Molecular Characterisation of spp. in Mozambican Children Younger than 5 Years Enrolled in a Matched Case-Control Study on the Aetiology of Diarrhoeal Disease.

is a leading cause of childhood diarrhoea and associated physical and cognitive impairment in low-resource settings. -positive faecal samples ( = 190) from children aged ≤ 5 years enrolled in the Global Enteric Multicenter Study (GEMS) in Mozambique detected by ELISA (11.5%, 430/3754) were successfully PCR-amplified and sequenced at the or rRNA loci for species determination and genotyping. Three species including (72.6%, 138/190), (22.6%, 43/190), and (4.2%, 8/190) were detected. Children ≤ 23 months were more exposed to spp. infections than older children. Both and were more prevalent among children with diarrhoeal disease compared to those children without it (47.6% vs. 33.3%, = 0.007 and 23.7% vs. 11.8%, = 0.014, respectively). A high intra-species genetic variability was observed within (subtype families Ia, Ib, Id, Ie, and If) and (subtype families IIb, IIc, IIe, and IIi) but not within (subtype family IIIb). No association between species/genotypes and child's age was demonstrated. The predominance of and IIc suggests that most of the infections were anthroponotically transmitted, although zoonotic transmission events also occurred at an unknown rate. The role of livestock, poultry, and other domestic animal species as sources of environmental contamination and human cryptosporidiosis should be investigated in further molecular epidemiological studies in Mozambique.