Defining the True Sensitivity of Culture for the Diagnosis of Melioidosis Using Bayesian Latent Class Models

BACKGROUND: Culture remains the diagnostic gold standard for many bacterial infections, and the method against which other tests are often evaluated. Specificity of culture is 100% if the pathogenic organism is not found in healthy subjects, but the sensitivity of culture is more difficult to determine and may be low. Here, we apply Bayesian latent class models (LCMs) to data from patients with a single Gram-negative bacterial infection and define the true sensitivity of culture together with the impact of misclassification by culture on the reported accuracy of alternative diagnostic tests. METHODS/PRINCIPAL FINDINGS: Data from published studies describing the application of five diagnostic tests (culture and four serological tests) to a patient cohort with suspected melioidosis were re-analysed using several Bayesian LCMs. Sensitivities, specificities, and positive and negative predictive values (PPVs and NPVs) were calculated. Of 320 patients with suspected melioidosis, 119 (37%) had culture confirmed melioidosis. Using the final model (Bayesian LCM with conditional dependence between serological tests), the sensitivity of culture was estimated to be 60.2%. Prediction accuracy of the final model was assessed using a classification tool to grade patients according to the likelihood of melioidosis, which indicated that an estimated disease prevalence of 61.6% was credible. Estimates of sensitivities, specificities, PPVs and NPVs of four serological tests were significantly different from previously published values in which culture was used as the gold standard. CONCLUSIONS/SIGNIFICANCE: Culture has low sensitivity and low NPV for the diagnosis of melioidosis and is an imperfect gold standard against which to evaluate alternative tests. Models should be used to support the evaluation of diagnostic tests with an imperfect gold standard. It is likely that the poor sensitivity/specificity of culture is not specific for melioidosis, but rather a generic problem for many bacterial and fungal infections

The Response of Lemna minor to Mixtures of Pesticides That Are Commonly Used in Thailand

In the field, aquatic organisms are exposed to multiple contaminants rather than to single compounds. It is therefore important to understand the toxic interactions of co-occurring substances in the environment. The aim of the study was to assess the effects of individual herbicides (atrazine, 2,4-D, alachlor and paraquat) that are commonly used in Thailand and their mixtures on Lemna minor. Plants were exposed to individual and binary mixtures for 7 days and the effects on plant growth rate were assesed based on frond area measurements. Experimental observations of mixture toxicity were compared with predictions based on single herbicide exposure data using concentration addition and independent action models. The single compound studies showed that paraquat and alachlor were most toxic to L. minor, followed by atrazine and then 2,4-D. For the mixtures, atrazine with 2,4-D appeared to act antagonistically, whereas alachlor and paraquat showed synergism

The burden of antimicrobial resistance in the Americas in 2019: a cross-country systematic analysis

Background Antimicrobial resistance (AMR) is an urgent global health challenge and a critical threat to modern health care. Quantifying its burden in the WHO Region of the Americas has been elusive—despite the region’s long history of resistance surveillance. This study provides comprehensive estimates of AMR burden in the Americas to assess this growing health threat. Methods We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with AMR for 23 bacterial pathogens and 88 pathogen–drug combinations for countries in the WHO Region of the Americas in 2019. We obtained data from mortality registries, surveillance systems, hospital systems, systematic literature reviews, and other sources, and applied predictive statistical modelling to produce estimates of AMR burden for all countries in the Americas. Five broad components were the backbone of our approach: the number of deaths where infection had a role, the proportion of infectious deaths attributable to a given infectious syndrome, the proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of pathogens resistant to an antibiotic class, and the excess risk of mortality (or duration of an infection) associated with this resistance. We then used these components to estimate the disease burden by applying two counterfactual scenarios: deaths attributable to AMR (compared to an alternative scenario where resistant infections are replaced with susceptible ones), and deaths associated with AMR (compared to an alternative scenario where resistant infections would not occur at all). We generated 95% uncertainty intervals (UIs) for final estimates as the 25th and 975th ordered values across 1000 posterior draws, and models were cross-validated for out-of-sample predictive validity. Findings We estimated 569,000 deaths (95% UI 406,000–771,000) associated with bacterial AMR and 141,000 deaths (99,900–196,000) attributable to bacterial AMR among the 35 countries in the WHO Region of the Americas in 2019. Lower respiratory and thorax infections, as a syndrome, were responsible for the largest fatal burden of AMR in the region, with 189,000 deaths (149,000–241,000) associated with resistance, followed by bloodstream infections (169,000 deaths [94,200–278,000]) and peritoneal/intra-abdominal infections (118,000 deaths [78,600–168,000]). The six leading pathogens (by order of number of deaths associated with resistance) were Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. Together, these pathogens were responsible for 452,000 deaths (326,000–608,000) associated with AMR. Methicillin-resistant S. aureus predominated as the leading pathogen–drug combination in 34 countries for deaths attributable to AMR, while aminopenicillin-resistant E. coli was the leading pathogen–drug combination in 15 countries for deaths associated with AMR. Interpretation Given the burden across different countries, infectious syndromes, and pathogen–drug combinations, AMR represents a substantial health threat in the Americas. Countries with low access to antibiotics and basic health-care services often face the largest age-standardised mortality rates associated with and attributable to AMR in the region, implicating specific policy interventions. Evidence from this study can guide mitigation efforts that are tailored to the needs of each country in the region while informing decisions regarding funding and resource allocation. Multisectoral and joint cooperative efforts among countries will be a key to success in tackling AMR in the Americas. Funding Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care using UK aid funding managed by the Fleming Fund

