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 1076-1084Subject Categories
Microbiology
DOI
10.1021/acsinfecdis.9b00464
PubMed
32294378