PhD Studentship (x4)

RESIST-AMRAntimicrobial 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 (mmartins@tcd.ie)
• 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 (renwickj@tcd.ie)
• 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 (corrsc@tcd.ie)
• 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 theagricultural practices and the regulatory environment that governs antimicrobial use in Ireland.

• Principal supervisors: Dr Elaine Moriarty (elaine.moriarty@tcd.ie)
• 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.

At Trinity, we are committed to equality, diversity, and inclusion. Trinity welcomes applications from all individuals, including those applicants with disabilities, those who may have had non-traditional career paths, those who have taken time out for reasons including family or caring responsibilities. We also welcome international applicants including those whom have been displaced due to war.

We are ranked 3rd in the world for gender equality (Times Higher Education Impact Rankings 2020) and we hold an Athena SWAN Bronze award, recognising our work to advance gender equality. The University is actively pursuing a Silver level award, which it has committed to achieving by 2025. Trinity is committed to supporting the work-life balance and to creating a family-friendly working environment.