Relationship between malaria vector survival, infectivity and insecticide treated net use in western Kenya.

Background: Much effort and resources have been invested to control malaria transmission in Sub-Saharan Africa, but it remains a major public health problem. For the disease to be transmitted from one person to another, the female Anopheles vector must survive 10-14 days following an infective bite for the Plasmodiumgametocytes to develop into infectious sporozoites which can be transmitted to the next person during a bloodmeal. The goal of this investigation was to assess factors associated with wild-caught Anopheles survival and infection following host-seeking and indoor resting. Methods: The study was conducted in a longitudinal cohort of 75 households in 5 villages including a total of 755 household members in Bungoma County, Kenya. Monthly adult mosquito collection was conducted by attenuated aspiration in all the enrolled households, and the mosquitoes were reared in the insectary for 7 days. The daily mortality rate was determined through day 7, and all the mosquitoes were morphologically identified. Female Anopheline mosquitoes were dissected, and species-level members of the Anopheles gambiae complex were resolved by molecular methods. The abdomen for all samples were processed for P. falciparum detection by PCR. Results: Within a period of 25 months, the total number of culex and Anopheles mosquitoes collected indoors were 12,843 and 712 respectively. Anopheles gambiaeand Anopheles funestus were the major vectors though their population varied between different villages. 61.2% (n=436/712) of the Anopheles species survived up to day 7 with the lowest mortality rate recorded on day 5 of captivity. The survival rate also varied between the different Anophelesspecies. 683 of 712 mosquito abdomens were tested for P. falciparumdetection and 7.8% (53/683) tested positive for P. falciparum with An. funestus having a higher (10%) prevalence than An. gambaie s.s.(6.0%, p=0.095, Pearson Chi square test). The proportion of household members sleeping under a bednet the night before mosquito collection varied across time and village. An. funestus survival times were refractory to household ITN coverage and An. gambaie s.s. survival was reduced only under very high (>95%) ITN coverage. Conclusion: Despite ITN coverage, mosquitoes still acquired bloodmeals and P. falciparum infections. Survival differed across species and was inversely correlated with high ITN exposure in the household, but not oocyst development.

Characterizing mobility patterns and malaria risk factors in semi-nomadic populations of Northern Kenya.

While many studies have characterized mobility patterns and disease dynamics of individuals from settled populations, few have focused on more mobile populations. Highly mobile groups are often at higher disease risk due to their regular movement that may increase the variability of their environments, reduce their access to health care, and limit the number of intervention strategies suitable for their lifestyles. Quantifying the movements and their associated disease risks will be key to developing intervention strategies more suitable for mobile populations. Here, we worked with four semi-nomadic communities in Central Turkana, Kenya to 1) characterize mobility patterns of travelers from semi-nomadic communities and 2) test the hypothesis that semi-nomadic individuals are at greater risk of exposure to malaria during seasonal migrations than when staying at their semi-permanent settlements. From March-October, 2021, we conducted a study in semi-nomadic households (n=250) where some members traveled with their herd while others remained at the semi-permanent settlement. Participants provided medical and travel histories, demographics, and a dried blood spot for malaria testing before and after the travel period. Further, a subset of travelers was given GPS loggers to document their routes. Four travel patterns emerged from the logger data, Long Term, Transient, Day trip, and Static, with only Long Term and Transient trips being associated with malaria cases detected in individuals who carried GPS devices. After completing their trips, travelers had a higher prevalence of malaria than those who remained at the household (9.2% vs 4.4%), regardless of gender, age group, and catchment area. These findings highlight the need to develop intervention strategies amenable to mobile lifestyles that can ultimately help prevent the transmission of malaria.

Detection of Anopheles stephensi Mosquitoes by Molecular Surveillance, Kenya.

The Anopheles stephensi mosquito is an invasive malaria vector recently reported in Djibouti, Ethiopia, Sudan, Somalia, Nigeria, and Ghana. The World Health Organization has called on countries in Africa to increase surveillance efforts to detect and report this vector and institute appropriate and effective control mechanisms. In Kenya, the Division of National Malaria Program conducted entomological surveillance in counties at risk for An. stephensi mosquito invasion. In addition, the Kenya Medical Research Institute conducted molecular surveillance of all sampled Anopheles mosquitoes from other studies to identify An. stephensi mosquitoes. We report the detection and confirmation of An. stephensi mosquitoes in Marsabit and Turkana Counties by using endpoint PCR and morphological and sequence identification. We demonstrate the urgent need for intensified entomological surveillance in all areas at risk for An. stephensi mosquito invasion, to clarify its occurrence and distribution and develop tailored approaches to prevent further spread.

