Background:

Malaria control strategies need to respond to geographical hotspots of transmission. Detection of hotspots depends on the sensitivity of the diagnostic tool used.
Methods:

We conducted cross-sectional surveys in three sites within Kilifi County, Kenya, at variable transmission intensities. RDT, Microscopy and PCR testing were used to detect asymptomatic parasitaemia and hotspots were detected using the spatial scan statistic.
Results:

8581 study participants were surveyed in three sites. There were statistically significant malaria hotspots by RDT, microscopy and PCR for all sites except by microscopy in one low transmission site. Pooled data analysis of hotspots by PCR overlapped with hotspots by microscopy at a moderate setting but not at two lower transmission settings. However, variations in degree of overlap was noted when data were analysed by year. Hotspots by RDT were predictive of PCR/microscopy at the moderate setting, but not at the two low transmission settings. We observed long-term stability of hotspots by PCR and microscopy except for RDT.
Conclusion:

Malaria control programmes may consider PCR testing to guide asymptomatic malaria hotspot detection once the prevalence of infection falls.