The prevalence and genetic characterisation of isolates from cattle in Kiruhura district, South Western Uganda.

is an emerging opportunistic zoonotic pathogen that causes diarrheal illness in a wide range of hosts including livestock and humans. This study set out to establish the prevalence of as well as the circulating genotypes in order to elucidate the potential role of cattle in the spread of human cryptosporidiosis. Rectal coprological samples from 363 cattle in 11 households in Kiruhura district, Southwestern Uganda were collected and screened for the presence of oocysts using the phenol auramine staining method followed by fluorescent microscopy. DNA was extracted from the microscopy positive samples and the COWP gene amplified using PCR. PCR products were sequenced and subjected to phylogenetic analysis. Additionally a multiplex realtime PCR was used to identify the . Multivariable mixed effect logistic regression models were used to identify potential risk factors for infection. The overall prevalence of was 7.7% (95% CI 5.1-10.9), and herd level prevalence was 33.3% (95% CI 18.5-52.2). We found a statistically significant difference (OR = 30.78, 95% CI 4.31-219.95,  = 0.001) between infection in bulls as compared to cows. There was no significant difference in the prevalence among the different cattle breeds sampled. All the sequenced COWP gene DNA amplicons were confirmed to be with 93%-100% identity to sequences in the GenBank. The amplification of the small subunit rRNA by multiplex realtime PCR further established that the isolates in this study are . This study represents the first time naturally occurring has been detected from cattle in Uganda.