Malaria parasite clearance rate regression: an R software package for a Bayesian hierarchical regression model.

BACKGROUND: Emerging resistance to anti-malarial drugs has led malaria researchers to investigate what covariates (parasite and host factors) are associated with resistance. In this regard, investigation of how covariates impact malaria parasites clearance is often performed using a two-stage approach in which the WWARN Parasite Clearance Estimator or PCE is used to estimate parasite clearance rates and then the estimated parasite clearance is regressed on the covariates. However, the recently developed Bayesian Clearance Estimator instead leads to more accurate results for hierarchial regression modelling which motivated the authors to implement the method as an R package, called "bhrcr". METHODS: Given malaria parasite clearance profiles of a set of patients, the "bhrcr" package performs Bayesian hierarchical regression to estimate malaria parasite clearance rates along with the effect of covariates on them in the presence of "lag" and "tail" phases. In particular, the model performs a linear regression of the log clearance rates on covariates to estimate the effects within a Bayesian hierarchical framework. All posterior inferences are obtained by a "Markov Chain Monte Carlo" based sampling scheme which forms the core of the package. RESULTS: The "bhrcr" package can be utilized to study malaria parasite clearance data, and specifically, how covariates affect parasite clearance rates. In addition to estimating the clearance rates and the impact of covariates on them, the "bhrcr" package provides tools to calculate the WWARN PCE estimates of the parasite clearance rates as well. The fitted Bayesian model to the clearance profile of each individual, as well as the WWARN PCE estimates, can also be plotted by this package. CONCLUSIONS: This paper explains the Bayesian Clearance Estimator for malaria researchers including describing the freely available software, thus making these methods accessible and practical for modelling covariates' effects on parasite clearance rates.

The effect of case management and vector-control interventions on space-time patterns of malaria incidence in Uganda.

BACKGROUND: Electronic reporting of routine health facility data in Uganda began with the adoption of the District Health Information Software System version 2 (DHIS2) in 2011. This has improved health facility reporting and overall data quality. In this study, the effects of case management with artemisinin-based combination therapy (ACT) and vector control interventions on space-time patterns of disease incidence were determined using DHIS2 data reported during 2013-2016. METHODS: Bayesian spatio-temporal negative binomial models were fitted on district-aggregated monthly malaria cases, reported by two age groups, defined by a cut-off age of 5 years. The effects of interventions were adjusted for socio-economic and climatic factors. Spatial and temporal correlations were taken into account by assuming a conditional autoregressive and a first-order autoregressive AR(1) process on district and monthly specific random effects, respectively. Fourier trigonometric functions were incorporated in the models to take into account seasonal fluctuations in malaria transmission. RESULTS: The temporal variation in incidence was similar in both age groups and depicted a steady decline up to February 2014, followed by an increase from March 2015 onwards. The trends were characterized by a strong bi-annual seasonal pattern with two peaks during May-July and September-December. Average monthly incidence in children < 5 years declined from 74.7 cases (95% CI 72.4-77.1) in 2013 to 49.4 (95% CI 42.9-55.8) per 1000 in 2015 and followed by an increase in 2016 of up to 51.3 (95% CI 42.9-55.8). In individuals ≥ 5 years, a decline in incidence from 2013 to 2015 was followed by an increase in 2016. A 100% increase in insecticide-treated nets (ITN) coverage was associated with a decline in incidence by 44% (95% BCI 28-59%). Similarly, a 100% increase in ACT coverage reduces incidence by 28% (95% BCI 11-45%) and 25% (95% BCI 20-28%) in children < 5 years and individuals ≥ 5 years, respectively. The ITN effect was not statistically important in older individuals. The space-time patterns of malaria incidence in children < 5 are similar to those of parasitaemia risk predicted from the malaria indicator survey of 2014-15. CONCLUSION: The decline in malaria incidence highlights the effectiveness of vector-control interventions and case management with ACT in Uganda. This calls for optimizing and sustaining interventions to achieve universal coverage and curb reverses in malaria decline.

Donor support for quality assurance and pharmacovigilance of anti-malarials in malaria-endemic countries.

