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

Research output: Contribution to journalArticle

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 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.

Details

Authors
  • Lena K. Nyberg
  • Saair Quaderi
  • Gustav Emilsson
  • Nahid Karami
  • Erik Lagerstedt
  • Vilhelm Müller
  • Charleston Noble
  • Susanna Hammarberg
  • Adam N. Nilsson
  • Fei Sjöberg
  • Joachim Fritzsche
  • Erik Kristiansson
  • Linus Sandegren
  • Tobias Ambjörnsson
  • Fredrik Westerlund
Organisations
External organisations
  • Chalmers University of Technology
  • University of Gothenburg
  • Uppsala University
  • Lund University
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Microbiology in the medical area
Original languageEnglish
Article number30410
JournalScientific Reports
Volume6
Publication statusPublished - 2016 Jul 27
Publication categoryResearch
Peer-reviewedYes