Combining school-catchment area models with geostatistical models for analysing school survey data from low-resource settings: Inferential benefits and limitations

School-based sampling has been used to inform targeted responses for malaria and neglected tropical diseases. Standard geostatistical methods for mapping disease prevalence use the school location to model spatial correlation, which is questionable since exposure to the disease is more likely to occur in the residential location. In this paper, we propose to overcome the limitations of standard geostatistical methods by introducing a modelling framework that accounts for the uncertainty in the location of the residence of the students. By using cost distance and cost allocation models to define spatial accessibility and in absence of any information on the travel mode of students to school, we consider three school catchment area models that assume walking only, walking and bicycling and, walking and motorized transport. We illustrate the use of this approach using two case studies of malaria in Kenya and compare it with the standard approach that uses the school locations to build geostatistical models. We argue that the proposed modelling framework presents several inferential benefits, such as the ability to combine data from multiple surveys some of which may also record the residence location, and to deal with ecological bias when estimating the effects of malaria risk factors. However, our results show that invalid assumptions on the modes of travel to school can worsen the predictive performance of geostatistical models. Future research in this area should focus on collecting information on the modes of transportation to school which can then be used to better parametrize the catchment area models.

Anaemia among Kenyan children: a call for improved monitoring and intervention in school-aged children

Background

Anaemia has long been recognised as a major public health problem among young children in lower- and middle-income countries and is an indicator of both poor nutrition and health status. There has been little progress towards improvement of anaemia in part due to its complex aetiology. An added impediment to the progress is that the monitoring of anaemia does not routinely target the whole population, with school-aged children (SAC) largely overlooked.

Methods

We re-examined data on the prevalence of anaemia among children aged <15 y sampled from 2008–2015 in Kenya.

Results

Approximately one in four Kenyan children aged <15 y were described as anaemic, including 12% with WHO-defined moderate anaemia and 1% who were severely anaemic. Average haemoglobin concentrations increased with age and the risk of having anaemia decreased with age. However, one in five SAC in Kenya were suffering from anaemia; most were either mild (11.4%) or moderately (10.9%) anaemic.

Conclusions

The monitoring of anaemia in SAC continues to be a neglected area limiting a careful articulation of the need to target interventions in this age group.

Geographic-genetic analysis of Plasmodium falciparum parasite populations from surveys of primary school children in Western Kenya

Background. Malaria control, and finally malaria elimination, requires the identification and targeting of residual foci or hotspots of transmission. However, the level of parasite mixing within and between geographical locations is likely to impact the effectiveness and durability of control interventions and thus should be taken into consideration when developing control programs.

Methods. In order to determine the geographic-genetic patterns of Plasmodium falciparum parasite populations at a sub-national level in Kenya, we used the Sequenom platform to genotype 111 genome-wide distributed single nucleotide polymorphic (SNP) positions in 2486 isolates collected from children in 95 primary schools in western Kenya. We analysed these parasite genotypes for genetic structure using principal component analysis and assessed local and global clustering using statistical measures of spatial autocorrelation. We further examined the region for spatial barriers to parasite movement as well as directionality in the patterns of parasite movement.

Results. We found no evidence of population structure and little evidence of spatial autocorrelation of parasite genotypes (correlation coefficients <0.03 among parasite pairs in distance classes of 1km, 2km and 5km; p value<0.01). An analysis of the geographical distribution of allele frequencies showed weak evidence of variation in distribution of alleles, with clusters representing a higher than expected number of samples with the major allele being identified for 5 SNPs. Furthermore, we found no evidence of the existence of spatial barriers to parasite movement within the region, but observed directional movement of parasites among schools in two separate sections of the region studied.

Conclusions. Our findings illustrate a pattern of high parasite mixing within the study region. If this mixing is due to rapid gene flow, then “one-off” targeted interventions may not be currently effective at the sub-national scale in Western Kenya, due to the high parasite movement that is likely to lead to re-introduction of infection from surrounding regions. However repeated targeted interventions may reduce transmission in the surrounding regions.

