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Evolutionary genomics of anthroponosis in Cryptosporidium

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Abstract

Human cryptosporidiosis is the leading protozoan cause of diarrhoeal mortality worldwide, and a preponderance of infections is caused by Cryptosporidium hominis and C. parvum. Both species consist of several subtypes with distinct geographic distributions and host preferences (i.e. generalist zoonotic and specialist anthroponotic subtypes). The evolutionary processes driving the adaptation to human host, and the population structure remain unknown. In this study, we analyse 21 whole genome sequences to elucidate the evolution of anthroponosis. We show that C. parvum splits into two subclades, and that the specialist anthroponotic subtype IIc-a shares a subset of loci with C. hominis that are undergoing rapid convergent evolution driven by positive selection. Subtype IIc-a also has an elevated level of insertion-deletion (indel) mutations in the peri-telomeric genes, which is characteristic also for other specialist subtypes. Genetic exchange between subtypes plays a prominent role throughout the evolution of Cryptosporidium. Interestingly, recombinant regions are enriched for positively selected genes and potential virulence factors, which indicates adaptive introgression. Analysis of 467 gp60 sequences collected across the world shows that the population genetic structure differs markedly between the main zoonotic subtype (isolation-by-distance) and the anthroponotic subtype (admixed population structure). Finally, we show that introgression between the four anthroponotic Cryptosporidium subtypes and species included in this study has occurred recently, probably within the past millennium.

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Original languageEnglish
Pages (from-to)826–836
JournalNature Microbiology
Volume4
DOIs
Publication statusPublished - 4 Mar 2019
Peer-reviewedYes

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