Genetic determinants 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.
The position
We are looking for a postdoctoral researcher in molecular microbiology to investigate the genetic basis of drug 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 across strains and drugs. 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, we now aim to identify the genetic determinants of bacterial survival and death and to build a species-wide tolerance atlas linking genotype to phenotype and clinical outcome. The work will provide fundamental insights into bacterial biology and identify targets for improved therapies.
Your role
You will generate and screen pooled CRISPRi libraries across multiple M. abscessus genetic backgrounds and infection-relevant conditions, using viability-based selection strategies to quantify bacterial killing at scale. You will integrate these results with genomic data from over 1,000 clinical isolates to build predictive models linking genotypes to tolerance phenotypes and clinical outcomes. You will lead the project and co-supervise a PhD student.
Your profile
We are looking for candidates with a strong track record in molecular microbiology.
-
PhD in molecular biology, microbiology, or a related discipline
-
Expertise in molecular bacteriology (e.g. CRISPRi, genetic manipulation)
-
Basic programming skills (Python or R) for data analysis
-
Ability to design and execute experiments independently
-
Strong motivation, scientific curiosity, and drive
-
Ability to work collaboratively and mentor junior researchers
-
Advantageous: experience with mycobacteria, high-content imaging, and screening approaches
We offer you
-
A fully funded 4-year postdoctoral position within an international consortium
-
Access to cutting-edge technologies (automation, sequencing, high-content imaging, etc.)
-
A project positioned to reshape how antibiotic efficacy is understood and measured
-
Close integration with drug development and clinical research
-
Support for independent funding and career development
-
Competitive salary and excellent quality of life in Switzerland
Application / Contact
Please upload a single PDF, including a motivation letter, a CV, contact details of at least two references and a short description of a project you would like to pursue. Applications will be reviewed on a rolling basis until the position is filled.