Plasmodium vivax Prevalence in Semiarid Region of Northern Kenya, 2019.

In urban and rural areas of Turkana County, Kenya, we found that 2% of household members of patients with Plasmodium falciparum infections were infected with P. vivax. Enhanced surveillance of P. vivax and increased clinical resources are needed to inform control measures and identify and manage P. vivax infections.

Experience and confidence in health technologies: evidence from malaria testing and treatment in Western Kenya.

BACKGROUND: Low adoption of effective health technologies increases illness morbidity and mortality worldwide. In the case of malaria, effective tools such as malaria rapid diagnostic tests (RDTs) and artemisinin-combination therapies (ACTs) are both under-used and used inappropriately. Individuals' confidence in RDTs and ACTs likely affects the uptake of these tools. METHODS: In a cohort of 36 households (280 individuals) in Western Kenya observed for 30 months starting in June 2017, we examined if experience with RDTs and ACTs changes people's beliefs about these technologies and how those beliefs affect treatment behavior. Household members requested a free RDT from the study team any time they suspected a malaria illness, and positive RDT results were treated with a free ACT. We conducted annual, monthly, and sick visit surveys to elicit beliefs about the accuracy of malaria RDT results and the effectiveness of ACTs. Beliefs were elicited on a 5-point Likert scale from "very unlikely" to "very likely." RESULTS: Over the study period, the percentage of survey respondents that said a hypothetical negative RDT result was "very likely" to be correct increased from approximately 55% to 75%. Controlling for initial beliefs, people who had been tested at least once with an RDT in the past year had 3.6 times higher odds (95% CI [1 1.718 7.679], P = 0.001) of saying a negative RDT was "very likely" to be correct. Confidence in testing was associated with treatment behavior: those who believed a negative RDT was "very likely" to be correct had 1.78 times higher odds (95% CI [1.079 2.934], P = 0.024) of adhering to a negative RDT result (by not taking ACTs) than those who were less certain about the accuracy of negative RDTs. Adherence to a negative test also affected subsequent beliefs: controlling for prior beliefs, those who had adhered to their previous test result had approximately twice the odds (OR = 2.19, 95% CI [1.661 2.904], P < 0.001) of saying that a hypothetical negative RDT was "very likely" to be correct compared to those who had not adhered. CONCLUSIONS: Our results suggest that greater experience with RDTs can not only increase people's confidence in their accuracy but also improve adherence to the test result.

Community-Based Malaria Testing Reduces Polypharmacy in a Population-Based Survey of Febrile Illness in Western Kenya.

Objective: The objective was to describe the relationship between the location of care, the malaria test result, and the type of medicine consumed for the fever, and to determine whether community-based access to malaria testing reduced polypharmacy. Methods: This is a secondary analysis of a cluster-randomized trial of an intervention designed to increase diagnostic testing and targeting of Artemesinin Combined Therapies (ACTs). Data collected at baseline, 12, and 18 months were analyzed to determine the impact of diagnostic testing on drug consumption patterns among febrile individuals. Results: Of the 5,756 participants analyzed, 60.1% were female, 42% were aged 5-17 years, and 58.1% sought care for fever in a retail outlet. Consumption of both ACT and antibiotics was 22.1% (n = 443/2008) at baseline. At endline, dual consumption had declined to 16.6%. There was reduced antibiotic consumption among those testing positive for malaria (39.5%-26.5%) and those testing negative (63.4%-55.1%), accompanied by a substantial decline in ACT use among malaria-negative participants. Conclusion: Diagnostic testing for malaria reduces dual consumption of ACTs and antibiotics, especially among those testing outside the formal healthcare sector.

How do malaria testing and treatment subsidies affect drug shop client expenditures? A cross-sectional analysis in Western Kenya.

