Using OMIC approaches to understand the genetic mechanisms controlling virulence in Trypanosoma brucei rhodesiense isolates

Due to the resurgence of human African trypanosomiasis (HAT), the world health organization (WHO) and various non-governmental organisations NGO’s have implemented strategies that have led to a significant drop in disease incidence, with only ~3,500 new HAT cases recorded in 2014. However the causative agent, T. brucei is still responsible for a heavy socio-economic burden, with T. brucei infections in cattle representing an estimated billion dollar loss annually. Of the two human infective T. brucei subspecies, T.b. rhodesiense is responsible for less than 3% of all HAT cases and is primarily considered a zoonosis. It causes acute disease comparative to the T.b. gambiense subspecies and two strains of differing phenotypes have been used to establish experimental infections, which reproduce the clinical manifestation observed in natural infections. This project utilized technological advances in order to understand the genetic mechanisms driving the phenotypic differences observed through the use of genomic, transcriptomic and metabolomic analysis. Firstly this work discusses the feasibility of sequencing directly from field samples by using Whatman FTA™ card and sequence capture in combination, and benchmarking the data against available whole genome sequence data. The resulting data showed both successful enrichment and lack of allelic drop out effect. This methodology was subsequently applied to multiple other strains and used to look at deleterious variants potentially giving rise to these phenotypic differences. Gross differences in the abundance of bloodstream forms in these strains were also observed, which indicated the phenotype of these strains may result from the regulation of differentiation. Transcriptomic and metabolomic data was also used to identify differential regulation driving these differences in virulence, and showed that only a small subset of genes were differentially regulated. Amongst these several candidate genes, which had previously been associated with drug resistance, were identified. Genomic and transcriptomic data also indicated that iron regulation is one of the key mechanisms driving this phenotypic change, with a high density of deleterious SNPs located in iron transport, and the greater than 10 fold increase in the expression of the transferrin receptor found in the transcriptomic data. However further analysis ideally on a larger set of strains, or SNPs derived from the entire genome rather than a subset, would be necessary to ascertain whether this is true