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Antibiotic resistant bacteria in Scottish surface waters

   School of Applied Sciences

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  Dr D Morrison, Dr F Stainsby  No more applications being accepted  Funded PhD Project (Students Worldwide)

About the Project

This project is one of 17 four year PhD Studentships funded by Medical Research Scotland (MRS) (https://www.medicalresearchscotland.org.uk) to be delivered jointly by the named University and External Partner Organisation (EPO). The Studentship will provide the first-class academic and additional training provided by the EPO needed to equip the successful candidate for a science career in an increasingly competitive market.

"The prevalence, sources and diversity of antibiotic resistant E. coli in Scottish surface waters: a baseline for risk assessment and intervention targets." to be delivered by the Edinburgh Napier University [Supervisors: Professor Donald Morrison and Dr Fiona Stainsby (both School of Applied Sciences, Edinburgh Napier University)] and Scottish Water (https://www.scottishwater.co.uk/) [External Partner Organisation supervisor: Mr George Ponton].

This PhD Studentships provide funding for a four year doctoral training programme delivered by a Scottish Universities in collaboration with an industrial partner. This will include 8 months training with Scottish Water and the Scottish Environment Protection Agency (SEPA) gaining valuable experience in public health microbiology and epidemiology. The combination of academic, industrial and commercial experiences will give the successful applicant an excellent opportunities for their future career.

The alarming rise in resistance to antibiotics is now widely accepted as being one of the most serious public health crises we face today. The use and overuse of antibiotics in human and animal medicine and especially the overuse in animal food production are the main drivers for the emergence of resistance. However, recent research suggests that the natural environment, and especially surface water, is the single largest source of antibiotic resistance. Surveillance is key to inform public health actions and strategies. A number of national monitoring schemes provide ongoing data on antibiotic resistance in human and animal settings, however, no such data is available on environmental antibiotic resistance. The urgency for such data has been recognised by an EU Committee who called for mandatory monitoring of antibiotic resistance in the environment at a national level to tackle the spread of antibiotic resistance from the environment to humans. This project will provide the first nationwide data on antibiotic resistance in Scottish surface waters. This baseline data will be used to assess the risk to human health and to determine if intervention measures are required to ensure that drinking water sources are protected.

The aim of the project is to determine the prevalence, major sources and diversity of antibiotic resistant E. coli in Scottish surface waters used for drinking water abstraction in order to provide a baseline for future risk assessment and intervention strategies. The Research Objectives are

1.         Determine the prevalence of antibiotic resistant E. coli in representative Scottish surface waters.

2.         Detect and quantify antibiotic resistant genes (ARG) in representative Scottish surface waters.

3.         Quantify the levels of antibiotic resistance selective chemicals in representative Scottish surface waters.

4.         Identify the major sources of antibiotic resistant E. coli present in Scottish surface waters using Microbial Source Tracking.

5.         Establish the population diversity of antibiotic resistant E. coli in Scottish surface waters by core genome and resistance genome analysis.


Enquiries should be sent by email to Dr Donald Morrision:

[Email Address Removed]


Applicants must have obtained, or expect to obtain, a first or 2.1 UK honours degree in biology, ideally in microbiology, with a good fundamental knowledge of techniques used to study microorganisms. Additional requirements follow:-

Essential attributes:

•           Experience of fundamental microbiology practical skills

•           Competent in research skills, data analysis and presentation, and problem-solving

•           Knowledge of molecular biology

•           Good written/oral communication skills

•           Strong motivation, with evidence of independent research skills relevant to the project

•           Good time management

Desirable attributes:

•           Experience in molecular microbiology and epidemiological typing of bacteria

•           Experience in chemical analysis

•          Experience of GIS-based spatial analysis

•           Experience of qPCR

•          Experience in whole genome sequencing and bioformatics analysis

•           Good statistical skills

•           Full clean driving licence

English language

•           IELTS score must be at least 6.5 (with not less than 6.0 in each of the four components). Equivalent qualifications will be accepted.

Applications are welcome from UK nationals, EU nationals that hold UK settled or pre-settled status and international students, but international students will be required to fund the difference between the Home/UK fee rate and international fee rate.


Checklist for your online application:

  • Apply via 'PhD APPLIED SCIENCES full-time' link, quoting application reference number 'SAS0171' on your form
  • Completed application form
  • CV
  • 2 academic references, using the Postgraduate Educational Reference Form (Found on the application process page)
  • A personal research statement (This should include (a) a brief description of your relevant experience and skills, (b) an indication of what you would uniquely bring to the project and (c) a statement of how this project fits with your future direction.)
  • Evidence of proficiency in English (if appropriate

Please note, your application may be shared with the funders of this PhD Studentship, Medical Research Scotland and Scottish Water.

Interviews are expected to take place approximately 3-4 weeks after the closing date for applications. Interviews may be conducted by video conference.

It is anticipated that the PhD Studentship will start 3 October 2022.

Funding Notes

PhD Studentship provides: an annual tax-free stipend of £18,500, increasing to £19,000 over the four years; tuition fees at home rates only; consumables; and generous travel allowance. International fees are not covered. International students applying for the Studentship must provide evidence by the date of interview that they are able to finance the fee top-up required to the international fee level.


Huijbers, P. M. C., Flach, C. F., & Larsson, D. G. J. (2019). A conceptual framework for the environmental surveillance of antibiotics and antibiotic resistance. Environment International, 130, 104880. https://doi.org/10.1016/j.envint.2019.05.074
Larsson, D. G. J., & Flach, C.-F. (2021). Antibiotic resistance in the environment. Nature Reviews Microbiology 2021, 1–13. https://doi.org/10.1038/s41579-021-00649-x
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