Genetic recombination plays a critical role in the emergence of pathogens with phenotypes such as drug resistance, virulence, and host adaptation. Here, we tested the hypothesis that recombination between sympatric ancestral populations leads to the emergence of divergent variants of the zoonotic parasite Cryptosporidium parvum with modified host ranges. Comparative genomic analyses of 101 isolates have identified seven subpopulations isolated by distance. They appear to be descendants of two ancestral populations, IIa in northwestern Europe and IId from southwestern Asia. Sympatric recombination in areas with both ancestral subtypes and subsequent selective sweeps have led to the emergence of new subpopulations with mosaic genomes and modified host preference. Subtelomeric genes could be involved in the adaptive selection of subpopulations, while copy number variations of genes encoding invasion-associated proteins are potentially associated with modified host ranges. These observations reveal ancestral origins of zoonotic C. parvum and suggest that pathogen import through modern animal farming might promote the emergence of divergent subpopulations of C. parvum with modified host preference.

Center for Epidemiology and Animal Health Veterinary Services Animal and Plant Health Inspection Service US Department of Agriculture Fort Collins CO USA

Department of Hygiene and Zoonoses Faculty of Veterinary Medicine Mansoura University Mansoura Egypt

Division of Foodborne Waterborne and Environmental Diseases Centers for Disease Control and Prevention Atlanta GA USA

Environmental Microbial and Food Safety Laboratory Beltsville Agricultural Research Center Agricultural Research Service US Department of Agriculture Beltsville MD USA

Guangdong Laboratory for Lingnan Modern Agriculture Center for Emerging and Zoonotic Diseases College of Veterinary Medicine South China Agricultural University Guangzhou China

Institute of Parasitology Biology Centre of the Czech Academy of Sciences Ceske Budejovice Czech Republic

State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing China

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Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States