Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum

Corsi, Giulia I., Tichkule, Swapnil, Sannella, Anna Rosa, Vatta, Paolo, Asnicar, Francesco, Segata, Nicola, Jex, Aaron R., van Oosterhout, Cock ORCID: and Cacciò, Simone M. (2023) Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum. Molecular Ecology, 32 (10). pp. 2633-2645. ISSN 0962-1083

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Cryptosporidium parvum is a globally distributed zoonotic pathogen and a major cause of diarrhoeal disease in humans and ruminants. The parasite's life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur between previously isolated lineages. Here, we compare 32 whole genome sequences from human- and ruminant-derived parasite isolates collected across Europe, Egypt and China. We identify three strongly supported clusters that comprise a mix of isolates from different host species, geographic origins, and subtypes. We show that: (1) recombination occurs between ruminant isolates into human isolates; (2) these recombinant regions can be passed on to other human subtypes through gene flow and population admixture; (3) there have been multiple genetic exchanges, and most are probably recent; (4) putative virulence genes are significantly enriched within these genetic exchanges, and (5) this results in an increase in their nucleotide diversity. We carefully dissect the phylogenetic sequence of two genetic exchanges, illustrating the long-term evolutionary consequences of these events. Our results suggest that increased globalization and close human-animal contacts increase the opportunity for genetic exchanges between previously isolated parasite lineages, resulting in spillover and spillback events. We discuss how this can provide a novel substrate for natural selection at genes involved in host–parasite interactions, thereby potentially altering the dynamic coevolutionary equilibrium in the Red Queens arms race.

Item Type: Article
Additional Information: Funding Information: This work was supported by the project “Collaborative management platform for detection and analyses of (re-) emerging and foodborne outbreaks in Europe” (COMPARE,, which has received funding from the European Union‘s Horizon 2020 research and innovation programme under grant agreement no. 643476 to S.M.C. A.R.J was funded through an Australian National Health and Medical Research Council Leadership grant (APP1194330). The Walter and Eliza Hall Institute of Medical Research receives support through the Victorian State Government Operational Infrastructure Support and Australian Government National Health and Medical Research Council Independent Research Institute Infrastructure Support Scheme. S.T. was supported by Walter and Eliza Hall International PhD Scholarship and Melbourne Research Scholarship (MRS).
Uncontrolled Keywords: cryptosporidium parvum,evolution, gene flow,population admixture,recombination,whole genome sequencing,ecology, evolution, behavior and systematics,genetics,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1100/1105
Faculty \ School: Faculty of Science > School of Environmental Sciences
UEA Research Groups: Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation
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Depositing User: LivePure Connector
Date Deposited: 07 May 2024 10:31
Last Modified: 07 May 2024 10:31
DOI: 10.1111/mec.16556


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