PhD in Antimicrobial Resistant Genes (ARG) and Pollutants – from Seabed to Seafood Platter - BBSRC FoodBio DTP

We are offering a BBSRC FoodBioSystems DTP-funded PhD position with our College of Health, Medicine and Life Sciences focusing on the impact of antimicrobial-resistant genes (ARG) and pollutants in marine ecosystems.

The research project, funded in partnership with the BBSRC FoodBio DTP, aims to investigate how ARGs in marine sediments enter the food chain and affect both wildlife and humans.

Project description

Municipal discharges and antibiotic use in aquaculture can lead to the enrichment of antimicrobial resistance genes (ARG) in aquatic ecosystems leading to contaminated fish entering the human food chain. However, Industrial discharges contain pollutants known to exert even greater selective pressure than antibiotics in driving the evolution of antimicrobial resistance (AMR). Decades of municipal and industrial discharging have rendered coastal sediments for decades as “pollution sinks” for antibiotics, heavy metals and organic pollutants. Persistent bioavailable pollutants in sediments bio-magnify in the marine food chain with the highest concentrations reaching apex predators.

Our preliminary studies have revealed a higher proportion of clinically-important ARGs in wild seals from the more industrialised polluted Tees Estuary compared with seals from control areas and this may explain increased AMR septicaemia mortality in seals from more polluted areas.

Similarly, in humans, ARG E coli infections were prevalent in surfers using more contaminated than cleaner beaches around the UK. Exposure to toxic pollutants from fish consumption can lead to toxic effects, including immunosuppression in humans, also immunosuppression occurs in seals induced by feeding them contaminated baltic herring dose-dependent with fish PCB concentration.

Little is known regards ARG transfer from the environment into and through the human food chain, and even less about concomitant immuno-toxic pollutant exposure which can exacerbate the pathogenicity of bacterial infections in humans and wildlife. The role of pollutants in ARG spread and its impacts on humans and wildlife clearly requires urgent attention. Seals are ideal sentinels for humans since they are long-lived apex predators with similar mammalian physiology and are exposed to pollutants concomitantly with ARGs via the food chain. However, due to their exclusively fish diet, exposures are significantly greater than humans, representing a worst-case exposure scenario to both health concerns and potential impacts.

What you will do

You will investigate how ARGs in marine sediments enter the marine food chain, contaminate fish and seals feeding on them, and, how ARG proliferation spreads in more polluted marine food chains. You will do this by quantifying ARGs and pollutants in sediments, fish and seal faeces sampled from polluted Estuaries versus cleaner control sites. Field sampling will be undertaken to collect samples which will be analysed using PCR techniques and analytical chemistry methods to quantify antibiotic and chemical pollutants.

Eligibility

Academic eligibility

An upper 2nd class degree (or equivalent) is required in a subject appropriate to the PhD projects applied for (see the project description for more information). Candidates with a lower-class bachelor's degree, but a good performance at the Masters level (merit or above) will also be considered.

To support accessibility to PhD training opportunities, these studentships are only available to applicants who have not previously obtained, or are about to obtain, a PhD degree (or equivalent).

Student profile

Knowledge of environmental chemistry and/or microbial ecology with genomics is required. Knowledge of real-time PCR, ELISA methods, HPLC and GC-MS are a bonus

Stipend (Salary)

FoodBioSystems DTP students receive an annual tax-free stipend (salary) that is paid in instalments throughout the year. For 2024/25 this is £19,237 (£21,237 at Brunel University) and it will increase slightly each year at the rate set by UKRI.

If you have an international qualification, please check the degree course eligibility information provided by the host universities before you apply to the DTP: Aberystswyth University, Brunel University, Cranfield University, University of Lincoln, Queen’s University Belfast, University of Reading, University of Surrey.

Funding eligibility

Home student applicants

The majority of our funding (minimum 70%) is available to students with UK/home fees status. To be classed as a home student, candidates must meet the following criteria:

Be a UK or Irish National (meeting residency requirements), or
Have settled status in the UK (under the EU Settlement Scheme), or
Have pre-settled status in the UK and meet residency requirements (under the EU Settlement Scheme) or
Have indefinite leave to remain or enter.

Further information about eligibility for UK home fee status

UK National
The UK includes the United Kingdom and Islands (i.e. the Channel Islands and the Isle of Man). In terms of residency requirements for UK and Irish nationals, candidates will be eligible for home fee status as long as:

They were living in the EEA or Switzerland on 31 December 2020, and have lived in the EEA, Switzerland, the UK or Gibraltar for at least the last 3 years before starting a course in the UK.
They have lived continuously in the EEA, Switzerland, the UK or Gibraltar between 31 December 2020 and the start of the course.

EU Settlement Scheme
EU, EEA or Swiss citizens can apply to the EU Settlement Scheme to continue living in the UK after 30 June 2021. If successful, applicants will get either settled or pre-settled status. Those with pre-settled status will qualify as a home student if they have 3 years of residency in the UK/EEA/Gibraltar/Switzerland immediately before the start of their course.

