Development of a single cell RNA sequencing platform for bacteria to delineate antibiotic hetero-resistance
Objective:
The primary goal of this project is to utilize single-cell RNA sequencing (scRNA-seq) to characterize bacterial populations displaying heterogeneous antibiotic resistance, specifically Staphylococcus aureus isolated from clinical samples. This includes establishing protocols for RNA stabilization, bacterial cell isolation, and sequencing to identify biomarkers for developing diagnostic kits.
Methods:
The methods single cell RNA sequencing has long been used to analyze eukaryotic cells and was recently applied to prokaryotes as well. This method will be specifically adapted to pathogenic bacteria from clinical settings.
Expected outcomes:
- Fixation protocols for bacterial RNA stabilization.
- Bioinformatics pipelines for single cell transcriptomic analysis in bacteria.
- A droplet-based scRNA seq platform tailored for bacterial cells.
- Identification of biomarkers for antibiotic-resistant subpopulations, leading to the development of diagnostic kits.
Significance:
This project addresses a critical gap in detecting and understanding bacterial heteroresistance, which is a significant challenge in treating bacterial infections. By developing advanced diagnostic tools and commercializing bacterial scRNA-seq services, this project aims to improve clinical outcomes and support optimal antimicrobial treatment strategies.
Keywords:
Single-cell RNA sequencing, heterogeneous antibiotic resistance, Staphylococcus aureus, diagnostic biomarkers, RNA stabilization
Ph.D candidate Freja C. Mikkelsen
In collaboration with Prof. Hanne Ingmer at University of Copenhagen.
Financed by Innovation Fund Denmark.