Geographic-genetic analysis of Plasmodium falciparum parasite populations from surveys of primary school children in Western Kenya

Background. Malaria control, and finally malaria elimination, requires the identification and targeting of residual foci or hotspots of transmission. However, the level of parasite mixing within and between geographical locations is likely to impact the effectiveness and durability of control interventions and thus should be taken into consideration when developing control programs. Methods. In order to determine the geographic-genetic patterns of Plasmodium falciparum parasite populations at a sub-national level in Kenya, we used the Sequenom platform to genotype 111 genome-wide distributed single nucleotide polymorphic (SNP) positions in 2486 isolates collected from children in 95 primary schools in western Kenya. We analysed these parasite genotypes for genetic structure using principal component analysis and assessed local and global clustering using statistical measures of spatial autocorrelation. We further examined the region for spatial barriers to parasite movement as well as directionality in the patterns of parasite movement. Results. We found no evidence of population structure and little evidence of spatial autocorrelation of parasite genotypes (correlation coefficients <0.03 among parasite pairs in distance classes of 1km, 2km and 5km; p value<0.01). An analysis of the geographical distribution of allele frequencies showed weak evidence of variation in distribution of alleles, with clusters representing a higher than expected number of samples with the major allele being identified for 5 SNPs. Furthermore, we found no evidence of the existence of spatial barriers to parasite movement within the region, but observed directional movement of parasites among schools in two separate sections of the region studied. Conclusions. Our findings illustrate a pattern of high parasite mixing within the study region. If this mixing is due to rapid gene flow, then “one-off” targeted interventions may not be currently effective at the sub-national scale in Western Kenya, due to the high parasite movement that is likely to lead to re-introduction of infection from surrounding regions. However repeated targeted interventions may reduce transmission in the surrounding regions.

Malaria in school-age children in Africa: an increasingly important challenge

School-age children have attracted relatively little attention as a group in need of special measures to protect them against malaria. However, increasing success in lowering the level of malaria transmission in many previously highly endemic areas will result in children acquiring immunity to malaria later in life than has been the case in the past. Thus, it can be anticipated that in the coming years there will be an increase in the incidence of both uncomplicated and severe malaria in school-age children in many previously highly endemic areas. In this review, which focuses primarily on Africa, recent data on the prevalence of malaria parasitaemia and on the incidence of clinical malaria in African school-age children are presented and evidence that malaria adversely effects school performance is reviewed. Long-lasting insecticide treated bednets (LLIN) are an effective method of malaria control but several studies have shown that school-age children use LLINs less frequently than other population groups. Antimalarial drugs are being used in different ways to control malaria in school-age children including screening and treatment and intermittent preventive treatment. Some studies of chemoprevention in school-age children have shown reductions in anaemia and improved school performance but this has not been the case in all trials and more research is needed to identify the situations in which chemoprevention is likely to be most effective and, in these situations, which type of intervention should be used. In the longer term, malaria vaccines may have an important role in protecting this important section of the community from malaria. Regardless of the control approach selected, it is important this is incorporated into the overall programme of measures being undertaken to enhance the health of African school-age children.

Reliability of school surveys in estimating geographic variation in malaria transmission in the western Kenyan highlands

Background

School surveys provide an operational approach to assess malaria transmission through parasite prevalence. There is limited evidence on the comparability of prevalence estimates obtained from school and community surveys carried out at the same locality.

Methods

Concurrent school and community cross-sectional surveys were conducted in 46 school/community clusters in the western Kenyan highlands and households of school children were geolocated. Malaria was assessed by rapid diagnostic test (RDT) and combined seroprevalence of antibodies to bloodstage Plasmodium falciparum antigens.

Results

RDT prevalence in school and community populations was 25.7% (95% CI: 24.4-26.8) and 15.5% (95% CI: 14.4-16.7), respectively. Seroprevalence in the school and community populations was 51.9% (95% CI: 50.5-53.3) and 51.5% (95% CI: 49.5-52.9), respectively. RDT prevalence in schools could differentiate between low (<7%, 95% CI: 0-19%) and high (>39%, 95% CI: 25-49%) transmission areas in the community and, after a simple adjustment, were concordant with the community estimates.

Conclusions

Estimates of malaria prevalence from school surveys were consistently higher than those from community surveys and were strongly correlated. School-based estimates can be used as a reliable indicator of malaria transmission intensity in the wider community and may provide a basis for identifying priority areas for malaria control.

Use of rapid diagnostic tests in malaria school surveys in Kenya: does their under-performance matter for planning malaria control?

