PhD Position in Experimental Microbiology: Antibiotic Tolerance in Mycobacterium abscessus University of Basel in Switzerland

The University of Basel is offering a PhD position in experimental microbiology focused on antibiotic tolerance in Mycobacterium abscessus, a bacterial pathogen known for its challenging treatment profile. This opportunity is part of a newly funded international consortium, bringing together experts in mycobacterial genetics, high-throughput phenotyping, structural biology, and clinical research from Switzerland, Israel, Australia, and the USA.

The project addresses a critical issue: antibiotic treatments for M. abscessus fail in more than half of patients, despite apparent drug activity in vitro. Drug tolerance, the ability of bacteria to survive antibiotic exposure without classical resistance, is a key factor. The Boeck Lab (boecklab.com) has developed a large-scale live-cell imaging platform capable of tracking hundreds of millions of bacteria during antibiotic exposure, enabling systematic analysis of killing dynamics. Using this platform, the lab has demonstrated that bacterial survival is strongly influenced by genetic background and can predict treatment outcomes (Nature Microbiology, 2026).

As a PhD student, you will use this advanced imaging platform to quantify bacterial survival at the single-cell level across various strains, drugs, and environmental conditions. Your research will focus on identifying the molecular mechanisms that shape drug tolerance during human infection. You will perform and analyze high-content live-cell imaging experiments to assess 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 pinpoint molecular mechanisms and M. abscessus genotypes underlying 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. The position offers a unique opportunity to work at the intersection of microbiology, genetics, and clinical research, with access to cutting-edge technology and international collaboration.

Applicants should have a strong background in microbiology, genetics, or a related field. Experience with experimental design, quantitative analysis, and large-scale dataset generation is desirable. Familiarity with live-cell imaging, CRISPRi, or transposon mutagenesis is advantageous. Candidates must be highly motivated, able to work collaboratively, and possess excellent analytical skills. No specific language or GPA requirements are mentioned.

To apply, use the University of Basel job portal link provided. Prepare your CV, cover letter, and relevant academic documents. Follow the instructions on the portal for submission. For further information about the lab and research, visit boecklab.com.