IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community

Who sleeps under bednets in Ghana? A doer/non-doer analysis of malaria prevention behaviours

BACKGROUND: Malaria prevention programmes should be based in part on knowledge of why some individuals use bednets while others do not. This paper identifies factors and characteristics of women that affect bednet use among their children less than five years of age in Ghana. METHODS: Data come from the baseline component of an evaluation of Freedom from Hunger's malaria curriculum. A quasi-experimental design was used to select clients (n = 516) of Credit with Education (an integrated package of microfinance and health education) and non-clients (n = 535). Chi-squares, Fisher's Exact tests and logistic regression were used to compare the characteristics of mothers whose children use bednets (doers) with those whose children do not (non-doers) and to identify factors associated with bednet use among children less than five years of age. RESULTS: The following factors were most closely associated with bednet use: region of residence; greater food security; and caregivers' beliefs about symptoms, causation and groups most vulnerable to malaria. Most respondents knew mosquitoes caused malaria; however, 20.6% of doers and 12.3% of non-doers (p = .0228) thought overworking oneself caused malaria. Ninety percent of doers and 77.0% of non-doers felt that sleeping under a net was protective against malaria (p = .0040). In addition, 16.5% of doers and 7.5% of non-doers (p = .0025) identified adult males as most vulnerable to malaria. CONCLUSION: Greater knowledge about malaria does not always translate into improved bednet use. Though culturally-based ideas about malaria may vary between communities, integrating them into traditional health education messages may enhance the effectiveness of public health efforts

The Diet of Diabetic Patients in Spain in 2008–2010: Accordance with the Main Dietary Recommendations—A Cross-Sectional Study

Background: No previous study has assessed the diet of the diabetic patients in the general population of an entire country in Europe. This study evaluates accordance of the diet of diabetic adults in Spain with nutritional recommendations of the European Association for the Study of Diabetes (EASD), American Diabetes Association (ADA), and the Mediterranean diet (MD). Methods and Findings: Cross-sectional study conducted in 2008-2010 among 12,948 persons representative of the population aged ≥18 years in Spain. Usual food consumption was assessed with a dietary history. EASD accordance was defined as ≥6 points on a score of 12 nutritional goals, ADA accordance as ≥3 points on a score of 6 goals, and MD accordance as ≥7 points on the Mediterranean Diet Adherence Screener. In the 609 diagnosed diabetic individuals, the diet was rich in saturated fat (11.2% of total energy), but trans fat intake was relatively low (1.1% energy) and monounsaturated fat intake was high (16.1% energy). Carbohydrate intake was relatively low (41.1% energy), but sugar intake was high (16.9% energy). Intake of cholesterol (322 mg/day) and sodium (3.1 g/day) was also high, while fiber intake was insufficient (23.8 g/day). EASD accordance was observed in 48.7% diabetic patients, ADA accordance in 46.3%, and MD accordance in 57.4%. The frequency of EASD, ADA and MD accordance was not statistically different between diagnosed and undiagnosed diabetic individuals. Conclusions: Only about half of diabetic patients in Spain have a diet that is consistent with the major dietary recommendations. The lack of dietary differences between diagnosed and undiagnosed diabetic individuals reflects deficiencies in diabetes managementThe ENRICA study is funded by Sanofi-Aventis. Additional funding is obtained from FIS grant PI09/1626 and from the ‘Cátedra UAM de Epidemiología y Control del Riesgo Cardiovascular

Staphylococcus warneri meningitis in a patient with Strongyloides stercoralis hyperinfection and lymphoma: first report of a case

A case of meningitis due to Staphylococcus warneri in a patient with a hyperinfection with Strongyloides stercoralis possibly associated with rituximab treatment for mantel cell lymphoma is reported for the first time in the literature. The patient was a 59-year-old woman, with a 3-year history of an apparently well controlled lymphoma after treatment with chemotherapy-immunotherapy and then immunotherapy alone, and diagnosis of strongyloidiasis. Meningitis was diagnosed by cerebrospinal fluid culture and tested with an automated plate system. The patient was successfully treated with vancomycin; although fever and productive cough persisted. Severe gastrointestinal symptoms and pneumonia developed three weeks later. Hyperinfection syndrome by S. stercoralis was diagnosed, with abundant larvae in feces and expectoration

Effects of pre-operative isolation on postoperative pulmonary complications after elective surgery: an international prospective cohort study

