Cultivation-Free Typing of Bacteria Using Optical DNA Mapping
Journal article, 2020

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.

diagnostics

nanofluidics

UTI

optical DNA mapping

bacteria

Author

Vilhelm Müller

Chalmers, Biology and Biological Engineering, Chemical Biology

My Nyblom

Chalmers, Biology and Biological Engineering, Chemical Biology

Anna Johnning

University of Gothenburg

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

Fraunhofer-Chalmers Centre

Marie Wrande

Uppsala University

Albertas Dvirnas

Lund University

Sriram Kesarimangalam

Chalmers, Biology and Biological Engineering, Chemical Biology

Christian G. Giske

Karolinska University Hospital

Karolinska Institutet

Tobias Ambjörnsson

Lund University

L. Sandegren

Uppsala University

Erik Kristiansson

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

University of Gothenburg

Fredrik Westerlund

Chalmers, Biology and Biological Engineering, Chemical Biology

ACS Infectious Diseases

2373-8227 (eISSN)

Vol. 6 5 1076-1084

Subject Categories

Microbiology

DOI

10.1021/acsinfecdis.9b00464

PubMed

32294378

More information

Latest update

8/4/2020 1