single Nucleotide , Sequence Analysis, DNA , South America/epidemiology , Staphylococcal Infections/epidemiology , Staphylococcal Infections/transmission , Time Factors , United States/epidemiology
16.
Malar J ; 8: 152, 2009 Jul 10.
Article in English | MEDLINE | ID: mdl-19589177

ABSTRACT

BACKGROUND: In Vietnam the blackwater fever syndrome (BWF) has been associated with malaria infection, quinine ingestion and G6PD deficiency. The G6PD variants within the Vietnamese Kinh contributing to the disease risk in this population, and more generally to haemoglobinuria, are currently unknown. METHOD: Eighty-two haemoglobinuria patients and 524 healthy controls were screened for G6PD deficiency using either the methylene blue reduction test, the G-6-PDH kit or the micro-methaemoglobin reduction test. The G6PD gene variants were screened using SSCP combined with DNA sequencing in 82 patients with haemoglobinuria, and in 59 healthy controls found to be G6PD deficient. RESULTS: This study confirmed that G6PD deficiency is strongly associated with haemoglobinuria (OR = 15, 95% CI [7.7 to 28.9], P < 0.0001). Six G6PD variants were identified in the Vietnamese population, of which two are novel (Vietnam1 [Glu3Lys] and Vietnam2 [Phe66Cys]). G6PD Viangchan [Val291Met], common throughout south-east Asia, accounted for 77% of the variants detected and was significantly associated with haemoglobinuria within G6PD-deficient ethnic Kinh Vietnamese (OR = 5.8 95% CI [114-55.4], P = 0.022). CONCLUSION: The primary frequency of several G6PD mutations, including novel mutations, in the Vietnamese Kinh population are reported and the contribution of G6PD mutations to the development of haemoglobinuria are investigated.


Subject(s)
Asian People/genetics , Glucosephosphate Dehydrogenase Deficiency/genetics , Glucosephosphate Dehydrogenase/genetics , Hemoglobinuria/genetics , Mutation/genetics , Asia, Southeastern , Case-Control Studies , Female , Genetic Variation , Glucosephosphate Dehydrogenase/metabolism , Glucosephosphate Dehydrogenase Deficiency/epidemiology , Glucosephosphate Dehydrogenase Deficiency/ethnology , Hemoglobinuria/epidemiology , Humans , Male , Methylene Blue , Molecular Sequence Data , Polymerase Chain Reaction , Polymorphism, Single-Stranded Conformational , Syndrome , Vietnam/epidemiology
17.
J Chem Inf Model ; 48(8): 1571-81, 2008 Aug.
Article in English | MEDLINE | ID: mdl-18661966

ABSTRACT

The SPECTRa (Submission, Preservation and Exposure of Chemistry Teaching and Research Data) project has investigated the practices of chemists in archiving and disseminating primary chemical data from academic research laboratories. To redress the loss of the large amount of data never archived or disseminated, we have developed software for data publication into departmental and institutional Open Access digital repositories (DSpace). Data adhering to standard formats in selected disciplines (crystallography, NMR, computational chemistry) is transformed to XML (CML, Chemical Markup Language) which provides added validation. Context-specific chemical metadata and persistent Handle identifiers are added to enable long-term data reuse. It was found essential to provide an embargo mechanism, and policies for operating this and other processes are presented.


Subject(s)
Combinatorial Chemistry Techniques , Crystallography, X-Ray , Models, Molecular , Software
18.
Int J Epidemiol ; 37(5): 978-87, 2008 Oct.
Article in English | MEDLINE | ID: mdl-18579574

ABSTRACT

BACKGROUND: Methods for assessing diet are prone to measurement error, which may be substantial in large cohort investigations. Biomarkers can be used as objective measures with which to compare estimates of nutritional exposure using different methods METHODS: Cross sectional comparisons in 12 474 men and women of regression between biomarkers for vitamin C, sodium, potassium, fibre, carbohydrate, fat and phytoestrogens with intakes derived from food diaries and food frequency questionnaires (FFQ), and odds ratios for risk of ischaemic heart disease (IHD) by dietary and plasma vitamin C. RESULTS: There were strong (P < 0.001) associations between biomarkers and intakes as assessed by food diary. Coefficients were markedly attenuated for data obtained from the FFQ, especially so for vitamin C, potassium and phytoestrogens (Z P < 0.05). Risk of IHD was associated with plasma vitamin C (P < 0.001) and intake of vitamin C and fruit and vegetables assessed by food diary (P quintile trends <0.001, 0.001) but not by the FFQ (P quintile trends 0.923, 0.186). CONCLUSIONS: Nutritional data that reflect the findings from biomarkers reduce measurement error and will thus improve statistical power in studies of gene nutrient interactions in cohort studies.


Subject(s)
Diet Surveys , Diet , Fruit , Myocardial Ischemia/etiology , Vegetables , Aged , Ascorbic Acid/administration & dosage , Ascorbic Acid/blood , Biomarkers/blood , Carotenoids/blood , Cohort Studies , Diet Records , England , Female , Humans , Male , Middle Aged , Myocardial Ischemia/blood , Surveys and Questionnaires , Vitamins/administration & dosage , Vitamins/blood
19.
Cancer Epidemiol Biomarkers Prev ; 17(5): 1074-81, 2008 May.
Article in English | MEDLINE | ID: mdl-18483328

ABSTRACT

Breast density is a well-known breast cancer risk factor. Most current methods of measuring breast density are area based and subjective. Standard mammogram form (SMF) is a computer program using a volumetric approach to estimate the percent density in the breast. The aim of this study is to evaluate the current implementation of SMF as a predictor of breast cancer risk by comparing it with other widely used density measurement methods. The case-control study comprised 634 cancers with 1,880 age-matched controls combined from the Cambridge and Norwich Breast Screening Programs. Data collection involved assessing the films based both on Wolfe's parenchymal patterns and on visual estimation of percent density and then digitizing the films for computer analysis (interactive threshold technique and SMF). Logistic regression was used to produce odds ratios associated with increasing categories of breast density. Density measures from all four methods were strongly associated with breast cancer risk in the overall population. The stepwise rises in risk associated with increasing density as measured by the threshold method were 1.37 [95% confidence interval (95% CI), 1.03-1.82], 1.80 (95% CI, 1.36-2.37), and 2.45 (95% CI, 1.86-3.23). For each increasing quartile of SMF density measures, the risks were 1.11 (95% CI, 0.85-1.46), 1.31 (95% CI, 1.00-1.71), and 1.92 (95% CI, 1.47-2.51). After the model was adjusted for SMF results, the threshold readings maintained the same strong stepwise increase in density-risk relationship. On the contrary, once the model was adjusted for threshold readings, SMF outcome was no longer related to cancer risk. The available implementation of SMF is not a better cancer risk predictor compared with the thresholding method.


Subject(s)
Breast Neoplasms/diagnostic imaging , Mammography/methods , Radiographic Image Interpretation, Computer-Assisted/methods , Aged , Case-Control Studies , Female , Humans , Logistic Models , Middle Aged , Predictive Value of Tests , Software
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