BACKGROUND: Malaria control efforts have been strengthened by funding from donor groups and government agencies. The Global Fund to Fight AIDS, Tuberculosis and the Malaria (Global Fund), the US President's Malaria Initiative (PMI) account for the majority of donor support for malaria control and prevention efforts. Pharmacovigilance (PV), which encompasses all activities relating to the detection, assessment, understanding, and prevention of adverse effects or any other drug-related problem, is a necessary part of efforts to reduce drug resistance and improve treatment outcomes. This paper reports on an analysis of PV plans in the Global Fund and PMI and World Bank's grants for malaria prevention and control. METHODS: All active malaria grants as of September 2015 funded by the Global Fund and World Bank, and fiscal year 2015 and 2016 PMI Malaria Operational Plans (MOP) were identified. The total amount awarded for PV-related activities and drug quality assurance was abstracted. A Key-Word-in-Context (KWIC) analysis was conducted for the content of each grant. Specific search terms consisted of pharmacovigilance, pregn*, registry, safety, adverse drug, mass drug administration, primaquine, counterfeit, sub-standard, and falsified. Grants that mentioned PV activities identified in the KWIC search, listed PV in their budgets, or included the keywords: counterfeit, sub-standard, falsified, mass drug administration, or adverse event were thematically coded using Dedoose software version 7.0. RESULTS: The search identified 159 active malaria grants including 107 Global Fund grants, 39 fiscal year 2015 and 2016 PMI grants and 13 World Bank grants. These grants were primarily awarded to low-income countries (57.2%) and in sub-Saharan Africa (SSA) (70.4%). Thirty-seven (23.3%) grants included a budget line for PV- or drug quality assurance-related activities, including 21 PMI grants and 16 Global Fund grants. Only 23 (14.5%) grants directly mentioned PV. The primary focus area was improving drug quality monitoring, especially among the PMI grants. CONCLUSIONS: The results of the analysis demonstrate that funding for PV has not been sufficiently prioritized by either the key malaria donor organizations or by the recipient countries, as reflected in their grant proposal submissions and MOPs.

Measuring the association between artemisinin-based case management and malaria incidence in southern Vietnam, 1991-2010.

In addition to being effective, fast-acting, and well tolerated, artemisinin-based combination therapies (ACTs) are able to kill certain transmission stages of the malaria parasite. However, the population-level impacts of ACTs on reducing malaria transmission have been difficult to assess. In this study on the history of malaria control in Vietnam, we assemble annual reporting on malaria case counts, coverage with insecticide-treated nets (ITN) and indoor residual spraying (IRS), and drug purchases by provincial malaria control programs from 1991 to 2010 in Vietnam's 20 southern provinces. We observe a significant negative association between artemisinin use and malaria incidence, with a 10% absolute increase in the purchase proportion of artemisinin-containing regimens being associated with a 29.1% (95% confidence interval: 14.8-41.0%) reduction in slide-confirmed malaria incidence, after accounting for changes in urbanization, ITN/IRS coverage, and two indicators of health system capacity. One budget-related indicator of health system capacity was found to have a smaller association with malaria incidence, and no other significant factors were found. Our findings suggest that including an artemisinin component in malaria drug regimens was strongly associated with reduced malaria incidence in southern Vietnam, whereas changes in urbanization and coverage with ITN or IRS were not.

In silico screening of antifolate based novel inhibitors from Brucea mollis Wall. ex kurz against quadruple mutant drug resistant PfDHFR.

Plasmodium falciparum is the most lethal form of the genus Plasmodium which causes malaria, a 'disease of antiquity'. Globally it affects the health and socio-economic development of a large population especially in Sub-Saharan Africa and Southeast Asia. The Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) is an important target of antimalarial drugs. Mutations at the active site of PfDHFR have resulted in decrease drug binding affinity of DHFR-inhibitors. In the present study we selected ten compounds of Brucea mollis Wall. Ex kurz and checked for their drug likeness using various computational tools and potential interactions with PfDHFR by molecular docking study. Soulameanone, a quassinoid of Brucea mollis Wall. Ex kurz showed better binding affinity when compared to pyrimethamine for both wild and quadruple mutant drug resistant PfDHFR. In addition, similar isomers of soulameanone were screened for their drug likeness and to study their interactions with PfDHFR. Twenty three compounds showed better binding affinity compared to soulameanone.

