Background: Giardia intestinalis, Cryptosporidium spp and Entamoeba histolytica are obligate pathogens and are the most common causative agents of childhood diarrhoea. The diagnosis of these parasitic infections was for a long time based on microscopic examination of stools that lacks sensitivity
and specificity and requires a highly trained staff. As a result of these limitations, DNA-based detection
methods exhibiting numerous advantages such as increased sensitivity and specificity, ability to combine
multiple targets in one multiplex assay have been developed for enteric parasites.
This study aimed to assess the epidemiology of these three-common diarrhoea-causing parasites in children under five years using microscopy vs. real time PCR assay.
Patients and Methods: A hospital-based cross-sectional survey for gastrointestinal parasites in children
under five years was conducted in Ouagadougou from January 2018 to December 2019. Stool samples
from 188 children presented with diarrhoea were processed using both light microscopy and real time
PCR techniques.
Results: Microscopy showed a 22.9% (43/188) overall prevalence of parasitosis with 10.1% (19/188) E.
histolytica/E. dispar and 6.9% (13/188) G. intestinalis. Real time PCR was positive in 26.1% (49/188) of
cases. G. intestinalis was the most common with a 22.9% (43/188) prevalence followed by Cryptosporidium spp 6.4% (12/188) and E. histolytica 1.6% (3/188).
Conclusions: Intestinal protozoan parasites mainly affect children aged 12-24 months. G. intestinalis
was identified as the leading cause of childhood diarrhoea. The real time PCR assay showed an excellent sensitivity detecting gastrointestinal parasites comparatively to microscopy that exhibited false positive or negative cases.

Children, Diarrhoea, Protozoan parasites, Real time PCR, Burkina Faso