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

Abstract

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 humanand 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.

Sympatric Recombination in Zoonotic Cryptosporidium Leads to Emergence of Populations with Modified Host Preference

“…Within Europe, Sweden is known to have a high occurrence of both IIa and IId subtypes in humans and cattle ( Lebbad et al 2021 ). Interestingly, several recently published C. parvum genomes from Italy and Slovenia, including IT-C395 (IIaA18R1), IT-C366 (IIdA17G2R1), and Slo4 (IIaA20G1R1), clustered with UKP8, supporting the conclusion from the present study ( Corsi et al 2022 ). In these European countries, IId subtypes are mainly seen in small ruminants ( Guo et al 2021 ; Lebbad et al 2021 ).…”

Analysis of genetic diversity and population structure of Babesia gibsoni

“…Gene flow is a driving force in the evolution of populations, which can increase the genetic diversity within populations but decrease the genetic difference between populations ( 58 , 59 ). In this study, the majority of genetic variation in Asia (99.55%) and the three continents (97.90%) were partitioned within populations, implying a high gene flow among these populations as found in other species such as Cryptosporidium parvum, Giardia duodenalis , and H. canis ( 27 , 60 , 61 ). High gene flow was also supported by the low pairwise Fst values, revealing that low genetic differentiation was found between the populations.…”

Conservation, abundance, glycosylation profile, and localization of the TSP protein family in Cryptosporidium parvum

“…Raw sequencing reads of 32 C. parvum genomes ( 60 , 61 , 62 ) were retrieved from the European Nucleotide Archive repository; filtered low-quality bases and trimmed adapters using Trimmomatic v.0.36 ( 63 ) and mapped to the C. parvum IOWA-ATCC reference genome ( 64 ) using BWA-MEM v.0.7 ( 65 ). SNPs were identified based on the variant calling protocol described in the study by Tichkule et al.…”