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

Zobrazit více v PubMed

Alves M, Xiao L, Sulaiman I, Lal AA, Matos O, Antunes F. 2003. Subgenotype analysis of PubMed DOI PMC

Baptista RP, Li Y, Sateriale A, Sanders MJ, Brooks KL, Tracey A, Ansell BRE, Jex AR, Cooper GW, Smith ED, et al. 2022. Long-read assembly and comparative evidence-based reanalysis of PubMed DOI PMC

Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, et al. 2021. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife 10: e65088. 10.7554/eLife.65088 PubMed DOI PMC

Beja-Pereira A, Caramelli D, Lalueza-Fox C, Vernesi C, Ferrand N, Casoli A, Goyache F, Royo LJ, Conti S, Lari M, et al. 2006. The origin of European cattle: evidence from modern and ancient DNA. Proc Natl Acad Sci 103: 8113–8118. 10.1073/pnas.0509210103 PubMed DOI PMC

Bhalchandra S, Cardenas D, Ward HD. 2018. Recent breakthroughs and ongoing limitations in PubMed DOI PMC

Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114–2120. 10.1093/bioinformatics/btu170 PubMed DOI PMC

Bowling GA. 1942. The introduction of cattle into colonial North America. J Dairy Sci 25: 129–154. 10.3168/jds.S0022-0302(42)95275-5 DOI

Braima K, Zahedi A, Oskam C, Reid S, Pingault N, Xiao L, Ryan U. 2019. Retrospective analysis of PubMed DOI

Cacciò SM, Chalmers RM. 2016. Human cryptosporidiosis in Europe. Clin Microbiol Infect 22: 471–480. 10.1016/j.cmi.2016.04.021 PubMed DOI

Chavez MA, White C Jr. 2018. Novel treatment strategies and drugs in development for cryptosporidiosis. Expert Rev Anti Infect Ther 16: 655–661. 10.1080/14787210.2018.1500457 PubMed DOI

Chessa B, Pereira F, Arnaud F, Amorim A, Goyache F, Mainland I, Kao RR, Pemberton JM, Beraldi D, Stear MJ, et al. 2009. Revealing the history of sheep domestication using retrovirus integrations. Science 324: 532–536. 10.1126/science.1170587 PubMed DOI PMC

Corsi GI, Tichkule S, Sannella AR, Vatta P, Asnicar F, Segata N, Jex AR, van Oosterhout C, Cacciò SM. 2023. Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen PubMed DOI

Csardi G, Nepusz T. 2006. The igraph software package for complex network research. InterJournal, Complex Systems: 1695. https://igraph.org.

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, et al. 2011. The variant call format and VCFtools. Bioinformatics 27: 2156–2158. 10.1093/bioinformatics/btr330 PubMed DOI PMC

Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, et al. 2021. Twelve years of SAMtools and BCFtools. GigaScience 10: giab008. 10.1093/gigascience/giab008 PubMed DOI PMC

Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B, Flouri T. 2020. ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Mol Biol Evol 37: 291–294. 10.1093/molbev/msz189 PubMed DOI PMC

Delsol N, Stucky BJ, Oswald JA, Cobb CR, Emery KF, Guralnick R. 2023. Ancient DNA confirms diverse origins of early post-Columbian cattle in the Americas. Sci Rep 13: 12444. 10.1038/s41598-023-39518-3 PubMed DOI PMC

DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491–498. 10.1038/ng.806 PubMed DOI PMC

Dumaine JE, Sateriale D, Gibson AR, Reddy AG, Gullicksrud JA, Hunter EN, Clark JT, Striepen B. 2021. The enteric pathogen PubMed DOI PMC

Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792–1797. 10.1093/nar/gkh340 PubMed DOI PMC

Emms DM, Kelly S. 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 20: 238. 10.1186/s13059-019-1832-y PubMed DOI PMC

Feng Y, Li N, Roellig DM, Kelley A, Liu G, Amer S, Tang K, Zhang L, Xiao L. 2017. Comparative genomic analysis of the IId subtype family of PubMed DOI PMC

Feng Y, Ryan UM, Xiao L. 2018. Genetic diversity and population structure of PubMed DOI