OBJECTIVES: To examine how drug shop clients' expenditures are affected by subsidies for malaria diagnostic testing and for malaria treatment, and also to examine how expenditures vary by clients' malaria test result and by the number of medications they purchased. DESIGN: Secondary cross-sectional analysis of survey responses from a randomised controlled trial. SETTING: The study was conducted in twelve private drug shops in Western Kenya. PARTICIPANTS: We surveyed 836 clients who visited the drug shops between March 2018 and October 2019 for a malaria-like illness. This included children >1 year of age if they were physically present and accompanied by a parent or legal guardian. INTERVENTIONS: Subsidies for malaria diagnostic testing and for malaria treatment (conditional on a positive malaria test result). PRIMARY AND SECONDARY OUTCOME MEASURES: Expenditures at the drug shop in Kenya shillings (Ksh). RESULTS: Clients who were randomised to a 50% subsidy for malaria rapid diagnostic tests (RDTs) spent approximately Ksh23 less than those who were randomised to no RDT subsidy (95% CI (-34.6 to -10.7), p=0.002), which corresponds approximately to the value of the subsidy (Ksh20). However, clients randomised to receive free treatment (artemisinin combination therapies (ACTs)) if they tested positive for malaria had similar spending levels as those randomised to a 67% ACT subsidy conditional on a positive test. Expenditures were also similar by test result, however, those who tested positive for malaria bought more medications than those who tested negative for malaria while spending approximately Ksh15 less per medication (95% CI (-34.7 to 3.6), p=0.102). CONCLUSIONS: Our results suggest that subsidies for diagnostic health products may result in larger household savings than subsidies on curative health products. A better understanding of how people adjust their behaviours and expenditures in response to subsidies could improve the design and implementation of subsidies for health products. TRIAL REGISTRATION NUMBER: NCT03810014.

The prevalence and density of asymptomatic Plasmodium falciparum infections among children and adults in three communities of western Kenya.

BACKGROUND: Further reductions in malaria incidence as more countries approach malaria elimination require the identification and treatment of asymptomatic individuals who carry mosquito-infective Plasmodium gametocytes that are responsible for furthering malaria transmission. Assessing the relationship between total parasitaemia and gametocytaemia in field surveys can provide insight as to whether detection of low-density, asymptomatic Plasmodium falciparum infections with sensitive molecular methods can adequately detect the majority of infected individuals who are potentially capable of onward transmission. METHODS: In a cross-sectional survey of 1354 healthy children and adults in three communities in western Kenya across a gradient of malaria transmission (Ajigo, Webuye, and Kapsisywa-Kipsamoite), asymptomatic P. falciparum infections were screened by rapid diagnostic tests, blood smear, and quantitative PCR of dried blood spots targeting the varATS gene in genomic DNA. A multiplex quantitative reverse-transcriptase PCR assay targeting female and male gametocyte genes (pfs25, pfs230p), a gene with a transcriptional pattern restricted to asexual blood stages (piesp2), and human GAPDH was also developed to determine total parasite and gametocyte densities among parasitaemic individuals. RESULTS: The prevalence of varATS-detectable asymptomatic infections was greatest in Ajigo (42%), followed by Webuye (10%). Only two infections were detected in Kapsisywa. No infections were detected in Kipsamoite. Across all communities, children aged 11-15 years account for the greatest proportion total and sub-microscopic asymptomatic infections. In younger age groups, the majority of infections were detectable by microscopy, while 68% of asymptomatically infected adults (> 21 years old) had sub-microscopic parasitaemia. Piesp2-derived parasite densities correlated poorly with microscopy-determined parasite densities in patent infections relative to varATS-based detection. In general, both male and female gametocytaemia increased with increasing varATS-derived total parasitaemia. A substantial proportion (41.7%) of individuals with potential for onward transmission had qPCR-estimated parasite densities below the limit of microscopic detection, but above the detectable limit of varATS qPCR. CONCLUSIONS: This assessment of parasitaemia and gametocytaemia in three communities with different transmission intensities revealed evidence of a substantial sub-patent infectious reservoir among asymptomatic carriers of P. falciparum. Experimental studies are needed to definitively determine whether the low-density infections in communities such as Ajigo and Webuye contribute significantly to malaria transmission.