Indefinite leave to remain (ILR) or Indefinite leave to enter (ILE)
Candidates with ILR or ILE can continue to live in the UK without applying to the EU Settlement Scheme.

International student applicants

We welcome applications from international students (any applicant who does not meet home fees eligibility criteria and requires a visa to study in the UK) and we receive many excellent applications each year. However, UKRI funding conditions mean that the DTP can only offer a maximum of 30% of the total number of studentships to international students. Between 2022 and 2024 approximately 1/100 international student applicants were successful.

Fees for International Students funded by FoodBioSystems DTP

We anticipate that DTP partner universities will be covering the difference in the UK/Republic of Ireland fees and international fees for international UKRI-funded students: Aberystwyth University, Brunel University, Cranfield University, University of Lincoln, Queen’s University Belfast, University of Reading and University of Surrey. For further information on this, please refer to the individual university websites.

Further funding eligibility information

Funding for PhD studentships from BBSRC is only available to successful candidates who meet the eligibility criteria set out in the UK Research and Innovation (UKRI) harmonised training terms and conditions. Offers of studentships to successful candidates will be conditional on acceptance onto PhD programmes as home fee students at the host universities.

Language proficiency

Candidates must show the necessary levels of English proficiency required by the university that will be hosting the PhD Studentship (the university where the project lead supervisor works). If you have completed a degree or higher degree in a course that was taught in English this may be sufficient evidence of your language proficiency. Please check the relevant university website for further details. If the website does not provide the information you are looking for, please contact the relevant university admissions office.
Aberystwyth University, Brunel University, Cranfield University, University of Lincoln, Queen’s University Belfast, University of Reading, and University of Surrey.

How to apply

All applications to FoodBioSystems DTP are made via the online application form, irrespective of the location of the specific project (Reading, Surrey, Cranfield, Lincoln, Queen’s, Aberystwyth or Brunel). You can apply to a maximum of TWO PhD projects. The application form will open at 17:00 on Friday 20 December 2024.

Project details are available in the project list further down this page. Each project description indicates the name and institution of the lead supervisor and has a project ID number. You are welcome and encouraged to email the lead supervisors of projects to ask them any questions you may have or to discuss the project.

You will need the following documents to support your application:

Official transcripts of your higher education qualifications, inclusive of grades
Evidence of your proficiency in English, if English is not your first language. (You can provide this later if you have not completed an IELTS test before the application closing date).

You must also provide the name and email address of someone who will provide a confidential academic reference letter. The DTP office will request a letter from your referee if you are shortlisted for an interview.

Equity, diversity and inclusion

The FoodBioSystems DTP is committed to equality, diversity and inclusion (EDI). We want to build a doctoral researcher and staff body that reflects the diversity of society and encourages applications from under-represented and disadvantaged groups.

Applicants with disabilities or specific learning differences

Applicants can choose to disclose a disability or specific learning difference on the application form. The DTP office will contact shortlisted applicants who have made this disclosure so we can offer reasonable adjustments to interviews. This information is kept confidential unless the applicant chooses to share it with the interview panels.

Guaranteed interview scheme

FoodBioSystems DTP is offering a guaranteed interview scheme (GIS) for candidates from eligible under-represented ethnic groups. This is an opt-in process. Applicants can participate in this scheme if they meet the following criteria:

Hold UK home student fee status for 2025 entry (details on UK fees status are available from UKCISA)
Identify as:
1. Black, African, Caribbean or Black British
2. Asian or Asian British
3. Belonging to mixed or multiple ethnic groups
Hold or expect to obtain a minimum of a 2.1 undergraduate degree in a relevant subject, or equivalent qualification

Candidates with a guaranteed interview must also provide full written answers to all questions about research and transferable skills in the application form. Assessment of written answers and interview performance are both considered when awarding studentships (see assessment criteria).

Applicant mentoring

We offer applicants, who meet GIS criteria, an opportunity to apply to our applicant mentoring programme. Applicants who are accepted onto the mentoring programme will receive four mentoring meetings, with a current DTP student with mentor training, during the application process.

Meeting one: (early in the week of 20 January 2025) A brief pre-application discussion with the mentor
Meeting two: (later in the week of 20 January 2025) An application writing support session
Meeting three: (mid-late February 2025) An interview preparation session
Meeting four: (after 14 April 2025) A post-application outcome reflection session

To be eligible to receive mentoring, applicants must:

Identify as:
1. Black, African, Caribbean or Black British
2. Asian or Asian British
3. Belonging to mixed or multiple ethnic groups
Hold or expect to obtain a minimum of a 2.1 undergraduate degree in a relevant subject, or equivalent qualification
Hold UK home student fee status for 2025 entry (details on UK fees status are available from UKCISA)

Priority will be given to applicants who meet the above criteria and also identify with one or more of the following:

Have ever been in receipt of free school meals
Are the first in their family to attend higher education
Have completed/are completing their undergraduate studies at a non-Russell Group university

How to request a mentor

If you are eligible to apply to the guaranteed interview scheme and would like to meet with a mentor, please complete the personal details and equality diversity and inclusion sections of the online application form. You must do this before 09.00 (GMT) on Friday 17 January 2025.

