As most endemic countries begin to re-focus their malaria control goals, including in some cases a target of elimination [1], contemporary maps that reliably define sub-national variation in disease risk are required to inform priority setting and the selection of appropriate suites of intervention. Recent efforts at developing empirical global maps of Plasmodium falciparum risk herald a new era of using maps to define regional populations at risk of malaria to guide the future global malaria control agenda [2]. However, the applicability of malaria risk mapping to make predictions at spatial scales and time points necessary for effective health service planning and review depends largely on the amount and resolution of information available. For example, it is recognized that continental risk maps may not provide sufficient detail and precision for national and sub-national level control priority setting [2].

Kenya is one of very few countries that have a plethora of malaria risk data, spanning over 30 years. The earliest attempts to describe the spatial distribution of malaria risk in Kenya were based on expert opinion of malaria seasons and climate [3]. Between 1998 and 2005 several attempts were made by our group to model the predictive accuracy of this historical map [4, 5] or use historical parasite prevalence data and remotely sensed proximates of climate to predict risk using sub-optimal spatial methods that were unable to define fully the uncertainty in the modeled maps [6, 7]. Here we present a more robust Bayesian model-based geo-statistical spatial-temporal method to predict the risk of malaria in Kenya in 2009 using the largest assembled contemporary empirical evidence for any country in Africa. As a new phase of malaria control in Kenya begins, the implications of the resulting malaria risk map for decision makers and the prospects for the future of malaria control nationwide are discussed.

We have assembled over 2,600 independent, empirical survey estimates of P. falciparum infection prevalence in Kenya and used these data to generate a contemporary map of infection prevalence at a 1 × 1 km resolution for the year 2009 using space-time geostatistical models within a Bayesian framework. The modeled distribution had a high predictive accuracy as shown by the low values of ME and MAE and high correlation between predicted and observed PfPR_2-10 (Table 3 & Figure 4). The probability of endemicity class membership were also generally moderate to high across the country with the exception of small pockets of the low population-density areas of the northern districts where there was relatively sparse distribution of input data in time and space (Figure 5). This mapped distribution of malaria risk represents the most accurate depiction of parasite exposure described for Kenya since efforts to map risk began in the 1950's [2, 3, 5, 6]. More importantly it represents a distribution of risk in 2009 serving as a contemporary basis upon which to design the future of malaria control in Kenya.

The use of a carefully selected suite of covariates to inform the prediction of risk is a departure from the current Malaria Atlas Project approach, with the exception of the use of urban-rural classification [2], but consistent with other approaches to modeling malaria distributions [5, 6, 15–17, 35]. In fact several discrete categories of the covariates were as different in infection prevalence as the differences described for urban versus rural surveys. We elected not to include a mask of zero or unstable transmission based upon temperature and aridity as developed previously by Guerra et al, [40]. Rather we have assumed that these climatic drivers of transmission would be captured within the model and have chosen to bin the risk classes within much smaller PfPR_2-10 ranges at the lowest end of the transmission spectrum. The lowest risk class encompasses predicted PfPR_2-10 between 0 and < 0.1% and covers approximately 91,000 km² within the Nairobi and Central provinces and small parts of Eastern and Rift Valley (Figure 3). Defining absolute zero transmission is conceptually difficult and practically impossible to measure empirically using PfPR_2-10 and we therefore feel that the more conservative and inclusive approach used here allows for the possibility of transmission until proven otherwise.

What is striking about the contemporary 2009 distribution of malaria infection risk is the enormity of Kenya's land surface under very low intensity transmission. Over 94% of Kenya's surface area is predicted to be exposed to a PfPR_2-10 of less than 5% and is home to 86% of Kenya's projected population in 2009 (Table 3). Approximately 66% of the 2009 population live in areas where infection prevalence is less than 1%, including a large majority where risks are hard to detect empirically (PfPR_2-10 < 0.1%) (Table 3). Conversely areas of high transmission, as defined by a PfPR_2-10 of ≥40%, representing areas expected to be intractable to immediate reductions in parasite prevalence with scaled-up use of insecticide treated nets [47] are located in the strip of land along the shores of Lake Victoria (Figure 3). In 2009 only 11% of Kenya's population was exposed to this highest transmission intensity class (Table 3). Historically holo-to-hyperendemic transmission (≥50% PfPR_2-10) was thought to exist across much larger reaches of the Kenyan coast, around Lake Victoria and along the Tana River [3, 51]. In the present modeled iteration of PfPR_2-10 holo-endemic transmission (>75% PfPR_2-10) no longer exists and hyper-endemic transmission is constrained to small pockets within the darkest red class shown in Figure 3. Although this study doesn't present change of infection risk over time, it seems plausible that across much of Kenya the extent and intensity of P. falciparum transmission has undergone a recent decline with increasing spatial areas and populations becoming exposed to lower and lower risks of parasite exposure. This has implications for a changing clinical epidemiology in areas undergoing transition, with older children becoming increasingly at risk of severe clinical outcomes [52–55] but more importantly as communities transition to very low levels of parasite exposure overall malaria morbidity and mortality will decline substantially [52, 56].

