Mining the Genome of Cryptosporidium

: Prospecting for Biomarkers

Abstract

Cryptosporidium is a protozoan parasite responsible for causing diarrhoeal disease in humans. Cryptosporidiosis is spread by contact with contaminated municipal water supplies or swimming pools, and can pose a serious health risk for individuals with weakened immune systems. This disease takes a massive toll on global public health, with over 200,000 deaths in children of less than two years old in Asia and Sub-Saharan Africa being attributed to it annually. Genomics can be a valuable asset in helping combat this parasite and the disease it causes. The primary focus of this project was to identify novel biomarkers around the genome of Cryptosporidium, using novel bioinformatics software, which can be used to furnish epidemiological surveys with high resolution data. This work necessitates generating high quality, reliable genome assemblies. Consequently, over 40 new Cryptosporidium genomes were sequenced and assembled. The biomarkers identified using these genomes provide a strong foundation upon which multiplicity of infection can be elucidated, using a novel in silico pipeline. The tools developed were designed with computational efficiency in mind, with the intention that they can be used by the Public Health Wales Cryptosporidium Reference Unit. This kind of computational efficiency was achieved, in part, by using alignment-free sequence analysis techniques to analyse raw read sets generated by Next-Generation sequencing projects, obviating the computationally intensive task of genome assembly. The results presented here shed light on the complex way this parasite is transmitted, and will facilitate the development of novel prevention strategies in the battle against Cryptosporidiosis

Date of Award	2021
Original language	English
Awarding Institution	Aberystwyth University
Sponsors	Knowledge Economy Skills Scholarships
Supervisor	Martin Swain (Supervisor), Justin Pachebat (Supervisor) & Rachel M Chalmers (Supervisor)