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Title: Use of whole genome sequencing in understanding transmission dynamics of tuberculosis
Author: Jones, Rhys C.
ISNI:       0000 0004 7431 6489
Awarding Body: Swansea University
Current Institution: Swansea University
Date of Award: 2018
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Mycobacterium tuberculosis is the leading cause of death from an infectious disease worldwide. An understanding of tuberculosis transmission dynamics in outbreak settings is vital for its control. The advent of affordable whole genome sequencing (WGS) has provided scope for superior resolution of tuberculosis outbreaks, compared to previous methods. However, the challenge lies in standardising the vast quantities of resulting data in a structured manner which lends itself to easy comparison of isolates. Gene-by-gene Multi-Locus Sequence Typing (MLST) methods of analysing WGS data, as opposed to Single Nucleotide Polymorphism (SNP) mapping, have shown promise in providing a uniform platform for outbreak resolution. WGS was performed on clinical isolates from three M. tuberculosis outbreaks in South West Wales. Molecular typing by MIRU-VNTR and epidemiological investigation had resulted in conflicting conclusions. Outbreak analysis and phylogenetic typing of all isolates was carried out using the WGS gene-by-gene MLST analysis method of core genome MLST (cgMLST) and traditional WGS SNP mapping. Where DNA quality was unsatisfactory, an ancient DNA library preparation was used successfully. Provean and BEAST software analysis provided physiological information and ancestral dating respectively on outbreak isolates. WGS successfully resolved all three outbreaks, with cgMLST providing clear conclusions across each outbreak. Traditional SNP mapping provided greater resolution than cgMLST in one outbreak. Ancestral dating also proved useful in understanding the outbreaks. Phylogenetically, the dataset was dominated by Euro-American lineage strains, providing the first snapshot of tuberculosis diversity within Wales. Provean analysis identified physiological features in isolates worthy of future research. In summary, WGS was successfully used to resolve three M. tuberculosis outbreaks across South West Wales and correlated better with the epidemiological data than molecular typing by MIRU-VNTR had done. The study highlighted the dominance of the Euro-American lineage within the outbreaks and included the first use of ancient DNA library preparation in a clinical outbreak.
Supervisor: Davies, Angharad ; Harris, Llinos ; Humphrey, Tomas Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral