A Hidden Epidemic of Misdiagnosis

A dangerous gap in Kenya's fight against malaria is widening, not in the field with mosquito nets, but within the walls of its health facilities. Inaccurate laboratory diagnosis is fuelling a silent epidemic of drug resistance, creating a significant public health crisis that threatens to reverse decades of progress. Stakeholders in Kenya's malaria control programme have issued warnings that persistent weaknesses in diagnostic capacity are leading to mismanagement of cases, where patients are either denied timely treatment or are prescribed powerful antimalarials unnecessarily. This dual-edged sword of over- and under-treatment is severely escalating the risk of drug resistance in malaria-endemic counties.

According to the Global Fund, Kenya contributes 1.4% to the world's malaria cases, with an estimated 3.4 million cases and over 11,000 deaths reported in 2023. While the proportion of suspected cases receiving a diagnostic test has impressively risen from 32% in 2010 to 92% in 2023, a 2022 study in Kisumu County found that the health facility misdiagnosis rate was a staggering 27.9%. This highlights a critical flaw in the system: even when tests are conducted, their accuracy is not guaranteed.

Regina Kandie, Head of Diagnostics at the Ministry of Health's National Malaria Control Programme (NMCP), confirmed the challenge. “Accurate results are key to effective case management. When diagnosis is delayed, patients may go untreated, and inaccurate results can lead to missed cases,” she stated in October 2025. “By the time some patients return, the infection may have progressed to severe malaria, which can be fatal.” This reality is most acute in high-burden areas like Busia and Siaya counties, which have malaria prevalence rates of 39% and 28.5% respectively, according to the 2020 Kenya Malaria Indicator Survey.

The Link to Antimicrobial Resistance

The primary driver of this crisis is the frequent breakdown in diagnostic quality. Weak microscopy skills, poor laboratory reporting, and delays in detection are common. David Isaboke, AMREF's Regional Laboratory Programme Manager, noted in October 2025 that this erodes trust between clinicians and laboratories, leading to a reliance on syndromic treatment—prescribing drugs based on symptoms like fever alone. This practice, coupled with self-medication, is a major contributor to the rise of drug-resistant malaria parasites. When patients without malaria are treated with Artemisinin-based Combination Therapies (ACTs), the current frontline treatment, it exposes parasites to the drugs without killing them, allowing the strongest, most resistant strains to survive and multiply.

This threat is no longer theoretical. The World Health Organization (WHO) has confirmed the emergence of partial artemisinin resistance in neighbouring Uganda and Tanzania, as well as in Rwanda and Eritrea. This development is a grave warning for Kenya, as the cross-border spread of resistant parasites is a significant risk. Kenya has already shifted to combination therapies because single-drug treatments became ineffective; now, even the efficacy of ACTs is under threat.

Compounding the Challenge: Faulty Rapid Tests

A further complication is the growing unreliability of some Rapid Diagnostic Tests (RDTs). Most RDTs work by detecting the Plasmodium falciparum histidine-rich protein 2 (PfHRP2). However, scientists at the Kenya Medical Research Institute (KEMRI) have confirmed the presence of malaria parasites with deletions of the *pfhrp2* and *pfhrp3* genes in the Lake Victoria region. These parasites are invisible to standard RDTs, leading to false-negative results. A patient can have malaria, be tested, receive a negative result, and be sent home untreated, allowing the disease to progress and transmission to continue. A December 2024 study of asymptomatic infections in the Lake Victoria region found that among RDT-negative but PCR-positive samples, 28.8% had these critical double gene deletions.

Economic and Regional Implications

The economic consequences are severe. Malaria already imposes a heavy burden on Kenya, causing the loss of an estimated 170 million working days annually and creating a "growth penalty" of up to 1.3% of GDP in some African nations. Faulty diagnosis exacerbates this by adding the cost of wasted medication and prolonged treatment for mismanaged cases. The rise of drug resistance threatens to make current treatments obsolete, which would necessitate a shift to newer, more expensive drugs, further straining the healthcare budget. The influx of counterfeit and substandard antimalarial drugs, some containing insufficient active ingredients, also contributes to both economic loss and the development of resistance.

The emergence of artemisinin resistance in East Africa demands a coordinated regional response. With significant cross-border movement, a resistant strain identified in Uganda or Tanzania today could be prevalent in western Kenya tomorrow. Collaborative surveillance and harmonized treatment policies are essential to contain this threat.

A Strategic Response

In response, Kenya's Ministry of Health has outlined a clear path in its **Kenya Malaria Strategy 2023–2027**. The strategy sets an ambitious target to reduce malaria incidence by 80% and deaths by 90% by 2027. A key pillar of this strategy is strengthening diagnostic capacity. Initiatives are underway, such as the intensive five-day malaria microscopy training for laboratory technologists from Busia and Siaya counties, supported by the NMCP and partners. This program focuses on enhancing practical skills like parasite detection, counting, and accurate reporting to rebuild confidence in laboratory results.

Furthermore, KEMRI is innovating to overcome diagnostic challenges. The institute has developed a new RDT, PlamoChek, which offers high sensitivity and is more affordable than imported kits. KEMRI is also actively involved in surveillance to monitor for drug resistance and *pfhrp2/3* gene deletions to inform national policy and ensure diagnostic tools remain effective. The ultimate success of these efforts hinges on sustained investment, rigorous implementation, and a commitment to ensuring every suspected malaria case in Kenya receives an accurate diagnosis before any treatment is administered.