Multicopy subtelomeric genes underlie animal infectivity of divergent Cryptosporidium hominis subtypes

The anthroponotic Cryptosporidium hominis differs from the zoonotic C. parvum in its lack of infectivity to rodents, but several divergent C. hominis subtypes have recently been found in nonhuman primates and equines. Here, we performed whole-genome sequencing of 17 animal C. hominis isolates and generated a chromosome-level C. hominis genome using PacBio and Illumina technologies. In a comparative analysis with 222 human isolates, the animal isolates showed significant genetic divergence, with genetic recombination among them. In addition, these animal isolates had additional insulinase and MEDLE genes as well as sequence differences in subtelomeric genes. In interferon-γ knockout mice, three monkey isolates showed differences in infectivity and induced higher and longer oocyst shedding than a reference C. parvum isolate. However, the growth of the IbA12G3 strain in GKO mice was significantly reduced by deletion of the subtelomeric MEDLE genes or partial deletion of the insulinase genes, and the former prevented the mice from losing body weight during infection. In addition, we provided experimental evidence for the conclusion that the co-infection of two C. hominis subtypes can produce genetic recombinants using the mouse model. These data provide insight into potential determinants of host infectivity in Cryptosporidium, and a convenient animal model for biological studies of C. hominis.