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4 PhD Positions: Agricultural practices and the regulatory environment that governs antimicrobial use in Ireland

   Natural Sciences

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  Prof T Hodkinson, Prof Elaine Moriarty, Prof Sinead Corr, Prof Julie Renwick, Dr Marta Martins  No more applications being accepted  Funded PhD Project (European/UK Students Only)

About the Project

4 PhD studentships available                                                        

Agricultural practices and the regulatory environment that governs antimicrobial use in Ireland

Fully funded 4 year PhDs available at Trinity College Dublin

RESIST-AMR Antimicrobial Resistance: Engineering Natural, One- Health, Systems Thinking Solutions to a Manmade Global Disaster

Antimicrobials are critical resources for human, animal and plant health. With emergence of antimicrobial resistance and lack of new antimicrobials, we face an unprecedented global environmental, food security and human health threat.   RESIST-AMR is a structured PhD training programme which umbrellas the Schools of Natural Sciences, Genetics & Microbiology, Medicine, Engineering, Social Science & Philosophy and Computer Science & Statistics, and outside partners, Teagasc agriculture and food development authority.   Applying a multidisciplinary approach and  performing active research at a Teagasc Research Farm, students will perform critical analyses of environmental and human ‘resistomes’ from agricultural settings and analyse agricultural stakeholders’ practices and policies to identify institutional reform implications. There are 4 PhD fellowships being offered to highly motivated and ambitious students as part of the RESIST-AMR programme. These are outlined below;

PhD1.  Characterisation of the microbiome and antimicrobial resistome in Irish soil, forage grasses and cereals.        

Principal supervisor: Dr Marta Martins ([Email Address Removed]

School/ Discipline: School of  Genetics and Microbiology/ Discipline of Microbiology

Co-supervisors: Prof Trevor Hodkinson (Sch. Natural Sciences) and Prof Simon Wilson (Sch. Computer Science)

There is a knowledge gap in our understanding of the antimicrobial resistome present in the farm environment. Applying cutting-edge metagenomic sequencing and advanced computational and statistical approaches the farm resistome will be profiled and predator species identified, while environmental persistence of AMR genes in soil, forage grasses and cereals will be determined and their risk of future transfer to humans analysed. 

PhD 2.  Farm-to-farmer, farm-to-air transfer of antimicrobial resistance during farming practices.

Principal supervisor: Dr Julie Renwick ([Email Address Removed])

School/ Discipline: School of Medicine/ Discipline of Clinical Microbiology

Co-supervisors: Dr Marta Martins and Dr Sinéad Corr (Sch. Genetics and Microbiology)

Transfer of the resistome from farm-to-farmer represents a large gap in our current knowledge. In particular, there is little knowledge of how aerosols generated during farming practices (slurry mixing, spreading) could be a mechanism of resistome transmission. Applying sampling, cultivation and resistance testing techniques alongside metagenomic sequencing and bioinformatics, this PhD project will focus on the transmission of the farm resistome (slurry/manure, animal, air) to the farmer during farming practices. 

PhD3. Modelling the microbiome in human in vitro organoid platforms.                               

Principal supervisor: Dr Sinéad Corr ([Email Address Removed]

School/ Discipline: School of Genetics and Microbiology/ Discipline of Microbiology

Co-supervisors: Dr Michael Monaghan (Sch. Engineering) and Dr Julie Renwick (Sch. Medicine) 

A major downside of current microbiome research is the lack of suitable models for studying mechanisms and causality. Two microbiome platforms (gut and lung) will be established with organ specific cells incorporated into tissue microenvironments engineered using advanced biomaterials and additive manufacturing processes; together with bioreactor technologies and used to test the vulnerability of the microbiome to the resistome and ecosystem stability. 

PhD4. Evaluating the agricultural practices and the regulatory environment that governs antimicrobial use in Ireland.                                                                                      

Principal supervisors: Dr Elaine Moriarty ([Email Address Removed]

School/ Discipline: Sch. of Social Science and Philosophy

Co-Supervisors: Prof Trevor Hodkinson (Sch. Natural Sciences); Prof. RoseAnne Kenny (Sch. Medicine)

There exists a knowledge gap with regards decision making on farms around antimicrobial usage. A whole population survey on the social and economic factors (e.g. gender, age, education) that influence the motivations and attitudes of farmers in Ireland towards the use of antimicrobials on their farms will be undertaken.  An extensive analysis of The Irish Longitudinal Study on Ageing, TCD (TILDA) dataset will be performed, while engagement with the stakeholders (vets, agri-business, policy regulators, will be conducted under the umbrella of the Policy Institute, a multi-disciplinary policy research institute, in Trinity College.

Standard Duties and Responsibilities of the Posts

The PhD student will participate fully in lab life, (PhDs 1-3) attending regular meetings and collaborating with other lab members. PhD 4 is not lab based. The structured PhD programme has a sustained enrolment of national and international students of high capability, and a structured approach to advanced research. All registered PhD students undertake and complete a taught module(s) that accrue in total a minimum of 10 ECT credits / maximum of 30 ECT credits.


Funding Information

The RESIST-AMR PhD training programme is funded by the Prendergast Challenge-Based Award.

Person Specification

The PhD studentship would be suited to someone who is highly motivated and can demonstrate a passion for microbiome-related research and tackling the global challenge of antimicrobial resistance. The student will join a large multidisciplinary team and should demonstrate the ability to work as part of a team while being independently driven.


·      For PhDs 1 to 3, a minimum of 2.1 Honours degree in Microbiology, Molecular Biology, Tissue engineering, Plant Science, or a related field is essential. (Lab based)

·      For PhD 4, a minimum of 2.1 Honours degree in Sociology, Social Sciences, Geography, Behavioural Science or a related field is essential. (Not lab based)


Knowledge & Experience (Essential & Desirable)


·      Candidates should demonstrate a high level of initiative, organisation and strong written and oral communication skills.

·      Candidates should have strong English language speaking and writing skills 


A prior MSc or evidence of research experience outside an undergraduate degree

Skills & Competencies

·      Strong English language speaking and writing skills 

The RESIST-AMR team will support opportunities during the course of each PhD to supplement the existing stipend (eg. Laboratory demonstration, exam invigilation, Scholars Ireland, Tutoring etc) and gain valuable transferable skills. 

Application Procedure

Applicants should submit a full Curriculum Vitae to include the names and contact details of 2 referees (including email addresses), and a 1-page statement specifying which PhD position/s they are applying for and why, (where an applicant is interested in more than 1 project, please state this in your cover letter/statement) to:- 

PhD1.  Principal supervisor. Dr Marta Martins ([Email Address Removed])

PhD2.  Principal supervisor. Dr Julie Renwick ([Email Address Removed])

PhD3. Principal supervisor. Dr Sinead Corr ([Email Address Removed])

PhD4.  Principal/Co-supervisors. Dr Elaine Moriarty ([Email Address Removed]) (cc’ Prof Trevor Hodkinson [Email Address Removed])


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