Population genomics of Cryptosporidium hominis across five continents identifies two subspecies that have diverged and recombined during 500 years of evolution
AbstractCryptosporidium is a significant public health problem and one of the primary causes of diarrhoea in humans, particularly in very young children living in low- and middle-income countries. While the zoonotic Cryptosporidium parvum and anthroponotic C. hominis species collectively account for most cases globally, the latter is predominant in low- and middle-income countries. Here, we present a comprehensive whole genome study of C. hominis, comprising 114 isolates from 16 countries within five continents. We detect two highly diverged lineages with a distinct biology and demography that have diverged circa 500 years ago. We consider these lineages as two subspecies, and provisionally propose the names C. hominis hominis (clade 1) and C. hominis aquapotentis (clade 2 or gp60 subtype IbA10G2). C. h. hominis is mostly found in low-income countries in Africa and Asia, and it appears to have recently undergone population contraction. In marked contrast, C. h. aquapotentis was found in high-income countries, mainly in Europe, North America and Oceania, and we reveal a signature of population expansion. Moreover, we detected genomic regions of introgression representing gene flow after a secondary contact between the subspecies from low- and high-income countries. We demonstrate that this gene flow resulted in genomic island of high diversity and divergence, and that this diversity at potential virulence genes is maintained by balancing selection, suggesting that they are involved in a coevolutionary arms race.