Microscopic and molecular identification of diarrhoea-causing intestinal protozoa among children in Guinea-Bissau

Background Gastrointestinal parasitic infections remain a major health burden in low- and middle-income countries (LMICs). Methods Overall, 1238 faecal samples (548 from healthcare-seeking children [Cohort 1] and 690 from children from the community [Cohort 2]) were examined by microscopy for Giardia duodenalis and Entamoeba species, and by PCR for G. duodenalis, Entamoeba histolytica, Entamoeba dispar and Cryptosporidium spp. Associations between symptoms, microscopy intensity and PCR cycle threshold (Ct) values were analysed. Children were matched by age, gender and residence. Results Giardia duodenalis was the most common, detected by PCR in 56.2% (Cohort 1) and 63.0% (Cohort 2) (p≤0.05), 2.5 times more often than by microscopy. Microscopy overestimated E. histolytica prevalence by 23% compared with PCR, due to non-pathogenic species. Four E. histolytica infections and one Cryptosporidium infection were PCR-confirmed. Ct values correlated with microscopy intensity (p<0.01), but detection was not linked to symptoms. The only cohort difference was water source: 48% in Cohort 2 vs 23% in Cohort 1 had private water posts. Conclusions Children in Bissau carry a high asymptomatic burden of G. duodenalis. Microscopy overestimates E. histolytica, while PCR improves specificity. Selective molecular testing with clinical assessment is recommended for rational treatment in high-endemic, resource-limited settings.