Tobias Ambjörnsson
Senior lecturer
Cultivation-Free Typing of Bacteria Using Optical DNA Mapping
Author
Summary, in English
A variety of pathogenic bacteria can infect humans, and rapid species identification is crucial for the correct treatment. However, the identification process can often be time-consuming and depend on the cultivation of the bacterial pathogen(s). Here, we present a stand-alone, enzyme-free, optical DNA mapping assay capable of species identification by matching the intensity profiles of large DNA molecules to a database of fully assembled bacterial genomes (>10 000). The assay includes a new data analysis strategy as well as a general DNA extraction protocol for both Gram-negative and Gram-positive bacteria. We demonstrate that the assay is capable of identifying bacteria directly from uncultured clinical urine samples, as well as in mixtures, with the potential to be discriminative even at the subspecies level. We foresee that the assay has applications both within research laboratories and in clinical settings, where the time-consuming step of cultivation can be minimized or even completely avoided.
Department/s
- Computational Biology and Biological Physics - Has been reorganised
Publishing year
2020-05-08
Language
English
Pages
1076-1084
Publication/Series
ACS Infectious Diseases
Volume
6
Issue
5
Document type
Journal article
Publisher
The American Chemical Society (ACS)
Topic
- Microbiology
- Microbiology in the medical area
- Biophysics
- Other Physics Topics
Keywords
- bacteria
- diagnostics
- nanofluidics
- optical DNA mapping
- UTI
Status
Published
ISBN/ISSN/Other
- ISSN: 2373-8227