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Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules

Nyberg, Lena K. LU ; Quaderi, Saair; Emilsson, Gustav; Karami, Nahid; Lagerstedt, Erik; Müller, Vilhelm; Noble, Charleston LU ; Hammarberg, Susanna; Nilsson, Adam N. LU and Sjöberg, Fei, et al. (2016) In Scientific Reports 6.
Abstract

The rapid spread of antibiotic resistance-currently one of the greatest threats to human health according to WHO-is to a large extent enabled by plasmid-mediated horizontal transfer of resistance genes. Rapid identification and characterization of plasmids is thus important both for individual clinical outcomes and for epidemiological monitoring of antibiotic resistance. Toward this aim, we have developed an optical DNA mapping procedure where individual intact plasmids are elongated within nanofluidic channels and visualized through fluorescence microscopy, yielding barcodes that reflect the underlying sequence. The assay rapidly identifies plasmids through statistical comparisons with barcodes based on publicly available sequence... (More)

The rapid spread of antibiotic resistance-currently one of the greatest threats to human health according to WHO-is to a large extent enabled by plasmid-mediated horizontal transfer of resistance genes. Rapid identification and characterization of plasmids is thus important both for individual clinical outcomes and for epidemiological monitoring of antibiotic resistance. Toward this aim, we have developed an optical DNA mapping procedure where individual intact plasmids are elongated within nanofluidic channels and visualized through fluorescence microscopy, yielding barcodes that reflect the underlying sequence. The assay rapidly identifies plasmids through statistical comparisons with barcodes based on publicly available sequence repositories and also enables detection of structural variations. Since the assay yields holistic sequence information for individual intact plasmids, it is an ideal complement to next generation sequencing efforts which involve reassembly of sequence reads from fragmented DNA molecules. The assay should be applicable in microbiology labs around the world in applications ranging from fundamental plasmid biology to clinical epidemiology and diagnostics.

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Scientific Reports
volume
6
publisher
Nature Publishing Group
external identifiers
  • scopus:84979783998
  • wos:000380330100001
ISSN
2045-2322
DOI
10.1038/srep30410
language
English
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yes
id
335b6cd4-e144-4704-a953-bf213ad5decb
date added to LUP
2016-12-19 15:23:03
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2017-09-18 11:32:25
@article{335b6cd4-e144-4704-a953-bf213ad5decb,
  abstract     = {<p>The rapid spread of antibiotic resistance-currently one of the greatest threats to human health according to WHO-is to a large extent enabled by plasmid-mediated horizontal transfer of resistance genes. Rapid identification and characterization of plasmids is thus important both for individual clinical outcomes and for epidemiological monitoring of antibiotic resistance. Toward this aim, we have developed an optical DNA mapping procedure where individual intact plasmids are elongated within nanofluidic channels and visualized through fluorescence microscopy, yielding barcodes that reflect the underlying sequence. The assay rapidly identifies plasmids through statistical comparisons with barcodes based on publicly available sequence repositories and also enables detection of structural variations. Since the assay yields holistic sequence information for individual intact plasmids, it is an ideal complement to next generation sequencing efforts which involve reassembly of sequence reads from fragmented DNA molecules. The assay should be applicable in microbiology labs around the world in applications ranging from fundamental plasmid biology to clinical epidemiology and diagnostics.</p>},
  articleno    = {30410},
  author       = {Nyberg, Lena K. and Quaderi, Saair and Emilsson, Gustav and Karami, Nahid and Lagerstedt, Erik and Müller, Vilhelm and Noble, Charleston and Hammarberg, Susanna and Nilsson, Adam N. and Sjöberg, Fei and Fritzsche, Joachim and Kristiansson, Erik and Sandegren, Linus and Ambjörnsson, Tobias and Westerlund, Fredrik},
  issn         = {2045-2322},
  language     = {eng},
  month        = {07},
  publisher    = {Nature Publishing Group},
  series       = {Scientific Reports},
  title        = {Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules},
  url          = {http://dx.doi.org/10.1038/srep30410},
  volume       = {6},
  year         = {2016},
}