| Summary: | <i>Cryptosporidium</i> is a leading cause of childhood diarrhoea and associated physical and cognitive impairment in low-resource settings. <i>Cryptosporidium</i>-positive faecal samples (<i>n</i> = 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 <i>gp60</i> or <i>ssu</i> rRNA loci for species determination and genotyping. Three <i>Cryptosporidium</i> species including <i>C. hominis</i> (72.6%, 138/190), <i>C. parvum</i> (22.6%, 43/190), and <i>C. meleagridis</i> (4.2%, 8/190) were detected. Children ≤ 23 months were more exposed to <i>Cryptosporidium</i> spp. infections than older children. Both <i>C. hominis</i> and <i>C. parvum</i> were more prevalent among children with diarrhoeal disease compared to those children without it (47.6% vs. 33.3%, <i>p</i> = 0.007 and 23.7% vs. 11.8%, <i>p</i> = 0.014, respectively). A high intra-species genetic variability was observed within <i>C. hominis</i> (subtype families Ia, Ib, Id, Ie, and If) and <i>C. parvum</i> (subtype families IIb, IIc, IIe, and IIi) but not within <i>C. meleagridis</i> (subtype family IIIb). No association between <i>Cryptosporidium</i> species/genotypes and child’s age was demonstrated. The predominance of <i>C. hominis</i> and <i>C. parvum</i> IIc suggests that most of the <i>Cryptosporidium</i> 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.
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