Development and application of a novel approach to profile bacterial response to antibiotics

Purpose and goal:

Antimicrobial drug resistance (AMR) is an emerging crisis of the 21st century. Efficient antibiotic susceptibility tests (AST) are needed that are fast, apply to bacterial species in complex samples, and are independent of the resistance mechanisms.

We propose to develop a novel approach to screen for bacterial response to anti- and pro-biotic treatments, independent of prior knowledge regarding drug action and resistance mechanisms. We aim to develop a data-driven approach to assess bacterial susceptibility accurately and quantitatively to various treatments.

Expected results and effects:

3N Bio is a start-up company formed on the basis of the research results demonstrating the potential capabilities of the metadegradomics technology. The work described in this project will enable the development of data-driven “drug signatures” generalizing the use of the technology to a wide range of microbial samples and treatments. The results of this project will be used for developing the first 3N Bio product for AST, and will help us translate the results of basic research into clinics.

Approach and implementation:

We will make use of novel technology, HT-5PSeq that enables us to capture patterns of mRNA degradation in response to antibiotic treatment within minutes. We will collect versatile data on response of various bacterial species to several treatment options. We will develop a data-driven “drug signature” for quantitative assessment of AST from HT-5PSeq response profiles. The drug signatures we obtain here will let us use them in settings where culture-based methods are not an option.