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Whole genome sequencing to investigate the mechanisms of fluoroquinolone-resistance in field isolates of Salmonella spp.: a nationwide study of recreational areas

Project Description

Research Group: Biomedical Research Group

Proposed supervisory team:
Dr Caray A. Walker (),
Dr Christopher O’Kane ()
Dr Helen McRobie ()
Dr Jim Sullivan ()

Theme: Microbiology (

Summary of the research project

The ’One Health’ concept recognises that human and animal health are interconnected and that bacteria can be transmitted from humans to animals and vice versa. The impact of this initiative is now even more apparent with the global burden of antimicrobial resistance (AMR). ’One Health’ also recognises that the environment is a key component of the link between humans, animals and the spread of new resistant microorganisms. Microbial source tracking has demonstrated how critical the environment is with regards to the persistence and re-infection potential of pathogens in animal reservoirs, such as bird faeces. Furthermore, research has shown that birds facilitate the spread of AMR through faeces.

The United Nations General Assembly underlined the threat of AMR and committed to join forces and prevent its spread. AMR is predicted to cause 10 million deaths and have a serious economic impact by 2050 if no action is taken. Fluoroquinolone-resistant Salmonella spp. are on the 2017 WHO list of pathogens in need of urgent research to develop new antibiotics. In order for such research efforts to take place, it is imperative that the mechanisms underlying fluoroquinolone-resistance in Salmonella spp. are elucidated. Thus, it is important to analyse field isolates which potentiate infection and resistance spread.

This PhD project will use whole-genome sequencing to determine fluoroquinolone-resistance profiles of field isolates collected from bird faeces in recreational areas around the UK. This monitoring is essential to evaluate how phylogenetically-related the isolates are and understand potential evolutionary patterns of the development of AMR in fluoroquinolone-resistant Salmonella spp. Preliminary work in our laboratory has identified ~50 isolates of Salmonella spp. collected from bird faeces in recreational areas. The project will use these samples but also perform further fieldwork therefore, some travelling around the UK will be necessary. The isolates have been phenotypically tested for resistance to fluoroquinolones using EUCAST standard procedures. A substantial part of the project will be analysing genome data, annotating and identifying resistance genes. Once the mechanisms of resistance have been identified allele-replacement mutagenesis will be used to knock out these mechanism(s) and the resistance phenotype will be re-tested to prove the involvement of specific genes.

Where you’ll study

Cambridge (

Next steps

If you wish to be considered for this project, you will need to apply for our Biomedical Science PhD ( In the section of the application form entitled ’Outline research proposal’, please quote the above title and include a research proposal.

Funding Notes

This project is self-funded.
Details of studentships for which funding is available are selected by a competitive process and are advertised on our jobs website (View Website) as they become available.

Related Subjects

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