The zoonotic parasite Cryptosporidium parvum is a global cause of gastrointestinal disease in humans and ruminants. Sequence analysis of the highly polymorphic gp60 gene enabled the classification of C. parvum isolates into multiple groups (e.g., IIa, IIc, Id) and a large number of subtypes. In Europe, subtype IIaA15G2R1 is largely predominant and has been associated with many water- and food-borne outbreaks. In this study, we generated new whole-genome sequence (WGS) data from 123 human- and ruminant-derived isolates collected in 13 European countries and included other available WGS data from Europe, Egypt, China, and the United States (n = 72) in the largest comparative genomics study to date. We applied rigorous filters to exclude mixed infections and analyzed a data set from 141 isolates from the zoonotic groups IIa (n = 119) and IId (n = 22). Based on 28,047 high-quality, biallelic genomic SNPs, we identified three distinct and strongly supported populations: Isolates from China (IId) and Egypt (IIa and IId) formed population 1; a minority of European isolates (IIa and IId) formed population 2; and the majority of European (IIa, including all IIaA15G2R1 isolates) and all isolates from the United States (IIa) clustered in population 3. Based on analyses of the population structure, population genetics, and recombination, we show that population 3 has recently emerged and expanded throughout Europe to then, possibly from the United Kingdom, reach the United States, where it also expanded. The reason(s) for the successful spread of population 3 remain elusive, although genes under selective pressure uniquely in this population were identified.

Animal Health Diagnostic Unit Finnish Food Authority FI 70210 Kuopio Finland

Cryptosporidium Reference Unit Public Health Wales Swansea SA2 8QA United Kingdom

Department of Biology and Biotechnology University of Pavia 27100 Pavia Italy

Department of Biology and Biotechnology University of Pavia 27100 Pavia Italy;

Department of Biosciences University of Milan 20133 Milan Italy

Department of Comparative Biomedical Sciences School of Veterinary Medicine University of Surrey Guildford GU2 7AL United Kingdom

Department of Infectious Diseases Istituto Superiore di Sanità 00161 Rome Italy

Department of Infectious Diseases Istituto Superiore di Sanità 00161 Rome Italy;

Department of Infectious Diseases Robert Koch Institute 13353 Berlin Germany

Department of Microbiology Public Health Agency of Sweden SE 171 82 Solna Sweden

Department of Parasitology and Invasive Diseases National Veterinary Research Institute 24 100 Pulawy Poland

Finnish Institute for Health and Welfare FI 00271 Helsinki Finland

IRCCS Fondazione Policlinico San Matteo 27100 Pavia Italy

Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche 06126 Perugia Italy

National Institute for Agricultural and Veterinary Research 1300 Lisbon Portugal

National Institute for Public Education Budapest 1007 Hungary

Norwegian Veterinary Institute N 1431 Ås Norway

Statens Serum Institut 2300 Copenhagen Denmark

Swansea Medical School Swansea University Swansea SA2 8PP United Kingdom

Swedish Veterinary Agency SE 751 89 Uppsala Sweden

UMR BIPAR Anses Laboratoire de Santé Animale INRAE École Nationale Vétérinaire d'Alfort 94700 Maisons Alfort France

Veterinary Research Institute Department of Food and Feed Safety 621 00 Brno Czech Republic

Viral Genetics and Biosecurity Unit 22440 Ploufragan France

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