Although the model is characterized by generally low uncertainties, the pockets of greatest predicted uncertainty are located in the northern districts of Turkana, Marsabit and Moyale (Figure 5). Surprisingly, pockets of risk >10% PfPR_2-10 were observed in these hot and generally arid parts of the country traditionally regarded to be of unstable low risk. These areas, which generally have low population densities and have traditionally not been targeted for scaling of malaria preventive interventions, exhibit highly focal transmission close to water features, such as the Turkwell, Tana and Kerio rivers and were referred to in historical maps as 'malarious near water' [3]. Because of their presumed low risk, few empirical studies of malaria have been undertaken in these areas. The malaria situation among these poor, pastoralist communities remains ill-defined. In addition there are some important methodological constraints to defining risk in areas of very low transmission and new approaches to micro-geographic Bayesian modeling of risk based upon a presence/absence criterion may be required to improve risk mapping in these areas where the majority risk is negligible, seasonal and exceptionally heterogeneous, associated with the presence of water features.

Further improvements in malaria risk mapping using PfPR_2-10 might be achieved if the prediction models were corrected for whether microscopy or RDT was used to examine parasitaemia given the varying sensitivities and specificities of the two methods [57]. In this study, however, this was not possible because information on the type of RDT used and the quality of microscopy was lacking for most surveys. In future, it may be feasible to develop universal models that correct for sensitivity/specificity differentials of the methods used to test for infection, preferably based on large-scale population surveys which have used both RDT and microscopy for the same individuals with the appropriate quality assurance and external validity.

The prospects for Kenya to transition the majority of its population living in high transmission areas in the next 10 years to areas of low (PfPR_2-10 <5%) or very low endemicity (PfPR_2-10 <1%) look promising. It is however important to emphasize the control implications of this low stable endemic control. There appear to be areas along the Kenyan coast that currently experience risks associated with a PfPR_2-10 <5% and are likely to have transitioned to this state from meso-hyperendemic conditions. If this has been achieved through the scaled-up use of insecticide treated nets (ITN) then universal coverage must be maintained as withdrawal of ITN would result in a devastating rebound where vectors persist but functional immunity has been modified among the human host population. Conversely in areas that have historically had low or very low transmission, for example in semi-arid areas, the adoption of ITN may not be the most cost-effective strategy. As such all areas of similar contemporary risk may not be equivalent in terms of strategic control. One therefore must interpret contemporary distributions of risk for control planning in concert with the potential vulnerabilities of transmission based upon vector distributions or historical descriptions of risk. For Kenya it is also important to recognize that there are vast areas where infection risks are low and have historically been low because of their ecological niches (arid, urban or at high elevation). While these communities enjoy a low risk of infection, risks are not absent and thus cost-efficient suites of interventions must be tailored to meet their needs. This poses a challenge where universal coverage of ITN and presumptive fever treatment with Artemisinin based combination therapy remain the single bedrock of most national malaria control strategies across Africa.

There remains some debate over the feasibility of malaria elimination in Africa [58–61]. Kenya is an example where infection prevalence is low across large parts of the country. However moderate-to-high risks remain in well defined areas, some of which share borders with neighboring countries and risks are not absent from marginalized hard-to-reach communities in semi-arid areas of the country. Successes in reducing infection prevalence in some areas [[55], Okiro EA, Alegana VA, Noor AM, Mutheu JJ, Juma E, Snow RW: Malaria paediatric hospitalization between 1999 and 2008 across Kenya. Submitted] that have led to reductions in disease burden [[54, 55], Okiro EA, Alegana VA, Noor AM, Mutheu JJ, Juma E, Snow RW: Malaria paediatric hospitalization between 1999 and 2008 across Kenya. Submitted] must be maintained and expanded and not viewed as 'job finished'. This alone may pose challenges for sustained financing. What is encouraging is that risks can be measured using survey data of infection prevalence; we have shown here that their spatial distribution can be modeled and mapped with accuracy; and that this can become the basis for judging the future success of control nationwide using data that does not depend upon opportunistic historical surveys. To this end the Kenyan Ministry of Health proposes to maintain annual surveys of malaria infection prevalence among school children as part of its monitoring of the revised national malaria strategy 2009-2017 (E Juma, personal communication). This will represent the first attempt in Africa to serially measure, map and model changing endemicity as part of scaled intervention coverage and where robust baseline endemicity for 2009 exists to judge success.