We aimed to determine the impact of pre-operative isolation on postoperative pulmonary complications after elective surgery during the global SARS-CoV-2 pandemic. We performed an international prospective cohort study including patients undergoing elective surgery in October 2020. Isolation was defined as the period before surgery during which patients did not leave their house or receive visitors from outside their household. The primary outcome was postoperative pulmonary complications, adjusted in multivariable models for measured confounders. Pre-defined sub-group analyses were performed for the primary outcome. A total of 96,454 patients from 114 countries were included and overall, 26,948 (27.9%) patients isolated before surgery. Postoperative pulmonary complications were recorded in 1947 (2.0%) patients of which 227 (11.7%) were associated with SARS-CoV-2 infection. Patients who isolated pre-operatively were older, had more respiratory comorbidities and were more commonly from areas of high SARS-CoV-2 incidence and high-income countries. Although the overall rates of postoperative pulmonary complications were similar in those that isolated and those that did not (2.1% vs 2.0%, respectively), isolation was associated with higher rates of postoperative pulmonary complications after adjustment (adjusted OR 1.20, 95%CI 1.05-1.36, p = 0.005). Sensitivity analyses revealed no further differences when patients were categorised by: pre-operative testing; use of COVID-19-free pathways; or community SARS-CoV-2 prevalence. The rate of postoperative pulmonary complications increased with periods of isolation longer than 3 days, with an OR (95%CI) at 4-7 days or ≥ 8 days of 1.25 (1.04-1.48), p = 0.015 and 1.31 (1.11-1.55), p = 0.001, respectively. Isolation before elective surgery might be associated with a small but clinically important increased risk of postoperative pulmonary complications. Longer periods of isolation showed no reduction in the risk of postoperative pulmonary complications. These findings have significant implications for global provision of elective surgical care

IMG/VR: A database of cultured and uncultured DNA viruses and retroviruses

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community

Community perceptions on malaria and care-seeking practices in endemic Indian settings: policy implications for the malaria control programme

<p>Abstract</p> <p>Background</p> <p>The focus of India’s National Malaria Programme witnessed a paradigm shift recently from health facility to community-based approaches. The current thrust is on diagnosing and treating malaria by community health workers and prevention through free provision of long-lasting insecticidal nets. However, appropriate community awareness and practice are inevitable for the effectiveness of such efforts. In this context, the study assessed community perceptions and practice on malaria and similar febrile illnesses. This evidence base is intended to direct the roll-out of the new strategies and improve community acceptance and utilization of services.</p> <p>Methods</p> <p>A qualitative study involving 26 focus group discussions and 40 key informant interviews was conducted in two districts of Odisha State in India. The key points of discussion were centred on community perceptions and practice regarding malaria prevention and treatment. Thematic analysis of data was performed.</p> <p>Results</p> <p>The 272 respondents consisted of 50% females, three-quarter scheduled tribe community and 30% students. A half of them were literates. Malaria was reported to be the most common disease in their settings with multiple modes of transmission by the FGD participants. Adoption of prevention methods was seasonal with perceived mosquito density. The reported use of bed nets was low and the utilization was determined by seasonality, affordability, intoxication and alternate uses of nets. Although respondents were aware of malaria-related symptoms, care-seeking from traditional healers and unqualified providers was prevalent. The respondents expressed lack of trust in the community health workers due to frequent drug stock-outs. The major determinants of health care seeking were socio-cultural beliefs, age, gender, faith in the service provider, proximity, poverty, and perceived effectiveness of available services.</p> <p>Conclusion</p> <p>Apart from the socio-cultural and behavioural factors, the availability of acceptable care can modulate the community perceptions and practices on malaria management. The current community awareness on symptoms of malaria and prevention is fair, yet the prevention and treatment practices are not optimal. Promoting active community involvement and ownership in malaria control and management through strengthening community based organizations would be relevant. Further, timely availability of drugs and commodities at the community level can improve their confidence in the public health system.</p

Pathways to malaria persistence in remote central Vietnam: a mixed-method study of health care and the community

<p>Abstract</p> <p>Background</p> <p>There is increasing interest in underlying socio-cultural, economic, environmental and health-system influences on the persistence of malaria. Vietnam is a Mekong regional 'success story' after dramatic declines in malaria incidence following introduction of a national control program providing free bed-nets, diagnosis and treatment. Malaria has largely retreated to pockets near international borders in central Vietnam, where it remains a burden particularly among impoverished ethnic minorities. In these areas commune and village health workers are lynchpins of the program. This study in the central province of Quang Tri aimed to contribute to more effective malaria control in Vietnam by documenting the <it>non-biological </it>pathways to malaria persistence in two districts.</p> <p>Methods</p> <p>Multiple and mixed (qualitative and quantitative) methods were used. The formative stage comprised community meetings, observation of bed-net use, and focus group discussions and semi-structured interviews with health managers, providers and community. Formative results were used to guide development of tools for the assessment stage, which included a provider quiz, structured surveys with 160 community members and 16 village health workers, and quality check of microscopy facilities and health records at district and commune levels. Descriptive statistics and chi-square analysis were used for quantitative data.</p> <p>Results</p> <p>The study's key findings were the inadequacy of bed-nets (only 45% of households were fully covered) and sub-optimal diagnosis and treatment at local levels. Bed-net insufficiencies were exacerbated by customary sleeping patterns and population mobility. While care at district level seemed good, about a third of patients reportedly self-discharged early and many were lost to follow-up. Commune and village data suggested that approximately half of febrile patients were treated presumptively, and 10 village health workers did not carry artesunate to treat the potentially deadly and common <it>P. falciparum </it>malaria. Some staff lacked diagnostic skills, time for duties, and quality microscopy equipment. A few gaps were found in community knowledge and reported behaviours.</p> <p>Conclusion</p> <p>Malaria control cannot be achieved through community education alone in this region. Whilst appropriate awareness-raising is needed, it is most urgent to address weaknesses at systems level, including bed-net distribution, health provider staffing and skills, as well as equipment and supplies.</p