Comparative study of microscopy and conventional PCR for Plasmodium Falciparum identification on patient samples from Gisagara and Huye districts, Southern Province, Rwanda

Abstract

Malaria is a critical global public health concern. Sub-Saharan African nations including Rwanda are known for high malaria cases and transmission. In Rwanda, particularly the districts of Gisagara and Huye are known for the endemic and seasonal transmission. To tackle high transmission and to apply early treatment, effective malaria management which depends on accurate and timely diagnosis is very imperative. Microscopy has been serving as the gold standard diagnostic technique due to its affordability, ability to detect and quantify Plasmodium species. However, factors such as technician skills, equipment quality and parasite density limit its effectiveness. Its low sensitivity, especially in detecting low- sensitive infections or lower ability in distinguishing between closely related species is also among its limitation. In contrary, conventional PCR, a molecular technique, offers superior sensitivity and specificity, especially for low parasitemia and mixed infections that microscopy often misses. Conventional PCR overcomes many of microscopy limitations through high sensitivity, targeting parasite DNA and enabling precise species identification even at low concentrations. This study is therefore, focused on comparison of microscopy with conventional PCR for successful identification of Plasmodium falciparum. It sought to determine prevalence of Plasmodium falciparum; to assess the diagnostic sensitivity; specificity of the two methods and evaluate their concordance. The study population includes RDT-positive patients identified by community health workers, then referred to health centers for screening to be recruited in ARMEA project. A sample size was determined using statistical calculations with Daniel’s formula. Ethical clearance was secured before data collection process begun. Blood samples undergone both microscopy (with thick and thin smear), and detection using conventional PCR. The raw data was recorded using Microsoft Excel and analyzed using SPSS Version 25. This study revealed that high prevalence rates were detected with both methods, though PCR detected slightly more cases. Microscopy demonstrated strong diagnostic performance with high sensitivity (95.26%) and positive predictive value (98.96%), but a lower negative predictive value (54.76%), reflecting its limitations in ruling out infection. Despite PCR's superior sensitivity, microscopy showed excellent diagnostic accuracy (AUC = 0.902) and substantial agreement with PCR (Cohen’s Kappa = 0.639), supporting its continued use in resource- limited, hightransmission settings. In conclusion, the study supported integrating microscopy with molecular tools like PCR for malaria diagnosis, as microscopy remains valuable due to its high sensitivity and accuracy.