Malaria rapid diagnostic tests (RDTs) are known to yield false-positive results, and their use in epidemiologic surveys will overestimate infection prevalence and potentially hinder efficient targeting of interventions. To examine the consequences of using RDTs in school surveys, we compared three RDT brands used during a nationwide school survey in Kenya with expert microscopy and investigated the cost implications of using alternative diagnostic approaches in identifying localities with differing levels of infection. Overall, RDT sensitivity was 96.1% and specificity was 70.8%. In terms of classifying districts and schools according to prevalence categories, RDTs were most reliable for the < 1% and > 40% categories and least reliable in the 1–4.9% category. In low-prevalence settings, microscopy was the most expensive approach, and RDT results corrected by either microscopy or polymerase chain reaction were the cheapest. Use of polymerase chain reaction–corrected RDT results is recommended in school malaria surveys, especially in settings with low-to-moderate malaria transmission.

Plasmodium infection, anaemia and mosquito net use among school children across different settings in Kenya

OBJECTIVE

To investigate risk factors, including reported net use, for Plasmodium infection and anaemia among school children and to explore variations in effects across different malaria ecologies occurring in Kenya.

METHODS

This study analysed data for 49 975 school children in 480 schools surveyed during a national school malaria survey, 2008-2010. Mixed effects logistic regression was used to investigate factors associated with Plasmodium infection and anaemia within different malaria transmission zones.

RESULTS

Insecticide-treated net (ITN) use was associated with reduction in the odds of Plasmodium infection in coastal and western highlands epidemic zones and among boys in the lakeside high transmission zone. Other risk factors for Plasmodium infection and for anaemia also varied by zone. Plasmodium infection was negatively associated with increasing socio-economic status in all transmission settings, except in the semi-arid north-east zone. Plasmodium infection was a risk factor for anaemia in lakeside high transmission, western highlands epidemic and central low-risk zones, whereas ITN use was only associated with lower levels of anaemia in coastal and central zones and among boys in the lakeside high transmission zone.

CONCLUSIONS

The risk factors for Plasmodium infection and anaemia, including the protective associations with ITN use, vary according to malaria transmission settings in Kenya, and future efforts to control malaria and anaemia should take into account such heterogeneities among school children.

Plasmodium-helminth coinfection and its sources of heterogeneity across East Africa

Background. Plasmodium–helminth coinfection can have a number of consequences for infected hosts, yet our knowledge of the epidemiology of coinfection across multiple settings is limited. This study investigates the distribution and heterogeneity of coinfection with Plasmodium falciparum and 3 major helminth species across East Africa.

Methods. Cross-sectional parasite surveys were conducted among 28 050 children in 299 schools across a range of environmental settings in Kenya, Uganda, and Ethiopia. Data on individual, household, and environmental risk factors were collected and a spatially explicit Bayesian modeling framework was used to investigate heterogeneities of species infection and coinfection and their risk factors as well as school- and individual-level associations between species.

Results. Broad-scale geographical patterns of Plasmodium–helminth coinfection are strongly influenced by the least common infection and by species-specific environmental factors. At the individual level, there is an enduring positive association between P. falciparum and hookworm but no association between P. falciparum and Schistosoma species. However, the relative importance of such within-individual associations is less than the role of spatial factors in influencing coinfection risks.

Conclusions. Patterns of coinfection seem to be influenced more by the distribution of the least common species and its environmental risk factors, rather than any enduring within-individual associations.

Preparing for national school-based deworming in Kenya: the validation and large-scale distribution of school questionnaires with urinary schistosomiasis

OBJECTIVE

School questionnaires of self-reported schistosomiasis provide a rapid and simple approach for identifying schools at high risk of Schistosoma haematobium and requiring mass treatment. This study investigates the reliability of school questionnaires to identify such schools and infected children within the context of a national school-based deworming programme in Kenya.

METHODS

Between November 2008 and March 2009, 6182 children from 61 schools in Coast Province, Kenya were asked by an interviewer whether they had blood in urine or urinary schistosomiasis (kichocho), and their results were compared with results from microscopic examination of urine samples. Subsequently, in 2009, a school-based questionnaire survey for self-reported schistosomiasis was distributed by the Ministry of Education to all schools in Coast Province, and its results were compared against results from the parasitological survey. The questionnaire survey results were linked to a schools database and mapped.

