Decline to near-zero malaria hospitalisation over 35 years on the Kenyan Coast

Background: Few longitudinal studies have examined the long-term health impact of changing malaria prevention and treatment strategies in Africa. This study analyses 35 years of clinical surveillance among paediatric malaria admissions in Kilifi, Kenya. Methods: Children aged 1 month to 14 years who were residents of rural Kilifi Health and Demographic Surveillance System and admitted to Kilifi County Hospital between January 1990 and December 2024 were included. Community malaria exposure was estimated using infection prevalence among children admitted for trauma, elective surgery, bites and neoplasms. Malaria admissions were defined as hospitalisations with a positive blood slide and a primary, secondary, or co-morbid malaria diagnosis. Severe malaria phenotypes including severe anaemia, cerebral malaria, hyper-parasitaemia and in-hospital mortality were also examined. Binomial and Poisson regression models assessed temporal differences, using 1990 to 1996 as the reference period Results: Community malaria prevalence declined from 35% (95% CI: 31, 39) in the 1990s to 2% (95% CI: 1, 4; p<0.001) in 2020 to 2024. Malaria hospitalisations declined from a peak of 25.5 per 1,000 children per annum (p.a.) (95% CI: 24.4, 26.6) in 1999 to 0.65 (95% CI: 0.59, 0.72; p<0.001) between 2020 and 2024. The median age of malaria increased from 19 months (IQR: 12, 39) between 1990 and 1996 to a peak of 48 months (IQR: 28, 78) between 2012 and 2019. Cerebral malaria became proportionally more common than severe anaemia over time. Malaria-specific hospitalised mortality rates declined from 0.43 per 1,000 children p.a. (95% CI: 0.38, 0.49) in the 1990s to 0.03 (95% CI: 0.02, 0.05; p<0.001) during the period 2020-2024. Conclusions: Hospital admission with malaria among children in Kilifi is now uncommon. Sustained reductions in parasite exposure have altered the clinical profile of disease presentation, including both phenotype and age distribution, without resulting in a cumulative increase in disease burden. Expanded and sustained coverage of effective long-lasting insecticidal nets, together with improved access to effective treatment, have likely contributed to this epidemiological transition.