Greta Bellinzona1, Tiago Nardi1, Michele Castelli1, Gherard Batisti Biffignandi1, Karim Adjou2, Martha Betson3, Yannick Blanchard4, Ioana Bujila5, Rachel Chalmers6,7, Rebecca Davidson8, Nicoletta D'Avino9, Tuulia Enbom10, Jacinto Gomes11, Gregory Karadjian2, Christian Klotz12, Emma Östlund13, Judith Plutzer14, Ruska Rimhanen-Finne15, Guy Robinson6,7, Anna Rosa Sannella16, Jacek Sroka17, Christen Rune Stensvold18, Karin Troell13, Paolo Vatta16, Barbora Zalewska19, Claudio Bandi20, Davide Sassera1,21 and Simone M. Cacciò16 1Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy; 2UMR BIPAR, Anses, Laboratoire de Santé Animale, INRAE, École Nationale Vétérinaire d'Alfort, 94700 Maisons-Alfort, France; 3Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, United Kingdom; 4Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Health Safety (ANSES), 22440 Ploufragan, France; 5Department of Microbiology, Public Health Agency of Sweden, SE-171 82 Solna, Sweden; 6Cryptosporidium Reference Unit, Public Health Wales, Swansea SA2 8QA, United Kingdom; 7Swansea Medical School, Swansea University, Swansea SA2 8PP, United Kingdom; 8Norwegian Veterinary Institute, N-1431 Ås, Norway; 9Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, 06126 Perugia, Italy; 10Animal Health Diagnostic Unit, Finnish Food Authority, FI-70210 Kuopio, Finland; 11National Institute for Agricultural and Veterinary Research, 1300 Lisbon, Portugal; 12Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany; 13Swedish Veterinary Agency, SE-751 89 Uppsala, Sweden; 14National Institute for Public Education, Budapest, 1007, Hungary; 15Finnish Institute for Health and Welfare, FI-00271 Helsinki, Finland; 16Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; 17Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, 24-100 Pulawy, Poland; 18Statens Serum Institut, 2300 Copenhagen, Denmark; 19Veterinary Research Institute, Department of Food and Feed Safety, 621 00 Brno, Czech Republic; 20Department of Biosciences, University of Milan, 20133 Milan, Italy; 21IRCCS Fondazione Policlinico San Matteo, 27100 Pavia, Italy Corresponding authors: davide.sasseraunipv.it, simone.caccioiss.it Abstract

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.

Footnotes

[Supplemental material is available for this article.]

Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.278830.123.

Freely available online through the Genome Research Open Access option.

Received December 11, 2023. Accepted June 5, 2024.