Progress toward elimination of malaria in Nigeria: uptake of artemisinin-based combination therapies for the treatment of malaria in households in Benin City.

BACKGROUND: The Roll Back Malaria (RBM) Partnership converged in Abuja in 2000. In 2005, Nigeria adopted artemisinin-based combination therapies (ACTs) as first-line therapy for uncomplicated malaria. It was determined that by 2010, 80% of persons with malaria would be effectively treated. OBJECTIVES: To describe household practices for malaria treatment in Benin City; to explore demographic characteristics that may influence use of ACTs. MATERIALS AND METHODS: Multistage sampling technique was used to select households from each of the three local government areas in Benin City. Adult respondents were interviewed. Household reference persons (HRPs) were defined by International Labour Organization categories. Data were collected between December 2009 and February 2010 and were analyzed using Statistical Package for the Social Sciences Version 16.0, at a significance level of P < 0.05 (2-tailed). RESULTS: Of the 240 households selected, 217 were accessible, and respondents from 90% of these recalled the most recent episode (s) of malaria. One-third of malaria episodes had occurred in children younger than 5 years. ACTs were used in 4.9% of households; sulfadoxine-pyrimethamine was the chief non-ACT antimalarial, followed by artemisinin monotherapies. Patent medicine stores were the most common sources of antimalarial medicines (38.2%), followed by private hospitals (20.3%) and private pharmacies (10.6%). Only 8.3% of households got their medicines from government hospitals. Having a HRP in managerial or professional categories was associated with a 6 times higher odds of using ACTs, compared to other occupational categories [odds ratio (OR) 5.8; confidence interval (CI) 1.470-20.758, P = 0.016]. Fathers' tertiary or higher education was significantly associated with ACT use, but not mothers' (OR 0.054, CI 0.006-0.510; P = 0.011 and OR 0.905, CI 0.195-4.198; P = 0.898, respectively). CONCLUSION: Ten years after the historic Abuja meeting, only 5% of households in Benin City used ACTs for the treatment of malaria, sourcing medicines chiefly from patent medicine stores and private hospitals. Fathers' level of education was significantly associated with ACT use. Interventions to eliminate malaria from Nigeria should mainstream the men folk and health care providers outside government hospitals, in line with the Nigerian reality.

Scientific research in malaria: bibliometric assessment of the Latin-American contributions.

BACKGROUND: Malaria is a parasitic disease of high global impact in public health, including Latin America. There should be more researched, particularly in this region. A bibliometric assessment of the Latin American contributions about malaria was done. METHODS: Bibliometric study at SCI (1980-2013), MEDLINE/ GOPUBMED (1802-2013), Scopus (1959-2013), SCIELO (2004-2013), LILACS (1980-2013). The studies were characterized by study type, year of publication, city/country of origin, journals and more productive authors, citations and H index. RESULTS: At SCI, 2,806 articles were retrieved (5.13% of the total). Brazil was the highest producer (31.41%), followed by Colombia (14.3%) and Mexico (9.5%). The region received 39,894 citations, 32.2% from Brazil (H index=51), 12.75% Mexico (H index=38), 11.2% Colombia (H index=33). At Scopus, there are 4,150 articles (4.9% of the total), 33.0% Brazil, 11.3% Colombia and 8.8% Mexico; 17% in Brazil were from Universidad de São Paulo; 23.6% of Colombia from Universidad de Antioquia; 15.4% of Mexico from Instituto Nacional de Salud Pública. At Medline there were 4,278 records (36.8% Brazil). At SciELO there are 792 records (45.3% Brazil). At LILACS there were 1744 records (34.3% Brazil). CONCLUSIONS: Brazil has the highest output of the region, as Venezuela the scientific production in Malaria was related with the burden of disease. This was not the case for Colombia. Scientific production at bibliographical databases, particularly regionals, is low, compared to the high incidence of this disease that requires more research and control.

