Diarrhoea is the second leading cause of under-five childhood mortality, being responsible for one in nine deaths worldwide, more than in malaria and HIV combined. The apicomplexan parasite Cryptosporidium causes prolonged and persistent diarrhoea in immunocompetent children and severe diarrhoea in immunocompromised individuals. The importance of Cryptosporidium infection as a significant cause of morbidity and mortality in infants and young children in the developing world has only been firmly established in the last few years. Birth cohort and case-control studies have identified a high burden of cryptosporidiosis in both immunocompromised and immunocompetent young children. Most symptomatic infections occur between 6 months to 2 years of age, after which incidence quickly declines, presumably because of the development of immunity with repeated exposure. Despite being among those pathogens with the highest attributable risk for diarrhoea in African children, cryptosporidiosis is still substantially underdiagnosed and preventive measures are almost absent. So far, 38 Cryptosporidium species have been recognized, of which more than 20 have been identified in humans, with most species or subspecies being restricted to specific hosts.

Previous studies have underlined the dominant role of human-to-human transmission as the major transmission route for children in endemic regions, despite close human-animal contact. Our research projects try to understand the genomic epidemiology of different Cryptosporidium species and the transmission dynamics among human and animal reservoirs in sub-Sahara Africa in order to identify more effective prevention strategies.