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GW4 FRESH CDT studentship: Bacterial fish pathogens: ignored threats for aquaculture and the environment

Project Description

In Wales, freshwater fish stocks are in general decline. Around 95% of the rivers are now categorise at risk for salmon stock with most salmon stocks in England and Wales in a depleted state. In parallel aquaculture, a diverse industry, is the fastest growing food sector. Both natural and farmed environments face multiple challenges from global warming to increased infection rates and multi-resistant drug pathogens. Surprisingly, the impact of bacterial fish pathogens and the physiopathology of infections is still poorly understood, few preventative or curative treatments are available. Edwardsiella spp. are well-recognised fish pathogens, particularly: E. tarda, E. piscicida, E. anguillarum and E. ictaluri. They infect a wild range of freshwater fish species from salmonids to catfish, but their impact is largely unknown. Over the last 4 years, progress has been made in understanding the infection mechanism of Edwardsiella spp. Genome sequencing has revealed the presence of type 3 and type 6 secretion system gene clusters. These secretion systems allow pathogens to translocate bacterial proteins, named effectors, directly from the bacterial cell into host cell cytoplasm. Following translocation, the effectors take control of cell signalling allowing the bacteria to invade and replicate inside the cells. But only a few effectors have been so far identified and the mechanism of action is poorly understood.

OBJECTIVE: To Investigate the burden of bacterial pathogens in freshwater fish stocks and identify conditions required for infection in order to identify risk factors for future emergence of fish pathogens and to prevent the disease. To answer these questions, the project is divided in three aims using the expertise of different supervisors.

1. IDENTIFICATION OF FISH BACTERIAL PATHOGENS ON FISH FARMS AND IN THE SURROUNDING ENVIRONMENT Necropsy of freshly dead fish will be performed and biopsies from different tissues will be taken to identify bacterial pathogens using deep sequencing. Virulence factors and antimicrobial resistance will be assessed using bioinformatic analyses. Faecal microbiota from fish presenting reduced growth will be compare to control fish. In addition, water and fish samples in the surrounding environment of the fish farm will be taken and microbiota analysed.
2. MODELLING THE FISH GROWTH DURING INFECTION We will establish an infection system (rainbow trout) in our aquarium as a model organism for studying Edwardsiella spp. We will assess different biotic and abiotic variables (temperature, fish density, water movement, infection dose and transmission routes) that control bacterial fish infections. Using different food supplements under various temperature regimes, we will investigate fish resistance to infection under changing climatic conditions. Using genetically modify bacteria expressing the Green Fluorescence Protein, we will track progression of bacterial infections in fish using confocal microscopy.
3. ELUCIDATING THE MOLECULAR MECHANISM OF PATHOGENICITY We will develop an in vitro cell culture model to study the molecular mechanisms of Edwardsiella spp. infection, particularly cell and tissue invasion processes. Using genomics and proteomics, we will identify new effectors and screen them using genetic deletion or transfection. Localization of the different host cell proteins required for infection will be evaluated by immunofluorescence.

Studentships will last for 3.5 years full-time or the equivalent period part-time.

The application deadline is 9am on 16th December 2019.


Applicants must apply directly to the CDT and not via Cardiff University’s online application system. Please use the below link which will take you to the relevant page to place an application to the CDT directly:

For more details on how to apply, please visit the GW4 Fresh website:

Funding Notes

Full UKRI stipend and fees to be funded for the duration of the studentship (3.5 years), plus RTSG of £11,000.

NERC-funded studentships are subject to UKRI eligibility requirements i.e. you should be a citizen of the UK or other EU country and have been residing in the UK for the last 3 years.

This project is in competition with others available across GW4 FRESH CDT; the projects which receive the best applicants will be awarded the funding. This year we are advertising 25 projects for 14 studentships.

Please note there are mandatory training activities during the first six months.

How good is research at Cardiff University in Biological Sciences?

FTE Category A staff submitted: 54.70

Research output data provided by the Research Excellence Framework (REF)

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