EASTBIO - Genomic analysis of Salmonella Blackisle including small colony variants

Funding

This 4-year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. This opportunity is open to UK and International students and provides funding to cover tuition fees at the UK rate, plus a stipend to support living costs.

The proportion of international students appointed through the EASTBIO DTP is capped at 30% by UKRI BBSRC. All students must meet the eligibility criteria as outlined in the UKRI guidance at UKRI Training Grant Terms and Conditions, esp. TGC 5.2 & Annex B. Please contact [Email Address Removed] if you are unsure of your fee status.

The Project

Salmonella is a genus of bacteria that are generally found in the enteric tract where they can cause enteritis and food poisoning. 

Salmonella enterica subsp. enterica serovar Blackisle (S. Blackisle) is a monophasic group B Salmonella that is host-adapted to harbour porpoises (Phocoena phocoena). There are several striking features of S. Blackisle that are unusual compared with other Salmonella enterica serovars. 

Salmonella Blackisle is detected, primarily in pulmonary tissues of harbour porpoises, though it has been recovered, less frequently, from the intestine and other body tissues, including septicaemic distribution. Furthermore, metabolic reactions of Salmonella Blackisle are atypical in comparison with those of most other Salmonella enterica serovars, with negative results for many biochemical tests, making identification using both commercial and in-house identification schemes, challenging to the unwary. 

Harbour porpoises are frequently infested with parasitic lungworm nematodes, and it was initially postulated that these parasites may act as a potential transmission vector, carrying Salmonella to lung tissue. There is a single report of the recovery of S. Blackisle from Pseudalius inflexus lungworms collected from the lung of a harbour porpoise carcase and molecular detection of P. inflexus from European plaice has been documented suggesting that this fish may act as an intermediate host. 

Recently, 16SrRNA sequencing has identified small colony variants of S. Blackisle, that have even fewer positive biochemical reactions than obtained with previous isolates of the serovar. Moreover, these small colony variants fail to agglutinate Salmonella antisera in slide agglutination tests. In some animals, small colony variants have been the only S. Blackisle colonies recovered from lung or other specific tissues, while in others, culture of individual tissues has resulted in growth of both colony types on the same culture plate. Each of the respective colony types retain their own characteristic colonial appearance, upon sub-culture. 

Like many bacteria, Salmonella interacts with bacteriophages (viruses which specifically infect bacteria) in a plethora of ways with concomitant impacts of either a lysis and release of amplified viral progeny by virulent phages or integration into the host bacterial chromosome by temperate phages. The integrated temperate phage (prophage) can facilitate the transfer of antibiotic resistance genes and virulence factors which influence the ecological fitness, physiology, diversity, evolution and pathogenicity of the new S. Blackisle phenotypes. Very little information is known on the diversity of the prophage elements encoded in the genomes of S. Blackisle strains and the potential role they play in the strains. 

Therefore, here, we aim to characterise the genomes of S. Blackisle isolates from harbour porpoises to ascertain their diversity, virulence factors and antimicrobial resistance genes. The prophage repertoire encoded in the genomes of the isolates will also be induced and characterised based on their morphology, completeness and to determine the potential role they play in the carriage and transmission of virulence genes S. Blackisle resulting the evolution of the new small colonies phenotypes.

Eligibility

Eligibility criteria are available on the EASTBIO how to apply webpage.

How to Apply

To apply for an EASTBIO PhD studentship, please follow the guidance on the EASTBIO how to apply webpage. EASTBIO can provide you with support for your application and details are available on the webpage.

Informal enquiries about the project and your application should be addressed to the project supervisor, Dr Geoffrey Foster - [Email Address Removed]

After you have approached the project supervisor and discussed your application with them, you should:

1) Download and complete the online EASTBIO Equality, Diversity and Inclusion survey; the survey will automatically generate a Unique Number that you should copy and paste on the relevant section of your EASTBIO Application Form.

2) Download and fill in the EASTBIO Application Form. You can only apply for one EASTBIO PhD project.

3) Download and send the EASTBIO Reference Form to your two academic/professional referees, and ask them to submit the references directly to [Email Address Removed] by 27 November 2023

4) Submit your complete application, along with academic transcripts and certificates to [Email Address Removed] by 27 November 2023

If you require any additional assistance in submitting your application or have any queries about the application process, please don't hesitate to contact us at [Email Address Removed]