Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules
Journal article, 2016
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.
Author
Lena Nyberg
Chalmers, Biology and Biological Engineering, Chemical Biology
Mahmood Saair Quaderi
Lunds Universitet
Chalmers University of Technology
Gustav Emilsson
Chalmers, Physics, Bionanophotonics
N. Karami
Sahlgrenska Academy
E. Lagerstedt
Lunds Universitet
Vilhelm Müller
Chalmers, Biology and Biological Engineering, Chemical Biology
C. Noble
Lunds Universitet
S. Hammarberg
Lunds Universitet
A. Nilsson
Lunds Universitet
F. Sjoberg
Sahlgrenska Academy
Joachim Fritzsche
Chalmers, Physics, Chemical Physics
Jerker Fick
Chalmers University of Technology
L. Sandegren
Uppsala Universitet
T. Ambjornsson
Lunds Universitet
Fredrik Westerlund
Chalmers, Biology and Biological Engineering, Chemical Biology
Scientific Reports
2045-2322 (ISSN)
Vol. 6 30410Driving Forces
Sustainable development
Innovation and entrepreneurship
Areas of Advance
Nanoscience and Nanotechnology
Life Science Engineering (2010-2018)
DOI
10.1038/srep30410
PubMed
27460437