Effect of health systems context on infant and child mortality in sub-Saharan Africa from 1995 to 2015, a longitudinal cohort analysis.

Each year, > 3 million children die in sub-Saharan Africa before their fifth birthday. Most deaths are preventable or avoidable through interventions delivered in the primary healthcare system. However, evidence regarding the impact of health system characteristics on child survival is sparse. We assembled a retrospective cohort of > 250,000 children in seven countries in sub-Saharan Africa. We described their health service context at the subnational level using standardized surveys and employed parametric survival models to estimate the effect of three major domains of health services-quality, access, and cost-on infant and child survival, after adjusting for child, maternal, and household characteristics. Between 1995 and 2015 we observed 13,629 deaths in infants and 5149 in children. In fully-adjusted models, the largest effect sizes were related to fees for services. Immunization fees were correlated with poor child survival (HR = 1.20, 95% CI 1.12-1.28) while delivery fees were correlated with poor infant survival (HR = 1.11, 95% CI 1.01-1.21). Accessibility of facilities and greater concentrations of private facilities were associated with improved infant and child survival. The proportion of facilities with a doctor was correlated with increased risk of death in children and infants. We quantify the impact of health service environment on survival up to five years of age. Reducing health care costs and improving the accessibility of health facilities should remain a priority for improving infant and child survival. In the absence of these fundamental investments, more specialized interventions may not achieve their desired impact.

Incentivizing appropriate malaria case management in the private sector: a study protocol for two linked cluster randomized controlled trials to evaluate provider- and client-focused interventions in western Kenya and Lagos, Nigeria.

BACKGROUND: A large proportion of artemisinin-combination therapy (ACT) anti-malarial medicines is consumed by individuals that do not have malaria. The over-consumption of ACTs is largely driven by retail sales in high malaria-endemic countries to clients who have not received a confirmatory diagnosis. This study aims to target ACT sales to clients receiving a confirmatory diagnosis using malaria rapid diagnostic tests (mRDTs) at retail outlets in Kenya and Nigeria. METHODS: This study comprises two linked four-arm 2 × 2 factorial cluster randomized controlled trials focused on malaria diagnostic testing and conditional ACT subsidies with the goal to evaluate provider-directed and client-directed interventions. The linked trials will be conducted at two contrasting study sites: a rural region around Webuye in western Kenya and the urban center of Lagos, Nigeria. Clusters are 41 and 48 participating retail outlets in Kenya and Nigeria, respectively. Clients seeking care at participating outlets across all arms will be given the option of paying for a mRDT-at a study-recommended price-to be conducted at the outlet. In the provider-directed intervention arm, the outlet owner receives a small monetary incentive to perform the mRDT. In the client-directed intervention arm, the client receives a free ACT if they purchase an mRDT and receive a positive test result. Finally, the fourth study arm combines both the provider- and client-directed interventions. The diagnosis and treatment choices made during each transaction will be captured using a mobile phone app. Study outcomes will be collected through exit interviews with clients, who sought care for febrile illness, at each of the enrolled retail outlets. RESULTS: The primary outcome measure is the proportion of all ACTs that are sold to malaria test-positive clients in each study arm. For all secondary outcomes, we will evaluate the degree to which the interventions affect purchasing behavior among people seeking care for a febrile illness at the retail outlet. CONCLUSIONS: If our study demonstrates that malaria case management can be improved in the retail sector, it could reduce overconsumption of ACTs and enhance targeting of publicly funded treatment reimbursements, lowering the economic barrier to appropriate diagnosis and treatment for patients with malaria. TRIAL REGISTRATION: ClinicalTrials.gov NCT04428307 , registered June 9, 2020, and NCT04428385 , registered June 9, 2020.

Does improving appropriate use of malaria medicines change population beliefs in testing and treatment? Evidence from a randomized controlled trial.

