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Background   Acanthamoeba  is an emerging potentially pathogenic amoeba that has been receiving increasing attention worldwide as a reservoir and potential vector for the transmission of pathogenic bacteria. It is also associated with brain cell damage, keratitis and skin irritation in humans. Its effects are more severe in immunocompromised individuals. This study provides for the first time in Uganda, information on the prevalence and genotypes of  Acanthamoeba  in environmental and domestic (tap) water.    Methods  A total of 324 environmental and 84 tap water samples were collected between November 2013 and September 2014. The samples were centrifuged, cultured (Non-Nutrient agar seeded with gram-negative bacteria) and observed under a microscope. After confirmation of  Acanthamoeba , genomic DNA was extracted for PCR assays by chemical lysis and purification with phenol/chloroform/isoamyl alcohol. Samples that showed the strongest positive bands (400–600 bp) were subjected to cycle sequencing.    Results  Among environmental and tap water samples, 107 (33 %) and 36 (42.9 %) tested positive for  Acanthamoeba  spp., respectively. Prevalence of  Acanthamoeba  from specific environmental locations was as follows; Kazinga channel banks (60.7 %), Fish landing sites (50 %), River Kyambura (39.6 %) and Kazinga mid channel (5.3 %). There was a significant difference ( p  = 0.001) in the prevalence of  Acanthamoeba  between sampling sites. The mean (Mean ± SE) occurrence of the organism was higher in Kazinga channel banks (3.44 ± 0.49) and Fish landing sites (3.08 ± 0.53). Correlation between in situ parameters and  Acanthamoeba  was insignificant except for the Dissolved Oxygen (mg/ML) which was negatively correlated ( r  = −0.231,  p  = 0.001) to  Acanthamoeba.  Six distinct partial  Acanthamoeba  T-genotype groups T1, T2, T4, T5, T6 and T11 were obtained. Ultimately,  Acanthamoeba  spp.,  Acanthamoeba hatchetti  and  Acanthamoeba polyphaga  were isolated in the current study.    Conclusions  There was a high prevalence of  Acanthamoeba  in communal piped tap and environmental water used by communities, indicating poor environmental and domestic water quality.

Occurrence and genetic characterisation of Acanthamoeba spp. from environmental and domestic water sources in Queen Elizabeth Protected Area, Uganda