Sub-microscopic schistosomiasis and soil-transmitted helminths in school children: molecular diagnostic evidence and implications for disease elimination

Schistosomiasis and soil-transmitted helminthiasis elimination programmes depend heavily on microscopic diagnostics, yet these methods may fail to detect low-intensity infections that sustain transmission. Molecular techniques could reveal the extent of submicroscopic infections missed by conventional approaches. To compare the detection rates of conventional microscopy with probe-based multiplex real-time PCR and quantitative real-time PCR (qPCR) for schistosomiasis and soil-transmitted helminths among primary school children in Plateau State, Nigeria, and to estimate the proportion of submicroscopic infections undetected by standard methods. In this cross-sectional study, 1,368 systematically sampled primary school children from six schools across six Local Government Areas provided urine and stool specimens. These were analysed using standard microscopy (urine filtration and Kato-Katz). A stratified subset of 585 samples (42.8%) underwent molecular analysis by probe-based multiplex real-time PCR for species detection and probe-based singleplex qPCR for quantification. Microscopy revealed an overall parasitic infection prevalence of 20.7% (95% CI: 18.6–22.9%). Among the 585 molecularly analysed samples, molecular methods detected 178 positive cases compared with 123 by microscopy, representing a 44.7% increase (95% CI: 36.2–53.8%, p < 0.001). An additional 9.4% of specimens (95% CI: 7.1–12.1%) were molecular-positive but microscopy-negative. For schistosomiasis, molecular methods identified 52 cases versus 36 by microscopy (44.4% increase), whilst soil-transmitted helminths showed 126 versus 87 molecular- and microscopy-positive cases respectively (44.8% increase). Molecular diagnostics identified 44.7% more infections than microscopy alone (95% CI: 36.2–53.8%, p < 0.001), indicating that conventional methods failed to detect a substantial proportion of low-intensity infections. These findings suggest that microscopy-based surveillance may underestimate infection prevalence in elimination programme settings. Integrating molecular methods into surveillance frameworks could improve the accuracy of elimination progress assessments.