Comparative genomics revealed adaptive admixture in Cryptosporidium hominis in Africa

Cryptosporidiosis is a major cause of diarrhoeal illness among African children, and associated with childhood mortality, malnutrition, cognitive development growth retardation. Cryptosporidium hominis the dominant pathogen in Africa, genotyping at glycoprotein 60 ( gp60 ) gene has revealed complex distribution different subtypes across this continent. However, comprehensive exploration metapopulation structure evolution based on whole-genome data yet to be performed. Here, we sequenced analysed genomes 26 C . isolates, representing subtypes, collected rural sites Gabon, Ghana, Madagascar Tanzania. Phylogenetic cluster analyses single-nucleotide polymorphisms showed that isolates predominantly clustered by their country origin, irrespective subtype. We found significant isolation-by-distance signature shows importance local transmission, but also detected evidence hybridization between geographical regions. identified 37 outlier genes exceptionally high nucleotide diversity, group significantly enriched for encoding extracellular proteins signal peptides. Furthermore, these are more often than expected recombinant regions, they show distinct positive or balancing selection. conclude that: (1) C. can only accurately captured analyses; (2) anthroponotic transmission underpins spread Africa; (3) occurs lineages; (4) genetic introgression provides novel substrate selection involved host–parasite coevolution.