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Cultivation-Free Typing of Bacteria Using Optical DNA Mapping

Müller, Vilhelm ; Nyblom, My ; Johnning, Anna ; Wrande, Marie ; Dvirnas, Albertas LU ; Kk, Sriram ; Giske, Christian G. ; Ambjörnsson, Tobias LU ; Sandegren, Linus and Kristiansson, Erik , et al. (2020) In ACS Infectious Diseases 6(5). p.1076-1084
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... (More)

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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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
bacteria, diagnostics, nanofluidics, optical DNA mapping, UTI
in
ACS Infectious Diseases
volume
6
issue
5
pages
9 pages
publisher
The American Chemical Society (ACS)
external identifiers
  • pmid:32294378
  • scopus:85084721005
ISSN
2373-8227
DOI
10.1021/acsinfecdis.9b00464
language
English
LU publication?
yes
id
29cd63bc-8505-4b61-9465-11fa5a9e92e1
date added to LUP
2020-06-09 09:27:53
date last changed
2024-04-03 06:48:22
@article{29cd63bc-8505-4b61-9465-11fa5a9e92e1,
  abstract     = {{<p>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 (&gt;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.</p>}},
  author       = {{Müller, Vilhelm and Nyblom, My and Johnning, Anna and Wrande, Marie and Dvirnas, Albertas and Kk, Sriram and Giske, Christian G. and Ambjörnsson, Tobias and Sandegren, Linus and Kristiansson, Erik and Westerlund, Fredrik}},
  issn         = {{2373-8227}},
  keywords     = {{bacteria; diagnostics; nanofluidics; optical DNA mapping; UTI}},
  language     = {{eng}},
  month        = {{05}},
  number       = {{5}},
  pages        = {{1076--1084}},
  publisher    = {{The American Chemical Society (ACS)}},
  series       = {{ACS Infectious Diseases}},
  title        = {{Cultivation-Free Typing of Bacteria Using Optical DNA Mapping}},
  url          = {{http://dx.doi.org/10.1021/acsinfecdis.9b00464}},
  doi          = {{10.1021/acsinfecdis.9b00464}},
  volume       = {{6}},
  year         = {{2020}},
}