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Cultivation-Free Typing of Bacteria Using Optical DNA Mapping

Journal article
Authors M. Nyblom
Anna Johnning
M. Wrande
A. Dvirnas
K. K. Sriram
C. G. Giske
T. Ambjornsson
L. Sandegren
Erik Kristiansson
F. Westerlund
Published in Acs Infectious Diseases
Volume 6
Issue 5
Pages 1076-1084
ISSN 2373-8227
Publication year 2020
Published at Department of Mathematical Sciences
Centre for antibiotic resistance research, CARe
Pages 1076-1084
Language en
Links dx.doi.org/10.1021/acsinfecdis.9b00...
Keywords nanofluidics, optical DNA mapping, diagnostics, bacteria, UTI, molecules, diagnosis, sequence, strains, binding, Pharmacology & Pharmacy, Infectious Diseases
Subject categories Infectious Medicine

Abstract

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.

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