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

Giulia I. Corsi, Swapnil Tichkule, Anna Rosa Sannella, Paolo Vatta, Francesco Asnicar, Nicola Segata, Aaron R. Jex, Cock van Oosterhout, Simone M. Cacciò

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)2633-2645
Number of pages13
JournalMolecular Ecology
Issue number10
Early online date2 Jun 2022
Publication statusPublished - May 2023


  • Cryptosporidium parvum
  • evolution, gene flow
  • population admixture
  • recombination
  • whole genome sequencing

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