Ficek RE. 2019. Cattle, capital, colonization. tracking creatures of the Anthropocene in and out of human projects. Current Anthropol 60: S260–S271. 10.1086/702788 DOI

Garcia-R JC, Hayman DTS. 2016. Origin of a major infectious disease in vertebrates: the timing of PubMed DOI

Gruber-Vodicka HR, Seah BKB, Pruesse E. 2020. phyloFlash: rapid small-subunit rRNA profiling and targeted assembly from metagenomes. mSystems 5: e00920-20. 10.1128/mSystems.00920-20 PubMed DOI PMC

Guo Y, Ryan U, Feng Y, Xiao L. 2022. Association of common zoonotic pathogens with concentrated animal feeding operations. Front Microbiol 12: 810142. 10.3389/fmicb.2021.810142 PubMed DOI PMC

Hadfield SJ, Pachebat JA, Swain MT, Robinson G, Cameron S, Alexander J, Hegarty MJ, Elwin K, Chalmers RM. 2015. Generation of whole genome sequences of new PubMed DOI PMC

Hemstrom W, Jones M. 2023. snpR: user friendly population genomics for SNP data sets with categorical metadata. Mol Ecol Res 23: 962–973. 10.1111/1755-0998.13721 PubMed DOI

Hijjawi N, Zahedi A, Al-Falah M, Ryan U. 2022. A review of the molecular epidemiology of PubMed DOI

Huang W, Guo Y, Lysen C, Wang Y, Tang K, Seabolt MH, Yang F, Cebelinski E, Gonzalez-Moreno O, Hou T, et al. 2023. Multiple introductions and recombination events underlie the emergence of a hyper-transmissible PubMed DOI PMC

Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254–267. 10.1093/molbev/msj030 PubMed DOI

Innes EA, Chalmers RM, Wells B, Pawlowic MC. 2020. A one health approach to tackle cryptosporidiosis. Trends Parasitol 36: 290–303. 10.1016/j.pt.2019.12.016 PubMed DOI PMC

Jann HW, Cabral-Castro MG, Barreto Costa JV, de Barros Alencar ACM, Peralta JM, Saramago Peralta RE. 2022. Prevalence of human cryptosporidiosis in the Americas: systematic review and meta-analysis. Rev Inst Med Trop Sao Paulo 64: e70. 10.1590/S1678-9946202264070 PubMed DOI PMC

Khalil IA, Troeger C, Rao PC, Blacker BF, Brown A, Brewer TG, Colombara DV, De Hostos EL, Engmann C, Guerrant RL, et al. 2018. Morbidity, mortality, and long-term consequences associated with diarrhoea from PubMed DOI PMC

Khan SM, Witola WH. 2023. Past, current, and potential treatments for cryptosporidiosis in humans and farm animals: a comprehensive review. Front Cell Infect Microbiol 13: 1115522. 10.3389/fcimb.2023.1115522 PubMed DOI PMC

Kotloff KL, Nataro JP, Blackwelder WC, Nasrin D, Farag TH, Panchalingam S, Wu Y, Sow SO, Sur D, Breiman RF, et al. 2013. Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the global enteric multicenter study, GEMS): a prospective, case-control study. Lancet 382: 209–222. 10.1016/S0140-6736(13)60844-2 PubMed DOI

Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357–359. 10.1038/nmeth.1923 PubMed DOI PMC

Long S, Anthony B, Drewry LL, Sibley LD. 2017. A conserved Ankyrin repeat-containing protein regulates conoid stability, motility and cell invasion in PubMed DOI PMC

Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G, O'Brien J, Djimde A, Doumbo O, Zongo I, et al. 2012. Analysis of PubMed DOI PMC

Martin DP, Murrell B, Golden M, Khoosal A, Muhire B. 2015. RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol 1: vev003. 10.1093/ve/vev003 PubMed DOI PMC

Mathur V, Wakeman KC, Keeling PJ. 2021. Parallel functional reduction in the mitochondria of apicomplexan parasites. Curr Biol 31: 2920–2928. 10.1016/j.cub.2021.04.028 PubMed DOI

McKerr C, O'Brien SJ, Chalmers RM, Vivancos R, Christley RM. 2018. Exposures associated with infection with PubMed DOI PMC

