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Single-cell analysis of antibiotic tolerance in mycobacteria
The Department of Biomedicine is a joint initiative of the University of Basel and the University Hospitals Basel. It unites basic and clinical scientists to advance our understanding of health and disease and to develop therapies for areas of unmet medical need. With over 70 research groups and 800 employees, the Department of Biomedicine is the largest department at the University, located across six sites in the city centre.
Your position
We are offering a PhD position in experimental microbiology to study antibiotic tolerance in Mycobacterium abscessus, one of the most challenging to treat bacterial pathogens. The position is part of a newly funded international consortium that brings together experts in mycobacterial genetics, high-throughput phenotyping, structural biology, and clinical research across Switzerland, Israel, Australia and the USA.
The project
Antibiotic treatments for M. abscessus fail in more than half of patients despite in vitro drug activity. A key reason is drug tolerance, the ability of bacteria to survive antibiotic exposure without classical resistance. Our lab (boecklab.com) has developed a large-scale live-cell imaging platform that tracks hundreds of millions of bacteria during antibiotic exposure, enabling systematic analysis of killing dynamics. Using this approach, we have shown that bacterial survival is strongly shaped by the bacterial genetic background and predicts treatment outcomes (Nature Microbiology, 2026). In this project, you will use this platform to quantify bacterial survival at the single-cell level across strains, drugs, and environmental conditions to identify the molecular mechanisms that shape drug tolerance during human infection.
Your role
You will perform and analyse high-content live-cell imaging experiments to quantify bacterial viability under antibiotic exposure across diverse conditions and clinical isolates. In close collaboration with postdoctoral researchers, you will integrate these data with results from CRISPRi and transposon mutagenesis screens to identify molecular mechanisms and M. abscessus genotypes that underlie tolerance phenotypes. Your work will involve systematic experimental design, generation of large-scale datasets, and quantitative analysis of single-cell time-kill dynamics. You will contribute to linking genetic variation to bacterial survival strategies and help build a comprehensive understanding of drug tolerance in clinically relevant settings.
Your profile
- MSc in molecular biology, microbiology, or a related discipline
- Experience in microbiology or molecular biology
- Interest in combining computational and experimental approaches
- Strong motivation, scientific curiosity, and drive
- Ability to work independently and as part of a team
- Good communication skills in English
We offer you
- A fully funded PhD position within a highly collaborative international consortium
- Training in cutting-edge technologies, including high-content imaging and automation workflows
- A project positioned to reshape how antibiotic efficacy is understood and measured
- A dynamic, international research environment in Basel
- Competitive salary and excellent quality of life in Switzerland
Application / Contact
Please upload a single PDF, including a motivation letter, a CV, and contact details of at least two references. Applications will be reviewed on a rolling basis until the position is filled.
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