The use of whole genome sequencing for the analysis of isolates belonging to the bacterial genus Salmonella
<p>The global burden of disease from Salmonella infections is substantial and the increase of trade and travel across borders presented very real challenges, such as the investigation of multi-country outbreaks. The primary aim of this thesis was to examine WGS for the analysis of Salmonella,...
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| Format: | Thesis |
| Language: | English |
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2018
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| _version_ | 1797107217348952064 |
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| author | Pearce, M |
| author2 | Maiden, M |
| author_facet | Maiden, M Pearce, M |
| author_sort | Pearce, M |
| collection | OXFORD |
| description | <p>The global burden of disease from Salmonella infections is substantial and the increase of trade and travel across borders presented very real challenges, such as the investigation of multi-country outbreaks. The primary aim of this thesis was to examine WGS for the analysis of Salmonella, especially in regard to the public health applications of sequencing. A review was conducted in Chapter Two to establish the impact of whole genome sequencing on public health to date.</p>
<p>The analyses undertaken here were primarily conducted by upscaling the MLST- approach. In Chapter Three cgMLST was shown to be highly congruent with SNP-based approaches for outbreak investigations. The use of cgMLST enabled easier communication across borders as it was reference free and readily available online.</p>
<p>In Chapter Four the current core scheme was shown to be problematic for whole genus analyses. A new scheme was therefore developed and used for the identification and analysis of isolates from across the genus. This included the identification of novel subspecies and the reclassification of subspecies IIIa as a separate species – S. arizonae, as demonstrated in Chapter Five. This in turn enabled more accurate reporting of the salmonellae.</p>
<p>WGS can also be used to characterise datasets of related organisms as demonstrated through an analysis of serovar Enteritidis isolates from New South Wales, as shown in Chapter Six. This analysis identified differences between regions and countries in serovar Enteritidis strains and their AMR profiles.</p>
<p>This work provided an overview of the utility of WGS for public health purposes and expanded the current understanding of the molecular epidemiology of Salmonella.</p> |
| first_indexed | 2024-03-07T07:11:40Z |
| format | Thesis |
| id | oxford-uuid:cdd3a991-b782-49af-8fe7-042b4c5cb4db |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T07:11:40Z |
| publishDate | 2018 |
| record_format | dspace |
| spelling | oxford-uuid:cdd3a991-b782-49af-8fe7-042b4c5cb4db2022-06-30T09:35:21ZThe use of whole genome sequencing for the analysis of isolates belonging to the bacterial genus SalmonellaThesishttp://purl.org/coar/resource_type/c_db06uuid:cdd3a991-b782-49af-8fe7-042b4c5cb4dbMicrobiologySpeciationGastrointestinal systemEpidemiologySalmonellaGenomicsEnglishHyrax Deposit2018Pearce, MMaiden, MGrant, KChattaway, MAlikhan, NLangridge, GLauer, ASintchenko, VColles, FWain, J<p>The global burden of disease from Salmonella infections is substantial and the increase of trade and travel across borders presented very real challenges, such as the investigation of multi-country outbreaks. The primary aim of this thesis was to examine WGS for the analysis of Salmonella, especially in regard to the public health applications of sequencing. A review was conducted in Chapter Two to establish the impact of whole genome sequencing on public health to date.</p> <p>The analyses undertaken here were primarily conducted by upscaling the MLST- approach. In Chapter Three cgMLST was shown to be highly congruent with SNP-based approaches for outbreak investigations. The use of cgMLST enabled easier communication across borders as it was reference free and readily available online.</p> <p>In Chapter Four the current core scheme was shown to be problematic for whole genus analyses. A new scheme was therefore developed and used for the identification and analysis of isolates from across the genus. This included the identification of novel subspecies and the reclassification of subspecies IIIa as a separate species – S. arizonae, as demonstrated in Chapter Five. This in turn enabled more accurate reporting of the salmonellae.</p> <p>WGS can also be used to characterise datasets of related organisms as demonstrated through an analysis of serovar Enteritidis isolates from New South Wales, as shown in Chapter Six. This analysis identified differences between regions and countries in serovar Enteritidis strains and their AMR profiles.</p> <p>This work provided an overview of the utility of WGS for public health purposes and expanded the current understanding of the molecular epidemiology of Salmonella.</p> |
| spellingShingle | Microbiology Speciation Gastrointestinal system Epidemiology Salmonella Genomics Pearce, M The use of whole genome sequencing for the analysis of isolates belonging to the bacterial genus Salmonella |
| title | The use of whole genome sequencing for the analysis of isolates belonging to the bacterial genus Salmonella |
| title_full | The use of whole genome sequencing for the analysis of isolates belonging to the bacterial genus Salmonella |
| title_fullStr | The use of whole genome sequencing for the analysis of isolates belonging to the bacterial genus Salmonella |
| title_full_unstemmed | The use of whole genome sequencing for the analysis of isolates belonging to the bacterial genus Salmonella |
| title_short | The use of whole genome sequencing for the analysis of isolates belonging to the bacterial genus Salmonella |
| title_sort | use of whole genome sequencing for the analysis of isolates belonging to the bacterial genus salmonella |
| topic | Microbiology Speciation Gastrointestinal system Epidemiology Salmonella Genomics |
| work_keys_str_mv | AT pearcem theuseofwholegenomesequencingfortheanalysisofisolatesbelongingtothebacterialgenussalmonella AT pearcem useofwholegenomesequencingfortheanalysisofisolatesbelongingtothebacterialgenussalmonella |