PhD scholarship in genetic epidemiology of antimicrobial resistance in animal production - DTU Food

At the DTU Food research group in Genetic Epidemiology, we are looking for a PhD student with an interest in quantitative epidemiology, bioinformatics and antimicrobial resistance.

The PhD project is part of our ongoing activities in how antimicrobial use in conventional animal production select for antimicrobial resistance genes (ARGs) in the microbiome of animals, and how these ARGs subsequent impose a risk for humans (One Health). The overall aim is to establish the scientific basis for predicting how interventions in antimicrobial usage in animal production influence the occurrence of ARGs that can impose human risk.

Responsibilities and qualifications
The specific objective of the PhD project is to study the quantitative effect of antimicrobial usage in animal production on the occurrence of ARGs in the microbiome related to animals and food products. The scientific work will focus on how to integrate results from DNA metagenome sequencing and bioinformatics for measuring occurrence of ARGs with data about farms and antimicrobial usage in a quantitative epidemiology approach and in a risk setting. The study will be utilizing sequencing data generated from samples collected in the Danish animal production both in routine surveillance programs and previous scientific studies. In addition, the study will contribute to the evaluation of metagenomics for future surveillance of AMR in livestock in Denmark as part of the Danmap program (www.danmap.org). 

In addition to scientific publication, the obtained quantitative epidemiological models should be integrated into a mathematical tool that can predict changes in occurrence of ARGs, given changes in AMU.

Responsibilities

• Apply bioinformatic tools to DNA sequencing data resulting in quantitative measures of ARGs in microbiomes.
• Manage data from many different sources into data frames that can be analyzed with biostatistical applications in the statistical software R/Python.
• Performing data analysis in accordance with time-structures and hierarchical structures of the data.
• Develop forecast models of AMR given the antimicrobial usage in animal production.
• Contributing to the teaching activities in the group, including supervision of students.
• Contribute to the dissemination of research findings through publications, presentations at national and international conferences and policy briefs.

You must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree.

Preference will be given to candidates with:

• Experience with management and manipulation of large data frames containing biological information.
• Experience in working simultaneously with more than one scientific field – in this case microbiome and quantitative epidemiology.  
• Experience in analyzing biological data in the context of surveillance in a one health perspective.
• Ideally experience with analyzing antimicrobial use data from Danish livestock.

Approval and Enrolment 
The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see DTU's rules for the PhD education. 

We offer
DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

Salary and appointment terms 
The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union. The period of employment is 3 years.

We aim for a starting date in August 2025 or according to mutual agreement. The PhD is a full-time position.

Preferred starting date for the PhD student will be August 2025 or according to mutual agreement. 

You can read more about career paths at DTU here.

Further information
Further information may be obtained from: Håkan Vigre, Associated Professor, hvig@food.dtu.dk

You can read more about the Research Group