Studies on waterborne parasites from natural environment and domestic water sources in Uganda are very scarce and unpublished. Water dwelling free-living amoebae (FLA) of the genus Acanthamoeba, Hartmannella, and Naegleria are often responsible for causing morbidities and mortalities in individuals with recent contact with contaminated water, but their presence in Uganda’s public water supply sources is not known. We cultivated and genotyped FLA from natural and domestic water from Queen Elizabeth Protected Area (QEPA) and Kampala (KLA). The cultivated parasites were observed microscopically and recorded. The overall prevalence of FLA in QEPA (Acanthamoeba spp., 35%; Hartmannella spp., 18.9%; Naegleria spp., 13.5%) and KLA (Acanthamoeba spp., 28.3%; Naegleria spp., 16.6%; Hartmannella spp., 23.1%) were not significantly different. The highest prevalence across water sources in QEPA and KLA was observed for Acanthamoeba spp., followed by Hartmannella spp., and Naegleria spp. Overall FLA mean (±SE) and mean (±SE) across water sources were highest for Acanthamoeba spp. compared to other FLA but were not statistically significant (p > 0.05). Analysis of the FLA sequences produced 1 Cercomonas, 1 Nuclearia, 1 Bodomorpha, 2 Hartmannella, 5 Echinamoeba, and 7 Acanthamoeba partial sequences, indicating a muliplicity of water contaminants that need to be controlled by proper water treatment.
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