Dynamic interactions between Schistosoma haematobium, Schistosoma mattheei and Schistosoma mansoni underscore the complex polyparasitism of intestinal schistosomiasis in southern Malawi.

Schistosomiasis is prevalent among school-aged children (SAC) in Mangochi District, Malawi, where both intestinal and urogenital forms are endemic. In 2024, we identified schistosomiasis cases predominantly associated with excretion of Schistosoma haematobium × Schistosoma mattheei ova in the faeces of two individuals from Samama village, Mangochi District. In this expanded cross-sectional study, we characterize the prevalence and species composition of Schistosoma infections among 247 SAC in Samama, using genus- and species-specific molecular diagnostics. We also present follow-up data from the two previous cases, showing natural mixed-species re-infection six months after treatment. Schistosomiasis prevalence among SAC was 62.3%. Schistosoma spp. DNA was detected in 50.6% of faecal samples and Schistosoma spp. ova were observed on 34.8% of urine filters. Species-specific assays detected S. haematobium, S. mattheei and S. mansoni DNA in 36.8%, 14.4% and 18.4% of faecal samples from children with intestinal schistosomiasis. Triple-species infections were identified in 10 children by faecal and urine testing. Notably, detection of S. haematobium DNA in faeces was strongly associated with S. mattheei co-infection (p = 0.006), highlighting potential cross-species interactions. Our findings underscore the need to integrate molecular diagnostics alongside routine testing strategies for enhanced surveillance of polyparasitic infections in zoonotic transmission zones across Africa. This article is part of the Royal Society Science+ meeting issue 'Parasite evolution and impact in action: exploring the importance and control of hybrid schistosomes in Africa and beyond'.