The genetic basis of host range and virulence in human-infective Cryptosporidium spp.

Nader, Johanna (2017) The genetic basis of host range and virulence in human-infective Cryptosporidium spp. Doctoral thesis, University of East Anglia.

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Abstract

Cryptosporidium is a leading cause of diarrhoeal disease worldwide. 26 species and more than 70 genotypes have been characterised to date, but only two species, Cryptosporidium hominis and Cryptosporidium parvum, account for a majority of human infections. Despite a close genomic relationship between these species (>96.0% nucleotide identities) the former propagates in a predominantly anthroponotic transmission cycle, while the latter exhibits a broad zoonotic host range and appears well-adapted to both humans and cattle. Intra-C. parvum host range differences have also been demonstrated through the existence of an anthroponotic subtype commonly referred to as ‘IIc’. Using a novel dataset of diverse C. hominis and C. parvum whole genome sequences to perform comparative genomics analyses between zoonotic and anthroponotic subtypes, a number of divergent loci are herein identified that are subject to heightened polymorphism and selective pressure in both C. hominis and C. parvum subtype IIc. Glycoproteins, multi-copy gene families and secreted proteins are predominant, and the subtelomeres houses a significant majority of these highly-variable putative virulence factors. A concatenated phylogeny of novel WGS reveals the existence of an anthroponotic subspecies within the C. parvum species clade, warranting re-classification of zoonotic versus anthroponotic strains as C. parvum parvum and C. parvum anthroponosum, respectively. The concatenated phylogeny also demonstrates a hybrid-type IIcA5G3j isolate, which contains a IIc-type GP60 locus but an otherwise predominantly C. parvum parvum-type genome. Recombination analyses between this hybrid strain and two common zoonotic (IIa-type) and anthroponotic (IIc-type) C. parvum WGS and a C. hominis (Ib-type) WGS shows extensive genome-wide recombination between all of these strains, and divergence dating using recombination data reveals a relatively recent estimated time of divergence (<1,000 years ago) between these species and subspecies. Population genetics analyses of C. hominis GP60 sequences reveals inter-family disparities in allelic divergence and selective pressure, with subtype famailies Ia and Id exhibiting significantly higher rates of diversification. Evidence of a recent population expansion event is also identified for these two subtypes in C. hominis populations from Central Asia and Sub-Saharan Africa. An updated look at whole genome divergence between a ‘virulent’ Ib-type and ‘avirulent’ Ia-type C. hominis WGS reveals structural changes at the subtelomeres resulting in subtype-specific coding sequences, and identifies the location, type and degree of polymorphism and selective pressure that accompanies lineage-specific strain emergence and evolution. Finally, the development of a novel In Situ PCR/Fluorescence In Situ Hybridization technique for sensitive and specific detection of C. p. parvum oocysts is hereby presented. This demonstrates how in silico findings from preceding chapters identified a suitable subspecies-specific target, and were subsequently translated into an applied molecular method for discrimination of lineages at a subspecific level. Taken together, the results from this thesis have contributed significantly towards increasing our understanding of the genomic factors driving evolution and adaptation in human-infective Cryptosporidium spp.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School
Depositing User:	Jackie Webb
Date Deposited:	10 May 2018 07:40
Last Modified:	30 Jun 2020 00:39
URI:	https://ueaeprints.uea.ac.uk/id/eprint/66995
DOI:

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