McTavish EJ, Decker JE, Schnabel RD, Taylor JF, Hillis DH. 2013. New World cattle show ancestry from multiple independent domestication events. Proc Natl Acad Sci 110: E1398–E1406. 10.1073/pnas.1303367110 PubMed DOI PMC

Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM, et al. 2015. Gene-wide identification of episodic selection. Mol Biol Evol 32: 1365–1371. 10.1093/molbev/msv035 PubMed DOI PMC

Nader JL, Mathers TC, Ward BJ, Pachebat JA, Swain MT, Robinson G, Chalmers RM, Hunter PR, van Oosterhout C, Tyler KM. 2019. Evolutionary genomics of anthroponosis in PubMed DOI

Nash JHE, Robertson J, Elwin K, Chalmers RA, Kropinski AM, Guy RA. 2018. Draft genome assembly of a potentially zoonotic PubMed DOI PMC

Peake L, Inns T, Jarvis C, King G, Rabie H, Henderson J, Wensley A, Jarratt R, Roberts C, Williams C, et al. 2023. Preliminary investigation of a significant national PubMed DOI PMC

Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945–959. 10.1093/genetics/155.2.945 PubMed DOI PMC

Puiu D, Enomoto S, Buck GA, Abrahamsen MS, Kissinger JC. 2004. CryptoDB: the PubMed DOI PMC

Rahman SU, Mi R, Zhou S, Gong H, Ullah M, Huang Y, Han X, Chen Z. 2022. Advances in therapeutic and vaccine targets for PubMed DOI

R Core Team. 2021. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. https://www.R-project.org/.

Ryan U, Xiao L, Read C, Zhou L, Lal AA, Pavlasek I. 2003. Identification of novel PubMed DOI PMC

Ryan UM, Feng Y, Fayer R, Xiao L. 2021a. Taxonomy and molecular epidemiology of PubMed DOI

Ryan U, Zahed A, Feng Y, Xiao L. 2021b. An update on zoonotic PubMed DOI PMC

Schaffner SF, Taylor AR, Wong W, Wirth DF, Neafsey DE. 2018. hmmIBD: software to infer pairwise identity by descent between haploid genotypes. Malaria J 17: 196. 10.1186/s12936-018-2349-7 PubMed DOI PMC

Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312–1313. 10.1093/bioinformatics/btu033 PubMed DOI PMC

Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B. 2006. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res 34: W435–W439. 10.1093/nar/gkl200 PubMed DOI PMC

Straschil U, Talman AM, Ferguson DJP, Bunting KA, Xu Z, Bailes E, Sinden RE, Holder AA, Smith EF, Coates JC, et al. 2010. The Armadillo repeat protein pf16 is essential for flagellar structure and function in PubMed DOI PMC

Troell K, Hallström B, Divne A, Alsmark C, Arrighi R, Huss M, Beser J, Bertilsson S. 2016. PubMed DOI PMC

Tůmová L, Ježková J, Prediger J, Holubová N, Sak B, Konečný R, Květoňová D, Hlásková L, Rost M, McEvoy J, et al. 2023. PubMed DOI PMC

Van der Auwera GA, Connor O, DB. 2020. Genomics in the cloud: using docker, GATK, and WDL in terra. O'Reilly Media, Sebastopol, CA.

Wang R, Zhang L, Axén C, Bjorkman C, Jian F, Amer S, Liu A, Feng Y, Li G, Lv C, et al. 2014. PubMed DOI PMC

Wang T, Guo Y, Roellig DM, Li N, Santín M, Lombard J, Kváč M, Naguib D, Zhang Z, Feng Y, et al. 2022. Sympatric recombination in zoonotic PubMed DOI PMC

Wick R, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13: e1005595. 10.1371/journal.pcbi.1005595 PubMed DOI PMC

Wickham H. 2016. ggplot2: elegant graphics for data analysis. Springer, Cham, Switzerland.

Xu Z, Guo Y, Roellig DM, Feng Y, Xiao L. 2019. Comparative analysis reveals conservation in genome organization among intestinal PubMed DOI PMC

Zahedi A, Ryan U. 2020. PubMed DOI

Zhang C, Dong S, Xu J, He W, Yang T. 2019. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics 35: 1786–1788. 10.1093/bioinformatics/bty875 PubMed DOI