A major puzzle in malaria treatment remains the dual problem of underuse and overuse of malaria medications, which deplete scarce public resources used for subsidies and lead to drug resistance. One explanation is that health behaviour, especially in the context of incomplete information, could be driven by beliefs, pivotal to the success of health interventions. The objective of this study is to investigate how population beliefs change in response to an experimental intervention which was shown to improve access to rapid diagnostic testing (RDT) through community health workers (CHWs) and to increase appropriate use of anti-malaria medications. By collecting data on individuals' beliefs on malaria testing and treatment 12 and 18 months after the experimental intervention started, we find that the intervention increases the belief that a negative test result is correct, and the belief that the first-line anti-malaria drugs (artemisinin-based combination therapies or ACTs) are effective. Using mediation analysis, we also explore some possible mechanisms through which the changes happen. We find that the experience and knowledge about RDT and experience with CHWs explain 62.4% of the relationship between the intervention and the belief that a negative test result is correct. Similarly, the targeted use of ACTs and taking the correct dose-in addition to experience with RDT-explain 96.8% of the relationship between the intervention and the belief that the ACT taken is effective. As beliefs are important determinants of economic behaviour and might guide individuals' future decisions, understanding how they change after a health intervention has important implications for long-term changes in population behaviour.

Mosquito Exposure and Malaria Morbidity: A Microlevel Analysis of Household Mosquito Populations and Malaria in a Population-Based Longitudinal Cohort in Western Kenya.

BACKGROUND: Malaria morbidity is highly overdispersed in the population. Fine-scale differences in mosquito exposure may partially explain this heterogeneity in individual malaria outcomes. METHODS: In 38 households we explored the effect of household-level mosquito exposure and individual insecticide-treated net (ITN) use on relative risk (RR) of confirmed malaria. We conducted monthly active surveillance (n = 254; 2624 person-months) and weekly mosquito collection (2092 household-days of collection), and used molecular techniques to confirm human blood feeding and exposure to infectious mosquitoes. RESULTS: Of 1494 female Anopheles (89.8% Anopheles gambiae sensu lato), 88.3% were fed, 51.9% had a human blood meal, and 9.2% were sporozoite infected. In total, 168 laboratory-confirmed malaria episodes were reported (incidence rate 0.064 episodes per person-month at risk; 95% confidence interval [CI], .055-.074). Malaria risk was directly associated with exposure to sporozoite-infected mosquitoes (RR, 1.24; 95% CI, 1.11-1.38). No direct effect was measured between ITN use and malaria morbidity; however, ITN use did moderate the effect of mosquito exposure on morbidity. CONCLUSIONS: Malaria risk increases linearly with vector density and feeding success for persons with low ITN use. In contrast, malaria risk among high ITN users is consistently low and insensitive to variation in mosquito exposure.

A mobile health technology platform for quality assurance and quality improvement of malaria diagnosis by community health workers.

BACKGROUND: Community health workers (CHWs) play an important role in improving access to services in areas with limited health infrastructure or workforce. Supervision of CHWs by qualified health professionals is the main link between this lay workforce and the formal health system. The quality of services provided by lay health workers is dependent on adequate supportive supervision. It is however one of the weakest links in CHW programs due to logistical and resource constraints, especially in large scale programs. Interventions such as point of care testing using malaria rapid diagnostic tests (RDTs) require real time monitoring to ensure diagnostic accuracy. In this study, we evaluated the utility of a mobile health technology platform to remotely monitor malaria RDT (mRDT) testing by CHWs for quality improvement. METHODS: As part of a large implementation trial involving mRDT testing by CHWs, we introduced the Fionet system composed of a mobile device (Deki Reader, DR) to assist in processing and automated interpretation of mRDTs, which connects to a cloud-based database which captures reports from the field in real time, displaying results in a custom dashboard of key performance indicators. A random sample of 100 CHWs were trained and provided with the Deki Readers and instructed to use it on 10 successive patients. The CHWs interpretation was compared with the Deki Reader's automatic interpretation, with the errors in processing and interpreting the RDTs recorded. After the CHW entered their interpretation on the DR, the DR provided immediate, automated feedback and interpretation based on its reading of the same cassette. The study team monitored the CHW performance remotely and provided additional support. RESULTS: A total of 1251 primary and 113 repeat tests were performed by the 97 CHWs who used the DR. 91.6% of the tests had agreement between the DR and the CHWs. There were 61 (4.9%) processing and 52 (4.2%) interpretation errors among the primary tests. There was a tendency towards lower odds of errors with increasing number and frequency of tests, though not statistically significant. Of the 62 tests that were repeated due to errors, 79% achieved concordance between the CHW and the DR. Satisfaction with the use of the DR by the CHWs was high. CONCLUSIONS: Use of innovative mHealth strategies for monitoring and quality control can ensure quality within a large scale implementation of community level testing by lay health workers.