Post-tsunami rehabilitation of fish cage farms on the Andaman coast of Thailand

A post-tsunami rehabilitation of cage culture along the Andaman Sea coast of Thailand was carried out in five provinces (Ranong, Phang-nga, Krabi, Trang and Satun) from September 2007 to February 2008. Based on the survey conducted, the money compensated subsequently used to buy materials for cage re-construction and cage repair accounted for 28.1% of the total, and to buy seed, feed and chemicals for culture operations, 15.8%. A surprising finding is that 56.1% of compensated money was used for other purposes. The analysis showed that the quality and quantity of equipment, seeds and feeds invested in aquaculture farms were increased in comparison with the pre-recovery period. Importantly, the farm area, growth rate, amount of product and revenue were improved during the post-tsunami rehabilitation period. Additionally, the area and quality of houses, household consumption, household infrastructures, health care and education were also improved. The satisfaction level of cage farmers in regard to the recovery programs was high (weigh average index = 3.88). The results from this study showed that the net economic profit (NEP) achieved was 41,030.49 baht/crop (33.9 baht = 1 US$) for sea bass culture, while NEP for grouper culture was 59,529.98 baht/crop. The result from the present study indicated that the economic value of cage culture farms was profitable. However, the seed shortage, high cost of trash fish, disease outbreak and marketing were among key problems and constraints encountered. In this study, we also found that the knowledge about fish marketing and culture techniques was poor. Therefore, technical, marketing and financial support are required for the future

A three-component hydrograph separation based on geochemical tracers in a tropical mountainous headwater catchment in northern Thailand

Land-use change in the mountainous parts of northern Thailand is reflected by an increased application of agrochemicals, which may be lost to surface and groundwater. The close relation between flow paths and contaminant transport within hydrological systems requires recognizing and understanding the dominant hydrological processes. To date, the vast majority of studies on runoff generation have been conducted in temperate regions. Tropical regions suffer from a general lack of data, and little is known about runoff generation processes. To fill this knowledge gap, a three-component hydrograph separation based on geochemical tracers was carried out in a steep, remote and monsoon-dominated study site (7 km2) in northern Thailand. Silica and electrical conductivity (EC) were identified as useful tracers and were applied to calculate the fractions of groundwater (similar to pre-event water), shallow subsurface flow and surface runoff on stormflow. K+ was a useful indicator for surface runoff dynamics, and Ca2+ provided insights into groundwater behaviour. Nevertheless, neither measure was applicable for the quantification of runoff components. Cl- and further parameters (e.g. Na+, K+, and Mg2+) were also not helpful for flow path identification, nor were their concentrations distinguishable among the components. Groundwater contributed the largest fractions to stormflow (62–80%) throughout all events, followed by shallow subsurface flow (17–36%) and surface runoff (2–13%). Our results provide important insights into the dynamics of the runoff processes in the study area and may be used to assess the transport pattern of contaminants (i.e. agrochemicals) here

A three-component hydrograph separation based on geochemical tracers in a tropical mountainous headwater catchment in northern Thailand

Land-use change in the mountainous parts of northern Thailand is reflected by an increased application of agrochemicals, which may be lost to surface and groundwater. The close relation between flow paths and contaminant transport within hydrological systems requires recognizing and understanding the dominant hydrological processes. To date, the vast majority of studies on runoff generation have been conducted in temperate regions. Tropical regions suffer from a general lack of data, and little is known about runoff generation processes. To fill this knowledge gap, a three-component hydrograph separation based on geochemical tracers was carried out in a steep, remote and monsoon-dominated study site (7 km2) in northern Thailand. Silica and electrical conductivity (EC) were identified as useful tracers and were applied to calculate the fractions of groundwater (similar to pre-event water), shallow subsurface flow and surface runoff on stormflow. K+ was a useful indicator for surface runoff dynamics, and Ca2+ provided insights into groundwater behaviour. Nevertheless, neither measure was applicable for the quantification of runoff components. Cl- and further parameters (e.g. Na+, K+, and Mg2+) were also not helpful for flow path identification, nor were their concentrations distinguishable among the components. Groundwater contributed the largest fractions to stormflow (62–80%) throughout all events, followed by shallow subsurface flow (17–36%) and surface runoff (2–13%). Our results provide important insights into the dynamics of the runoff processes in the study area and may be used to assess the transport pattern of contaminants (i.e. agrochemicals) here.Water ManagementCivil Engineering and Geoscience