Postdoctoral Position in Molecular Microbiology

Postdoctoral Position in Molecular Microbiology

University of Basel

Basel, Switzerland

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 position

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.