Exploring the ‘Nemabiome’: Deep Amplicon Sequencing to Investigate Community Structure and Drug Resistance in Parasitic Gastrointestinal Nematodes of Livestock
Creators: name: Avramenko, Russell
Publisher: name: Graduate Studies
Year: 2018
Subjects: subject: Nematode
subject: Nemabiome
subject: next-generation sequencing
subject: anthelmintic resistance
subject: deep-amplicon sequencing
subject: Cooperia
subject: Haemonchus
subject: Trichostrongylus
subject: Ostertagia ostertagi
subject: Bioinformatics
subject: FOS: Computer and information sciences
subject: Genetics
subject: FOS: Biological sciences
subject: Biology--Molecular
subject: Parasitology
subject: Veterinary Science
subject: Epidemiology

description: Parasitic gastrointestinal nematodes are one of the most important pathogen groups impacting livestock health, welfare and production worldwide. Control in both animals and humans is heavily dependent on the prophylactic administration of anthelmintic drugs. However, there are widespread and increasing reports of anthelmintic drug resistance in many parasitic nematode species making current approaches to control unsustainable. Consequently, there is an urgent need for better tools for diagnosis, surveillance and research to support the development of sustainable approaches to parasite control. Although co-infection with multiple nematode species within a single host is common, there are few tools with which to study the composition of these complex parasite communities. Nematode species vary in their pathogenicity, epidemiology and drug sensitivity and the interactions that occur between co-infecting species and their hosts are poorly understood. This thesis introduces the concept of the ‘nemabiome’ as the community of mixed nematode species inhabiting the gastrointestinal tract of the host. Chapter 2 presents the development of a deep-amplicon (metabarcoding) sequencing approach, targeting the ITS-2 rDNA locus, to define the species composition of the nemabiome. This approach is analogous to deep-amplicon sequencing methodologies used to study the bacterial ‘microbiome’. Chapter 3 uses this methodology to assess the species composition of nematode communities in cattle from Canada, the United States and Brazil. It also describes changes in the nemabiome before and after anthelmintic treatment in Canadian cattle. Chapter 4 illustrates the ability of this approach to describe the nemabiome of commercial and conservation bison herds in western Canada, which previously had little information regarding species prevalence. Chapter 5 introduces another deep-amplicon sequencing application; screening for DNA sequence polymorphisms associated with benzimidazole drug resistance in mixed nematode infections. The isotype-1 β-tubulin locus is screened for three polymorphisms associated with benzimidazole resistance. Chapter 6 describes the application of this approach to screen for benzimidazole resistance associated polymorphisms in the cattle and bison parasite populations characterised in Chapters 3 and 4. These approaches represent vital tools needed to conduct epidemiological studies, surveillance of parasite species, improve the sensitivity of drug efficacy testing and assess anthelmintic resistance on a large scale.