PhD scholarship in Antifungal Resistance at the Food–Environment Interface – DTU Food

Antimicrobial resistance is not just a bacterial problem. Antifungal resistance is an emerging threat to human health, yet we still know remarkably little about the occurrence and spread of resistant fungi across food production and associated environments, or what these reservoirs mean for human exposure and public health. Do you enjoy the lab bench as much as the command line, and would you like to help develop a new One Health surveillance framework? Then join us at DTU National Food Institute.

In this PhD project, you will investigate antifungal resistance at the food–environment interface, combining fungal isolation and susceptibility testing with genomics, bioinformatics and quantitative risk assessment. You will explore how resistant fungi occur and spread in food-production environments, investigate the genomic basis of antifungal resistance, and help translate surveillance data into estimates of human exposure and public-health impact. You will have real influence on the scientific direction of the project and help turn new knowledge into evidence that can support public-health and food-safety advice.

You will be supervised by an interdisciplinary team bringing together expertise in antimicrobial resistance, microbial genomics, bioinformatics and machine learning, quantitative risk assessment and burden-of-disease modelling.

Responsibilities and qualifications
Your overall focus will be to generate new knowledge on antifungal resistance at the food–environment interface and assess its relevance for public health. You will be based in the Research Group for Global Capacity Building, collaborate closely with the Research Group for Risk-Benefit, and work in both the wet and the dry lab throughout the project. Your primary tasks will be to:

• Collect samples and isolate and characterise fungi from food and food-production environments, including antifungal susceptibility testing
• Generate and analyse whole-genome sequencing data to investigate antifungal resistance and genomic epidemiology in priority fungal pathogens, particularly Aspergillus fumigatus and Candida spp.
• Analyse complex microbial datasets, including metagenomic data where relevant
• Apply statistical and machine-learning approaches to investigate genotype–phenotype relationships and predict antifungal resistance from genomic data
• Contribute to probabilistic exposure and risk-assessment models linking surveillance data to public-health impact
• Communicate your research through publications and conferences, contribute to scientific advice, teaching, and co-supervision of BSc and MSc students

We are looking for a curious and motivated candidate who is interested in working across experimental microbiology and computational analysis. You do not need to be an expert in all aspects of the project when you start, but you should be enthusiastic about developing skills across both the wet and dry lab. You have:

• A master’s degree in microbiology, molecular biology, biotechnology, bioinformatics, computational biology, or a related field
• Experience with bioinformatics and sequence analysis, including the analysis and interpretation of biological sequence data
• Experience with command-line computing, for example in a Linux environment
• Experience with scripting or statistical programming in a language such as Python or R
• Some hands-on experience with microbiological laboratory work, for example microbial cultivation, isolation, or phenotypic characterisation, together with an interest in further developing these skills
• An understanding of experimental design and basic statistical data analysis
• Good written and spoken English and the ability to work both independently and collaboratively

Experience with one or more of the following would be an advantage, but is not required: fungal microbiology, antimicrobial or antifungal susceptibility testing, whole-genome sequencing, metagenomics, microbial genomics, machine learning, or quantitative risk assessment.

In your cover letter, please describe your experience with laboratory and computational work and what interests you about combining these approaches in this project.

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.

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.

Assessment
The assessment of the applicants will be made by Joana Mourão, Sara Monteiro Pires and René S. Hendriksen.

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. Please see DTU’s salary structure for scientific staff: www.inside.dtu.dk/en/human-resources/during-employment/salary/salary-structures

The period of employment is 3 years.

Starting date is 1 January 2027 (or according to mutual agreement). The position is a full-time position.

You can read more about career paths at DTU here.

Further information
Further information may be obtained from the main supervisor, Joana Mourão (joam@food.dtu.dk), or the co-supervisors, Senior Researcher Sara Monteiro Pires (smpi@food.dtu.dk) and Professor René S. Hendriksen (rshe@food.dtu.dk).

Read more about the Research Group for Global Capacity Building and the Research Group for Risk Benefit at https://orbit.dtu.dk/en/organisations/research-group-for-global-capacity-building/ and https://orbit.dtu.dk/en/organisations/research-group-for-risk-benefit/, respectively.

You can read more about DTU National Food Institute at www.food.dtu.dk/english

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark. Furthermore, you have the option of joining our monthly free seminar “PhD relocation to Denmark and startup “Zoom” seminar” for all questions regarding the practical matters of moving to Denmark and working as a PhD at DTU.

Application procedure
Your complete online application must be submitted no later than 21 October 2026 (23:59 Danish time).

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link “Apply now”, fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

• A letter motivating the application (cover letter)
• Curriculum vitae
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale
• List of publications (if applicable)

You may apply prior to obtaining your master’s degree but cannot begin before having received it.

Applications received after the deadline will not be considered.

All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply. As DTU works with research in critical technology, which is subject to special rules for security and export control, open-source background checks may be conducted on qualified candidates for the position.

DTU National Food Institute
DTU National Food Institute conducts research into and disseminates – through advice, innovation and teaching – sustainable and value-creating solutions in the area of food and health for the benefit of society. The vision is to make a difference by generating future prosperity through research into food and health. The institute works to prevent disease and promote health, develop new and better food products for a growing population and create sustainable technological solutions, including biosolutions. The institute’s tasks are carried out in interdisciplinary collaboration within e.g. nutrition, chemistry, toxicology, microbiology, epidemiology, modelling, and technology. This is achieved through a strong academic environment of international top class with correspondingly skilled researchers and employees. The Institute employs approximately 390 staff members.

DTU – For the benefit of society since 1829
DTU is one of Europe’s leading elite technical universities. Through research and education at an international top level, we create solutions to the major societal challenges of our time and help secure Europe’s global leadership in sustainable technological development. Since Hans Christian Ørsted founded DTU almost 200 years ago, our mission has remained the same: We develop and create value through the natural and technical sciences for the benefit of society. DTU has 13,800 students, 1,600 PhD students, and 6,500 employees. We work in an international environment and have an inclusive, stimulating, and informal work culture. DTU has campuses in all parts of Denmark and in Greenland and collaborates with the best universities around the world.