Household beliefs about malaria testing and treatment in Western Kenya: the role of health worker adherence to malaria test results.

BACKGROUND: Although use of malaria diagnostic tests has increased in recent years, health workers often prescribe anti-malarial drugs to individuals who test negative for malaria. This study investigates how health worker adherence to malaria case management guidelines influences individuals' beliefs about whether their illness was malaria, and their confidence in the effectiveness of artemisinin-based combination therapy (ACT). METHODS: A survey was conducted with 2065 households in Western Kenya about a household member's treatment actions for a recent febrile illness. The survey also elicited the individual's (or their caregiver's) beliefs about the illness and about malaria testing and treatment. Logistic regressions were used to test the association between these beliefs and whether the health worker adhered to malaria testing and treatment guidelines. RESULTS: Of the 1070 individuals who visited a formal health facility during their illness, 82% were tested for malaria. ACT rates for malaria-positive and negative individuals were 89 and 49%, respectively. Overall, 65% of individuals/caregivers believed that the illness was "very likely" malaria. Individuals/caregivers had higher odds of saying that the illness was "very likely" malaria when the individual was treated with ACT, and this was the case both among individuals not tested for malaria [adjusted odds ratio (AOR) 3.42, 95% confidence interval (CI) [1.65 7.10], P = 0.001] and among individuals tested for malaria, regardless of their test result. In addition, 72% of ACT-takers said the drug was "very likely" effective in treating malaria. However, malaria-negative individuals who were treated with ACT had lower odds of saying that the drugs were "very likely" effective than ACT-takers who were not tested or who tested positive for malaria (AOR 0.29, 95% CI [0.13 0.63], P = 0.002). CONCLUSION: Individuals/caregivers were more likely to believe that the illness was malaria when the patient was treated with ACT, regardless of their test result. Moreover, malaria-negative individuals treated with ACT had lower confidence in the drug than other individuals who took ACT. These results suggest that ensuring health worker adherence to malaria case management guidelines will not only improve ACT targeting, but may also increase patient/caregivers' confidence in malaria testing and treatment.

Contribution of urinary tract infection to the burden of febrile illnesses in young children in rural Kenya.

INTRODUCTION: The clinical features of UTI in young children may not localize to the urinary tract and closely resemble other febrile illnesses. In malaria endemic areas, a child presenting with fever is often treated presumptively for malaria without investigation for UTI. Delayed or inadequate treatment of UTI increases the risk of bacteremia and renal scarring in young children and subsequently complications as hypertension and end stage renal disease in adulthood. METHODS: A cross-sectional study was carried out in a hospital in western Kenya. Inpatients and outpatients 2 months to five years with axillary temperature ≥37.5°C and no antibiotic use in the previous week were enrolled between September 2012 and April 2013. Urine dipstick tests, microscopy, and cultures were done and susceptibility patterns to commonly prescribed antibiotics established. UTI was defined as presence of pyuria (a positive urine dipstick or microscopy test) plus a positive urine culture. RESULTS: A total of 260 subjects were recruited; 45.8% were female and the median age was 25months (IQR: 13, 43.5). The overall prevalence of UTI was 11.9%. Inpatients had a higher prevalence compared to outpatients (17.9% v 7.8%, p = 0.027). UTI co-existed with malaria but the association was not significant (OR 0.80, p = 0.570). The most common organisms isolated were Escherichia coli (64.5%) and Staphylococcus aureus (12.9%) and were sensitive to ciproflaxin, cefuroxime, ceftriaxone, gentamycin and nitrofurantoin but largely resistant to more commonly used antibiotics such as ampicillin (0%), amoxicillin (16.7%), cotrimoxazole (16.7%) and amoxicillin-clavulinate (25%). CONCLUSION: Our study demonstrates UTI contributes significantly to the burden of febrile illness in young children and often co-exists with other infections. Multi-drug resistant organisms are common therefore choice of antimicrobial therapy should be based on local sensitivity pattern.