CRIMALDDI: a prioritized research agenda to expedite the discovery of new anti-malarial drugs.

The CRIMALDDI Consortium has been a three-year project funded by the EU Framework Seven Programme. It aimed to develop a prioritized set of recommendations to speed up anti-malarial drug discovery research and contribute to the setting of the global research agenda. It has attempted to align thinking on the high priority issues and then to develop action plans and strategies to address these issues. Through a series of facilitated and interactive workshops, it has concluded that these priorities can be grouped under five key themes: attacking artemisinin resistance; creating and sharing community resources; delivering enabling technologies; exploiting high throughput screening hits quickly; and, identifying novel targets. Recommendations have been prioritized into one of four levels: quick wins; removing key roadblocks to future progress; speeding-up drug discovery; and, nice to have (but not essential). Use of this prioritization allows efforts and resources to be focused on the lines of work that will contribute most to expediting anti-malarial drug discovery. Estimates of the time and finances required to implement the recommendations have also been made, along with indications of when recommendations within each theme will make an impact. All of this has been collected into an indicative roadmap that, it is hoped, will guide decisions about the direction and focus of European anti-malarial drug discovery research and contribute to the setting of the global research agenda.

CRIMALDDI: platform technologies and novel anti-malarial drug targets.

The Coordination, Rationalization, and Integration of antiMALarial drug Discovery & Development Initiatives (CRIMALDDI) Consortium, funded by the EU Framework Seven Programme, has attempted, through a series of interactive and facilitated workshops, to develop priorities for research to expedite the discovery of new anti-malarials. This paper outlines the recommendations for the development of enabling technologies and the identification of novel targets.Screening systems must be robust, validated, reproducible, and represent human malaria. They also need to be cost-effective. While such systems exist to screen for activity against blood stage Plasmodium falciparum, they are lacking for other Plasmodium spp. and other stages of the parasite's life cycle. Priority needs to be given to developing high-throughput screens that can identify activity against the liver and sexual stages. This in turn requires other enabling technologies to be developed to allow the study of these stages and to allow for the culture of liver cells and the parasite at all stages of its life cycle.As these enabling technologies become available, they will allow novel drug targets to be studied. Currently anti-malarials are mostly targeting the asexual blood stage of the parasite's life cycle. There are many other attractive targets that need to be investigated. The liver stages and the sexual stages will become more important as malaria control moves towards malaria elimination. Sexual development is a process offering multiple targets, even though the mechanisms of differentiation are still not fully understood. However, designing a drug whose effect is not curative but would be used in asymptomatic patients is difficult given current safety thresholds. Compounds active against the liver schizont would have a prophylactic effect and Plasmodium vivax elimination requires effectors against the dormant liver hypnozoites. It may be that drugs to be used in elimination campaigns will also need to have utility in the control phase. Compounds with activity against blood stages need to be screened for activity against other stages.Natural products should also be a valuable source of new compounds. They often occupy non-Lipinski chemical space and so may reveal valuable new chemotypes.

In vitro antimicrobial assessment of Cuban propolis extracts

Propolis is a resinous mixture of different plant exudates collected by honeybees. Currently, propolis is widely used as a food supplement and in folk medicine. We have evaluated 20 Cuban propolis extracts of different chemical types, brown (BCP), red and yellow (YCP), with respect to their in vitro antibacterial, antifungal and antiprotozoal properties. The extracts inhibited the growth of Staphylococcus aureus and Trichophyton rubrum at low µg/mL concentrations, whereas they were not active against Escherichia coli and Candida albicans. The major activity of the extracts was found against the protozoa Leishmania, Trypanosoma and Plasmodium, although cytotoxicity against MRC-5 cells was also observed. The BCP-3, YCP-39 and YCP-60 extracts showed the highest activity against P. falciparum, with 50% of microbial growth (IC50) values of 0.2 µg/mL. A positive correlation between the biological activity and the chemical composition was observed for YCP extracts. The most promising antimicrobial activity corresponds to YCP subtype B, which contains acetyl triterpenes as the main constituents. The present in vitro study highlights the potential of propolis against protozoa, but further research is needed to increase selectivity towards the parasite. The observed chemical composition-activity relationship of propolis can contribute to the identification of the active principles and standardisation of this bee product.