RESULTS

Prevalence of self-reported blood in urine was lower among girls than boys among all ages. The use of a 30% threshold of reported blood in urine was both highly sensitive (91.7%) and specific (100%) in identifying high (>50%) prevalence schools in Coast Province. Questionnaires were however less reliable in diagnosing S. haematobium infection in individuals, particularly among young girls. Comparable levels of reliability were observed when the questionnaire was distributed through the existing education systems and administered by class teachers.

CONCLUSIONS

The results confirm that blood in urine questionnaires can be reliably used to target mass treatment with praziquantel at national scales. The mapped results of the Ministry of Education survey serve to describe the spatial variation of urinary schistosomiasis and identify schools requiring mass treatment.

Spatial modelling of soil-transmitted helminth infections in Kenya: a disease control planning tool

BACKGROUND

Implementation of control of parasitic diseases requires accurate, contemporary maps that provide intervention recommendations at policy-relevant spatial scales. To guide control of soil transmitted helminths (STHs), maps are required of the combined prevalence of infection, indicating where this prevalence exceeds an intervention threshold of 20%. Here we present a new approach for mapping the observed prevalence of STHs, using the example of Kenya in 2009.

METHODS AND FINDINGS

Observed prevalence data for hookworm, Ascaris lumbricoides and Trichuris trichiura were assembled for 106,370 individuals from 945 cross-sectional surveys undertaken between 1974 and 2009. Ecological and climatic covariates were extracted from high-resolution satellite data and matched to survey locations. Bayesian space-time geostatistical models were developed for each species, and were used to interpolate the probability that infection prevalence exceeded the 20% threshold across the country for both 1989 and 2009. Maps for each species were integrated to estimate combined STH prevalence using the law of total probability and incorporating a correction factor to adjust for associations between species. Population census data were combined with risk models and projected to estimate the population at risk and requiring treatment in 2009. In most areas for 2009, there was high certainty that endemicity was below the 20% threshold, with areas of endemicity ≥ 20% located around the shores of Lake Victoria and on the coast. Comparison of the predicted distributions for 1989 and 2009 show how observed STH prevalence has gradually decreased over time. The model estimated that a total of 2.8 million school-age children live in districts which warrant mass treatment.

CONCLUSIONS

Bayesian space-time geostatistical models can be used to reliably estimate the combined observed prevalence of STH and suggest that a quarter of Kenya's school-aged children live in areas of high prevalence and warrant mass treatment. As control is successful in reducing infection levels, updated models can be used to refine decision making in helminth control.

The use of artemether-lumefantrine by febrile children following national implementation of a revised drug policy in Kenya

OBJECTIVES

To examine access to, timing and use of artemisinin-based combination therapy among rural Kenyan febrile children before and following the introduction of artemether-lumefantrine (AL) as first-line antimalarial drug policy.

METHODS

In August 2006, a cohort was established within 72 rural clusters in four sentinel districts to monitor the period prevalence of fever and treatment in children aged 0-4 years through four repeat cross-sectional surveys (one prior to introduction of AL and three post-AL introduction: January-June 2007). Mothers/guardians of children were asked about fever in the last 14 days and related treatment actions including the timing, drugs used, dosing and adherence supported by visual aids of commonly available drug products.

RESULTS

A total of 2526 child-observations were recorded during the four survey rounds. The period prevalence of fever was between 20% and 26% with little variation between survey rounds. The overall proportion of children with fever receiving antimalarial drugs for their fever was 31 % (95% CI, 26-36%) and the proportion of febrile children receiving antimalarial drugs within 48 h was 23.3% (95% CI, 18.6-28.0%). The proportion of febrile children who received first-line recommended AL within 48 h was 10.2% (95% CI, 7.0-13.4%), compared to only 4.6% (95% CI, 3.8-5.4%) of children receiving sulphadoxine-pyrimethamine first-line therapy in 2001.

CONCLUSIONS

Although Kenya was less than a year into the new policy implementation and AL is restricted to the public formal sector, access to antimalarial drugs among children within 48 h and to the first-line therapy has improved. But it remains well below national and international targets. The continued use of amodiaquine and artemisinin monotherapies constrains effective implementation of artemisinin-based combination therapy policy in Kenya.