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PhD Quantifying antibiotic resistance and antibiotic resistance selective chemicals in the River Almond Catchment Area – a baseline for risk assessment and intervention targets

School of Applied Sciences

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Dr D Morrison , Dr R Briers , Dr A Blaud , Prof F Henriquez No more applications being accepted Funded PhD Project (Students Worldwide)
Edinburgh United Kingdom Environmental Biology Microbiology

About the Project

The alarming rise in resistance to antibiotics is now widely accepted as being one of the most serious public health crises we face today. Recent studies indicate that the natural environment is a significant contributor to the emergence and transmission of resistant pathogens. Resistance is selected in environments polluted with antibiotic residues, heavy metals and other chemicals of emerging concern. The River Almond catchment area has all the ingredients of an antibiotic resistance transmission and selection “hotspot”. Including nine waste-water treatment plants, numerous combined sewer overflows and septic tanks, farm animal waste, mining discharge and landfill sites. 

This projects will quantify the levels of antibiotic resistant bacteria and genes in a river catchment, evaluate potential sources of antibiotic resistance pollution and assess links between potential sources, prevalence of resistance and concentration of chemicals which select resistance. Such surveillance is key to inform public health interventions and the baseline data gathered in this project will inform suitable intervention targets. 


To determine the abundance of antibiotic resistance bacteria (ARB) and genes (ARG) and investigate the links with antibiotic resistance selective chemicals along a river impacted by multiple pollution sources in order to provide a baseline for future risk assessment and intervention strategies. 


1. Use culture dependent and qPCR to detect and quantify ARB and ARG along the length of the River Almond.

2. Identify the major sources of antibiotic resistance pollution in the River Almond, focusing on point sources (WWTP, combined Sewer Overflow, mining discharge) and diffuses sources (agricultural sites) using GIS data and Microbial Source Tracking.

3. Determine the potential relationship between the abundance of ARB and ARG and the concentration of antibiotic resistance selective chemicals.

4. Using metataxonomic and WGS investigate whether “naturalized” (environmental) E. coli, as distinct from enteric E. coli, can be used as indicators of environmental selection of resistance.

This NERC funded SUPER-DTP studentship (The Scottish Universities Partnership for Environmental Research - Doctoral Training Partnership) is a highly prized integrated PhD training programme. The SUPER training approach to your professional development is formalised in an innovative PGCert programme, it also includes an opportunity for an industrial internship and presentation of your work at conferences. All of which will enhance your employment potential across a range of different disciplines and sectors (e.g. academic, industry, regulatory). As a SUPER DTP student, you will also benefit from inter- institutional support and shared training through the Marine Alliance for Science and Technology for Scotland. In addition, this is a CASE-studentship with the Scottish Environment Protection Agency (SEPA), the Scottish environment regulator. The CASE studentship will further enhance your employment opportunities providing you with experience in bathing water analysis, shadowing SEPAs regulatory teams, in depth knowledge of SEPA monitoring programmes, interpretation of data and responses to adverse incidents and events. You will be based at Edinburgh Napier University, with frequent visits to the University of the West of Scotland and in various SEPA locations. 

Academic qualifications 

A first degree (at least a 2.1) ideally in Biology/Microbiology/Environmental Microbiology, or a Master’s degree in a relevant field with good practical knowledge/experience of techniques used to study microorganisms. 

English language requirement 

IELTS score must be at least 6.5 (with not less than 6.0 in each of the four components). Other, equivalent qualifications will be accepted. Full details of the University’s policy are available online. 

Essential attributes: 

 Experience of fundamental microbiology practical skills

 Competent in data management and analysis

 Knowledge of molecular biology

 Willingness to work in an interdisciplinary environment with good communication skills

 Good written and oral communication skills

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

 Good time management

Desirable attributes:

 Experience of GIS-based spatial analysis

 Experience of qPCR

 Experience of chemical analysis

 Experience of whole genome sequencing and bioinformatics analysis

 Good statistical skills

 Full clean driving license

Please quote project code SAS0094 n your enquiry and application.


 •     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)

Funding Notes

This studentship forms part of the NERC-funded Doctoral training partnership SUPER ( )
Start date: 27 September 2021
The 3.5-year studentship covers:
 Tuition fees (UK fee rate only*)
 A stipend (around £15,000 p.a. for full-time study)
 Funding for research training/consumables
 Part-time study optional, a minimum of 50% of full- time effort being required.
* International candidates will be required to cover the difference between UK fees and full international fees


 Marano, R. B. M., Fernandes, T., Manaia, C. M., Nunes, O., Morrison, D., et al. (2020). A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants. Environmental International, 144, 106035.
 Kraemer, S., Ramachandran, A. & Perron, G. Antibiotic pollution in the environment: From microbial ecology to public policy. Microorganisms 7, (2019).
 Singer, A. C., Shaw, H., Rhodes, V. & Hart, A. Review of antimicrobial resistance in the environment and its relevance to environmental regulators. Front. Microbiol. 7, (2016).
 Proia, L. et al. Antibiotic resistance along an urban river impacted by treated wastewaters. Sci. Total Environ. 628–629, (2018).
 Bengtsson-Palme, J., Kristiansson, E. & Larsson, D. G. J. Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiol Rev 42, (2018).
 Oliver, D. M. et al. A catchment-scale model to predict spatial and temporal burden of E. coli on pasture from grazing livestock. Sci. Total Environ. 616–617, 678–687 (2018).
 Smalla, K., Cook, K., Djordjevic, S. P., Klümper, U. & Gillings, M. Environmental dimensions of antibiotic resistance: assessment of basic science gaps. FEMS Microbiol. Ecol. 94, fiy195–fiy195 (2018).

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