In vitro antimicrobial assessment of Cuban propolis extracts.

Propolis is a resinous mixture of different plant exudates collected by honeybees. Currently, propolis is widely used as a food supplement and in folk medicine. We have evaluated 20 Cuban propolis extracts of different chemical types, brown (BCP), red and yellow (YCP), with respect to their in vitro antibacterial, antifungal and antiprotozoal properties. The extracts inhibited the growth of Staphylococcus aureus and Trichophyton rubrum at low µg/mL concentrations, whereas they were not active against Escherichia coli and Candida albicans. The major activity of the extracts was found against the protozoa Leishmania, Trypanosoma and Plasmodium, although cytotoxicity against MRC-5 cells was also observed. The BCP-3, YCP-39 and YCP-60 extracts showed the highest activity against P. falciparum, with 50% of microbial growth (IC50) values of 0.2 µg/mL. A positive correlation between the biological activity and the chemical composition was observed for YCP extracts. The most promising antimicrobial activity corresponds to YCP subtype B, which contains acetyl triterpenes as the main constituents. The present in vitro study highlights the potential of propolis against protozoa, but further research is needed to increase selectivity towards the parasite. The observed chemical composition-activity relationship of propolis can contribute to the identification of the active principles and standardisation of this bee product.

Prospects for malaria elimination in non-Amazonian regions of Latin America.

Latin America contributes 1-1.2 million clinical malaria cases to the global malaria burden of about 300 million per year. In 21 malaria endemic countries, the population at risk in this region represents less than 10% of the total population exposed worldwide. Factors such as rapid deforestation, inadequate agricultural practices, climate change, political instability, and both increasing parasite drug resistance and vector resistance to insecticides contribute to malaria transmission. Recently, several malaria endemic countries have experienced a significant reduction in numbers of malaria cases. This is most likely due to actions taken by National Malaria Control Programs (NMCP) with the support from international funding agencies. We describe here the research strategies and activities to be undertaken by the Centro Latino Americano de Investigación en Malaria (CLAIM), a new research center established for the non-Amazonian region of Latin America by the National Institute of Allergy and Infectious Diseases (NIAID). Throughout a network of countries in the region, initially including Colombia, Guatemala, Panama, and Peru, CLAIM will address major gaps in our understanding of changing malaria epidemiology, vector biology and control, and clinical malaria mainly due to Plasmodium vivax. In close partnership with NMCPs, CLAIM seeks to conduct research on how and why malaria is decreasing in many countries of the region as a basis for developing and implementing new strategies that will accelerate malaria elimination.

A research agenda for malaria eradication: modeling.

Malaria modeling can inform policy and guide research for malaria elimination and eradication from local implementation to global policy. A research and development agenda for malaria modeling is proposed, to support operations and to enhance the broader eradication research agenda. Models are envisioned as an integral part of research, planning, and evaluation, and modelers should ideally be integrated into multidisciplinary teams to update the models iteratively, communicate their appropriate use, and serve the needs of other research scientists, public health specialists, and government officials. A competitive and collaborative framework will result in policy recommendations from multiple, independently derived models and model systems that share harmonized databases. As planned, modeling results will be produced in five priority areas: (1) strategic planning to determine where and when resources should be optimally allocated to achieve eradication; (2) management plans to minimize the evolution of drug and pesticide resistance; (3) impact assessments of new and needed tools to interrupt transmission; (4) technical feasibility assessments to determine appropriate combinations of tools, an associated set of target intervention coverage levels, and the expected timelines for achieving a set of goals in different socio-ecological settings and different health systems; and (5) operational feasibility assessments to weigh the economic costs, capital investments, and human resource capacities required.

A mathematical model for antimalarial drug resistance.

