Using whole genome sequencing to investigate the inter-species transmission dynamics of Mycobacterium bovis

Crispell, Joseph (2017) Using whole genome sequencing to investigate the inter-species transmission dynamics of Mycobacterium bovis. PhD thesis, University of Glasgow.

Abstract

Bovine tuberculosis (bTB), a disease of cattle caused by Mycobacterium bovis, presents considerable health and economic burdens in many countries. In the United Kingdom and New Zealand, wildlife reservoirs are implicated in the spread and persistence of bTB in cattle populations. Where multi-host systems exist, understanding the roles of different host species in the spread and persistence of M. bovis infection in livestock is paramount. This thesis describes how Whole Genome Sequenced (WGS) M. bovis data can be used to investigate inter-species transmission of bTB between livestock and wildlife populations.

WGSdata must be processed before it can be used in downstream analyses. A filter sensitivity analysis was used to investigate whether the selection of quality criteria to be used in the processing of WGS data, could be informed by epidemiological data describing the sampled bTB system. WGS M. bovis data were available from three different bTB systems: in Northern Ireland, England and New Zealand. By using agreement between the genetic data, resulting from applying different quality filters, and the epidemiological data as an indication of the appropriateness of filtering, it was demonstrated that epidemiological data could inform the selection of quality criteria.

With appropriately processed WGSdata from infected cattle and wildlife in New Zealand, the role of wildlife reservoirs was investigated. In addition, the WGS data were compared to the types defined by a different molecular typing method used heavily in New Zealand until 2012. The high resolution WGS data agreed well with the previous typing method, and was used to demonstrate that inter-species transmission had occurred between the sampled cattle and wildlife populations.

The large spatial range of the data available from New Zealand made it difficult to determine the direction of inter-species transmission. In the southwest of England, Woodchester Park is home to a badger population that is naturally infected with M. bovis and living in close proximity to many cattle herds. WGS M. bovis data, for infected cattle and badgers sampled from this system, combined with detailed epidemiological data, were used to provide evidence of inter-species transmission in both directions. The sampled badger population was also shown to be acting as a maintenance reservoir for bTB.

This thesis describes how WGSdata can be used to investigate inter-species transmission, but also highlights how the underlying bTB systems must be sampled appropriately for these data to be most informative. Future work will involve addressing the limitations of the available data and the analyses conducted, as well as analysis of new data and implementation of new methods.

• Item Type: Thesis (PhD)
• Qualification Level: Doctoral
• Subjects: Q Science > QH Natural history > QH426 Genetics; Q Science > QR Microbiology
• Colleges/Schools: College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine; College of Medical Veterinary and Life Sciences > School of Life Sciences
• Funder's Name: Biotechnology and Biological Sciences Research Council (BBSRC)
• Supervisor's Name: Kao, Prof. Rowland and Zadoks, Prof. Ruth
• Date of Award: 2017
• Depositing User: Mrs Marie Cairney
• Unique ID: glathesis:2017-8254
• Copyright: Copyright of this thesis is held by the author.
• Date Deposited: 07 Jun 2017 09:58
• Last Modified: 05 Feb 2025 14:01
• Thesis DOI: 10.5525/gla.thesis.8254
• URI: https://theses.gla.ac.uk/id/eprint/8254