A retrospective cohort study to quantify the contribution of health systems to child survival in Kenya: 1996-2014.

Globally, the majority of childhood deaths in the post-neonatal period are caused by infections that can be effectively treated or prevented with inexpensive interventions delivered through even very basic health facilities. To understand the role of inadequate health systems on childhood mortality in Kenya, we assemble a large, retrospective cohort of children (born 1996-2013) and describe the health systems context of each child using health facility survey data representative of the province at the time of a child's birth. We examine the relationship between survival beyond 59 months of age and geographic distribution of health facilities, quality of services, and cost of services. We find significant geographic heterogeneity in survival that can be partially explained by differences in distribution of health facilities and user fees. Higher per capita density of health facilities resulted in a 25% reduction in the risk of death (HRR = 0.73, 95% CI:0.58 to 0.91) and accounted for 30% of the between-province heterogeneity in survival. User fees for sick-child visits increased risk by 30% (HRR = 1.30, 95% CI:1.11 to 1.53). These results implicate health systems constraints in child mortality, quantify the contribution of specific domains of health services, and suggest priority areas for improvement to accelerate reductions in child mortality.

Overlap Extension Barcoding for the Next Generation Sequencing and Genotyping of Plasmodium falciparum in Individual Patients in Western Kenya.

Large-scale molecular epidemiologic studies of Plasmodium falciparum parasites have provided insights into parasite biology and transmission, can identify the spread of drug resistance, and are useful in assessing vaccine targets. The polyclonal nature infections in high transmission settings is problematic for traditional genotyping approaches. Next-generation sequencing (NGS) approaches to parasite genotyping allow sensitive detection of minority variants, disaggregation of complex parasite mixtures, and scalable processing of large samples sets. Therefore, we designed, validated, and applied to field parasites an approach that leverages sequencing of individually barcoded samples in a multiplex manner. We utilize variant barcodes, invariant linker sequences and modular template-specific primers to allow for the simultaneous generation of high-dimensional sequencing data of multiple gene targets. This modularity permits a cost-effective and reproducible way to query many genes at once. In mixtures of reference parasite genomes, we quantitatively detected unique haplotypes comprising as little as 2% of a polyclonal infection. We applied this genotyping approach to field-collected parasites collected in Western Kenya in order to simultaneously obtain parasites genotypes at three unlinked loci. In summary, we present a rapid, scalable, and flexible method for genotyping individual parasites that enables molecular epidemiologic studies of parasite evolution, population structure and transmission.

Development and validation of a rapid assessment tool for malaria prevention.

BACKGROUND: Insecticide-treated bed nets (ITN) have been shown to be efficacious in reducing malaria morbidity and mortality in many regions. Unfortunately in some areas, malaria has persisted despite the scale up of ITNs. Recent reports indicate that human behaviour and mosquito behaviour are potential threats to the efficacy of ITNs. However, these concerns are likely highly heterogeneous even at very small scales. This study aimed at developing, testing and validating a rapid assessment tool to collect actionable information at local levels for a quick evaluation of potential barriers to malaria prevention. METHODS: The study was conducted at the Webuye Health and Demographic Surveillance Site in Bungoma East Sub-County, Kenya. Based on the findings from the case-control study, 12 primary surveillance components that encompass the major impediments to successful prevention were identified and used to develop a rapid assessment tool. Twenty community health volunteers were trained to identify patients with laboratory-confirmed malaria in six peripheral health facilities located within six sub locations and subsequently followed them up to their homes to conduct a rapid assessment. Sampling and analysis of the results of the survey are based on Lot Quality Assurance. RESULTS: The tool was able to detect local heterogeneity in bed net coverage, bed net use and larval site abundance in the six health facility catchment areas. Nearly all the catchment areas met the action threshold for incomplete household coverage (i.e. not all household members not using a net the previous night) except the peri-urban area. Although the threshold for nets not in good condition was set very high (≥50%), only two catchment areas failed to meet the action threshold. On the indicator for "Net not used every day last week", half of the areas failed, while for net ownership, only two areas met the action threshold. CONCLUSION: The rapid assessment tool was able to detect marked heterogeneity in key indicators for malaria prevention between patients attending health facilities, and can distinguish between priority areas for intervention. There is need to validate it for use in other contexts.