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Global investigation into the population genetic structure of Ciyptosporidium hominis based on a whole genome multi-locus SNP-typing scheme; inferences about the existence of biogeographical partitions Williamson, Jill Marie

Abstract

Previously considered a disease of importance strictly to veterinary medicine Cryptosporidium has emerged as a highly successful opportunistic parasitic protozoan posing a significant threat to public health. Intricate transmission dynamics, a complex epidemiology, and parasite robustness and persistence have all hampered efforts for the prevention and control of Cryptosporidium. Genetic diversity is a prerequisite to better understand the role of parasite variation in disease etiology and pathobiology. The extent of genetic structure among C. hominis and C. parvum, the two most prevalent species of Ciyptosporidium, is insufficiently understood with the population structure still largely suspect. We report on the distribution of genetic diversity and possible existence of geographic partitions among C. hominis subpopulations from Australia, Kenya, Peru and Scotland. We studied C. hominis population genetic structure using a multi-locus SNP-type (M1St) established from 45 single nucleotide polymorphic loci covering 13 bio-functionally relevant proteins. A total of 77 isolates from 4 intercontinental subpopulations were genetically typed. Twenty-four unique M1St’s were identified, 25% of which were found to be located within one or more subpopulations. Diversity statistical tests to discern the degree of ultrapopulation and inter-population diversity, genetic distance, and genetic identity variation were used to examine the population genetic structure. Within-population differences among subpopulations account for 69.6% of genetic variation; differentiation among subpopulations constitute 30.4%. Genetic distances among subpopulations averaged 0.048 and varied from 0.03 4 between the Australian and Scotland subpopulations to 0.061 between Scotland and Kenya. More broadly, our results argue that too wide of a geographic boundary can impede rather than advance genetic population studies and that the practice of sampling more regional subpopulations be adopted. A fifth subpopulation, a combination of C. hominis and C. parvum isolates, was drawn upon to determine whether or not a pre-defined allelic profile of single nucleotide polymorphisms (SNPs) was an efficient and reliable means for species specific identification. Results showed the SNP-typing approach’s ability to distinguish between different species as well as being capable of uncovering potential novel SNPs within an individual isolate. We propose that the patterns of genetic variation are influenced by geography and that the identification of host adapted geographically conserved sub-genotypes within a defined geographic cohort versus widespread dissemination of genetically stable isolates could ultimately provide a valuable basis for the predictive epidemiology of Cryptosporidiwn infection. Our fmdings provide an alternative method for species detection, a crucial element to epidemiological investigations.

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