Multiple introductions and recombination events led to emergence of a hyper-transmissible Cryptosporidium hominis subtype in the United States
Description
Abstract: Cryptosporidium hominis is a leading cause of severe diarrhea globally. In the United States, the incidence of cryptosporidiosis has increased substantially since 2005. Here we show the newly emerged IfA12G1R5 is now the dominant C. hominis subtype. In comparative analyses of 127 newly sequenced C. hominis genomes and 95 published ones, IfA12G1R5 isolates are placed in three of 14 clusters, indicating this subtype in the United States has multiple ancestral origins. Among the three variants, Pop6 has an East Africa origin and has gone through recombination with autochthonous subtypes after its arrival. In contrast, Pop13 is imported from Europe, where it has gone through recombination with the prevalent local subtype, while Pop14 is a progeny of secondary recombination between Pop6 and Pop13. Selective sweeps in invasion-associated genes have accompanied the emergence of the dominant Pop14 variant. These observations offer insights into the emergence and evolution of hyper-transmissible pathogens.