If you are eligible for the scheme, we will contact you shortly after 20 January with details of your proposed mentor. Please note: We will only share your name and email address with mentors. Other personal information will be kept confidential and used by the DTP office if we need to prioritise applications according to the eligibility scheme criteria.
Please do not request a mentor after the closing date for this scheme (09:00 on 17 January 2025). We will not be able to assign you a mentor after this date.

Part-time registration

Our studentships are offered on a part-time basis in addition to full-time registration. The minimum registration is 50% FT and the studentship end date and stipend payments will be amended to reflect the part-time registration. We recommend that if part-time studentships are combined with paid employment, the combined time commitment does not exceed 48 hours per week. Candidates who are awarded a studentship, and wish to register part-time, must discuss arrangements with the project supervisor and DTP office before enrolment.

Please go to the end of the project summary table to read important information about applicant eligibility and our selection process before you apply for a studentship.

Meet the Supervisor(s)

Gera Troisi - Dr Gera M. Troisi is a Senior Lecturer in the Department of Mechanical & Aerospace Engineering in the College of Engineering & Design at Brunel University London, since 2001, responsible for the deliver of undergraduate and postgraduate modules on Environmental, Health & Safety Management towards Sustainable Engineering Solutions. She has supervised postgraduate students to successful completion of PhD-doctoral degrees, MPhil and MRes. She is a Chartered Toxicologist-Ecotoxicologist (UK & Europe) and is former member of the Risk Assessment Committee (RAC) of the European Chemicals Agency (ECHA) administering European Union chemicals regulations (REACH and CLP). Dr Troisi's principal research interests include environmental toxicology (ecotoxicology, endocrine disruption, biomonitoring, biosensors, environmental analysis); Risk Assessment and Aquaculture. She has coordinated research and consultancy projects related to environmental toxicology funded by both non-governmental, governmental agencies and industry. Before her academic career, Dr Troisi was a Senior Scientific Officer forthe Medical Research Council (MRC) Institute for Environment & Health. Her consultancy services include: Medical Device Risk Management; Environmental Risk Assessment (ERA); Health Risk Assessment (HRA); Life Cycle Assessment (LCA with simapro, gabi to ISO14040); Environmental Impact Assessment (EIA); Environmental (ISO14001) Management, Occupational Health & Safety Management (OHSAS 45001) Management, Quality Management (FMEA, FMECA, FTA, probabilistic Risk Management). Sustainability Analysis (environmental, socia-economic impacts and compliance) of products and processes (procurement, manufacturing, end of life sustainable logistics) for Triple Bottom Line accounting and reporting and complaince of emissions with REACH, HSE, WEL, EPR under IED, WFD.

Ashley Houlden - I am a Microbial Ecologist in the Division of Biosciences, within the College of Health and Life Sciences at the University of Brunel London. My research interests lie in the assessment of microbial community structure and function using high throughput sequencing and molecular microbiological techniques. Focusing on the Host microbiome their interaction with one another in this community and changes as a result of disease or injury, this characterisation of the communities allows the identification of functionally important changes in microbial assemblages and detection of Antimicrobial Resistance. My research has included work on the impact of stroke, brain injury, parasitic intestinal infections, and dementia on the interactions with the host and its microbiome. One of my Current research focus areas is women's health, I am studying bacterial vaginosis, the interaction of microbes present in the vagina, detection of potential pathogens, and the development of an in-house in vitro model system using Organ on a Chip technology for 3D tissue culture to simulate the vaginal environment. Linked to this I am interested in the impact that space travel and microgravity has on microbial populations and implications for health. I am also interested in antimicrobial resistance (AMR) and detection of AMR in bacterial communities with a focus on the environmental impact and ecological implications of this. It is becoming increasing an issue that AMR organisms are colonising animal populations and if these pathogens are accumulated in Apex predators via food chain acquisition. My Doctorial training was in soil microbial ecology carrying out risk assessments and the efficacy of using bacterial biological control agents against fungi diseases of crops in laboratory, glass house and field experiments while at CEH-Oxford/Cardiff University. I then undertook postdoctoral research at The University of Sheffield followed by The University of Manchester continuing research into environmental microbiology looking a biogeochemical cycling of Nitrogen and sulphur. While at Manchester I moved into medical microbiome research as Researcher Co-Investigator on a grant on T. Muris and the impact on the microbiome and host. As a result of this I have formed a number of collaborations involving microbiome research.

Related Research Group(s)

Sustainable Energy Use in Food Chains - Energy demand and GHG emissions reduction in all stages of the food chain; optimal ways the food chain can utilise different energy sources and interact with the energy supply system; resource efficiency through intensification of food processing.