Exploring the ‘Nemabiome’: Deep Amplicon Sequencing to Investigate Community Structure and Drug Resistance in Parasitic Gastrointestinal Nematodes of Livestock

Simple item page
dc.contributor.advisorGilleard, John
dc.contributor.authorAvramenko, Russell
dc.contributor.committeememberColwell, Douglas
dc.contributor.committeememberDe Buck, Jeroen
dc.contributor.committeememberWasmuth, James
dc.date2018-02-16
dc.date.accessioned2018-01-25T19:16:48Z
dc.date.available2018-01-25T19:16:48Z
dc.date.issued2018-01-12
dc.description.abstractParasitic 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.en_US
dc.identifier.citationAvramenko, R. W. (2018). Exploring the ‘Nemabiome’: Deep Amplicon Sequencing to Investigate Community Structure and Drug Resistance in Parasitic Gastrointestinal Nematodes of Livestock (Doctoral thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca. doi:10.11575/PRISM/5420en_US
dc.identifier.doihttp://dx.doi.org/10.11575/PRISM/5420
dc.identifier.urihttp://hdl.handle.net/1880/106339
dc.language.isoeng
dc.publisher.facultyGraduate Studies
dc.publisher.facultyVeterinary Medicine
dc.publisher.institutionUniversity of Calgaryen
dc.publisher.placeCalgaryen
dc.rightsUniversity of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.
dc.subjectNematode
dc.subjectNemabiome
dc.subjectnext-generation sequencing
dc.subjectanthelmintic resistance
dc.subjectdeep-amplicon sequencing
dc.subjectCooperia
dc.subjectHaemonchus
dc.subjectTrichostrongylus
dc.subjectOstertagia ostertagi
dc.subject.classificationBioinformaticsen_US
dc.subject.classificationGeneticsen_US
dc.subject.classificationBiology--Molecularen_US
dc.subject.classificationParasitologyen_US
dc.subject.classificationVeterinary Scienceen_US
dc.subject.classificationEpidemiologyen_US
dc.titleExploring the ‘Nemabiome’: Deep Amplicon Sequencing to Investigate Community Structure and Drug Resistance in Parasitic Gastrointestinal Nematodes of Livestock
dc.typedoctoral thesis
thesis.degree.grantorUniversity of Calgary
thesis.degree.nameDoctor of Philosophy (PhD)
ucalgary.item.requestcopytrue
ucalgary.thesis.checklistI confirm that I have submitted all of the required forms to Faculty of Graduate Studies.en_US
Files
Original bundle
Now showing 1 - 5 of 5
Thumbnail Image
Name:
ucalgary_2018_avramenko_russell.pdf
Size:
14.9 MB
Format:
Adobe Portable Document Format
Description:
Thesis
Download
No Thumbnail Available
Name:
ucalgary_2018_avramenko_russell_appendixc.fasta
Size:
685.32 KB
Format:
Unknown data format
Description:
Appendix C
Download
No Thumbnail Available
Name:
ucalgary_2018_avramenko_russell_appendixd.fasta
Size:
797.68 KB
Format:
Unknown data format
Description:
Appendix D
Download
No Thumbnail Available
Name:
ucalgary_2018_avramenko_russell_appendixe.fasta
Size:
237.21 KB
Format:
Unknown data format
Description:
Appendix E
Download
No Thumbnail Available
Name:
ucalgary_2018_avramenko_russell_appendixf.fasta
Size:
4.84 KB
Format:
Unknown data format
Description:
Appendix F
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.74 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Open Theses and Dissertations