Files
Abstract
Cryptosporidium is a diverse genus of parasites that causes severe diarrhea, particularly in infants and immunocompromised individuals in low- to middle-income countries. Due to the challenges of obtaining sufficient pure parasites, the genomic diversity of Cryptosporidium species remains poorly understood. Furthermore, there is evidence of multiple subtypes within a single population. This increases the likelihood of genomic recombination events, further contributing to this parasite's complex diversity. This dissertation explores the challenges hindering research on Cryptosporidium diversity and proposes potential solutions.The first chapter reviews the current knowledge, advances, and applications of genomics in Cryptosporidium research. Although progress has been made in genomic research, approximately 50% of the Cryptosporidium genomic assemblies in the National Center for Biotechnology Information (NCBI) database consist of only two species. The second chapter evaluates Multiple Displacement Amplification (MDA) in association with whole-genome Oxford Nanopore Technology (ONT) sequencing. I assessed its efficiency with varying DNA inputs and sequencing output. ONT rapid libraries were successfully generated from starting DNA inputs as low as 0.025 ng using MDA.
Considering the evidence of mixed infections, the third chapter assesses recombination events within samples from a single host. Single oocysts from a mouse model infected with C. parvum and C. tyzzeri were sequenced and analyzed. Despite the limited breadth of coverage in the single oocyst assembly, recombination events were identified, indicating genetic exchange between species or subtypes during mixed infection.
In Chapter 4, I conducted a comparative genomic analysis of whole-genome SNP data from Cryptosporidium parvum SRA datasets, revealing two major clades: Africa–China and Europe–USA, with minimal differentiation between the latter. Chinese samples (subtype IId) were highly clonal, while African samples showed divergent subgroups and possible gene flow. Samples from the USA showed signatures suggesting recent introduction from Europe, whereas European populations were diverse and recombining. Positive selection signals on chromosome 6, in Africa–USA comparisons, identified genes linked to host and environmental adaptation. These findings highlight the role of geography and evolution in shaping C. parvum diversity and provide a framework for surveillance and control.