We formulate and analyze a mathematical model for malaria with treatment and the well-known three levels of resistance in humans. The model incorporates both sensitive and resistant strains of the parasites. Analytical results reveal that the model exhibits the phenomenon of backward bifurcation (co-existence of a stable disease-free equilibrium with a stable endemic equilibrium), an epidemiological situation where although necessary, having the basic reproduction number less than unity, it is not sufficient for disease elimination. Through quantitative analysis, we show the effects of varying treatment levels in a high transmission area with different levels of resistance. Increasing treatment has limited benefits in a population with resistant strains, especially in high transmission settings. Thus, in a cost-benefit analysis, the rate of treatment and percentage to be treated become difficult questions to address.

[Global trends in malaria control. Progress and topical tasks in malaria control programs].

This communication is the first in the series consisting of two publications describing the present state of malaria control and elimination in the world. The global malaria situation in 2009-2010 demonstrated a considerable situation as compared to the previous years. This improvement is associated with a considerable global increase of investments made by both national governments and world society to the malaria control programs. Spectacular progress has been achieved even in the areas of the most infection-affected African countries situated to the south of the Sahara Desert. It has been estimated that malaria cases in the world declined from 233, 000,000 in 2000 to 225,000,000 in 2009. Malaria mortality decreased from 985,000 in 2000 to 781,000 in 2009. To maintain the results achieved and to further reduce the problem of malaria worldwide, it is necessary to ensure a long-term political and financial support for malaria control programs at the national and international levels.

A situational analysis of pharmacovigilance plans in the Global Fund Malaria and U.S. President's Malaria Initiative proposals.

BACKGROUND: Pharmacovigilance programmes can monitor and help ensure the safe use of medicines that are critical to the success of global public health programmes. The widespread deployment of artemisinin-based combination therapy (ACT) by national malaria control programmes as part of the overall Global Malaria Action Plan for malaria control to elimination and eradication makes ACT an excellent candidate for pharmacovigilance activities. In 2008, The Roll Back Malaria partnership issued guidelines for inclusion of pharmacovigilance in Global Fund and other related proposals. In light of this recommendation and the rapid scale-up of ACT worldwide, an analysis of Global Fund Round 8 proposals and the President's Malaria Initiative (PMI) 2009 Malaria Operational Plans was conducted to assess if and how pharmacovigilance has been incorporated into countries' national malaria plans and donor budget requests. METHODS: The Global Fund-Malaria Round 8 proposals for the 26 countries and the PMI Malaria Operational Plans (MOPs) for fiscal year 2009 for the 15 countries that were approved and received funding from either the Global Fund-Malaria Round 8 or PMI were accessed through the programme websites. The analysis consisted of conducting word counts and key word in context analyses of each proposal and plan. RESULTS: Twelve out of 26 (46%) of the Global Fund proposals mentioned that established pharmacovigilance systems were present in their countries. Four of the fifteen PMI MOPs (27%) mentioned that established pharmacovigilance systems were present in their countries. Only seven of the 26 (27%) Global Fund proposals included a request for funding for new or current pharmacovigilance activities. Seven of 15 (47%) MOPs included a request for funding for pharmacovigilance activities. CONCLUSIONS: There were relatively few requests for funding for pharmacovigilance activities, demonstrating a lack of emphasis placed on pharmacovigilance systems in recipient countries. The findings stress the need for more active direction to strengthen active surveillance and passive adverse event reporting systems to augment the issuance of guidance documents.

New medicines to improve control and contribute to the eradication of malaria.

Despite being one of the most prevalent tropical diseases, for many years malaria was not a commercial priority for the pharmaceutical industry. However, in response to the emergence and spread of resistance to the available antimalarial drugs, there has been a renaissance in the discovery and development of new medicines to control the disease in the last few years. The persistent threat of resistance means that new molecules with novel mechanisms of action are continually required. Furthermore, the recent call for the elimination and eradication of malaria has prompted an extension of the stages of the life cycle of malaria parasites that should be targeted by new molecules. Recent advances in genome-based technologies and in in vitro screening of whole parasites have broadened the range of therapeutic targets and are accelerating the development of a new generation of treatments for both malaria control and eradication.