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  • 1.
    Frykholm, K.
    et al.
    Department of Biology and Biological Engineering, Chalmers University of Technology.
    Nyberg, L. K.
    Department of Biology and Biological Engineering, Chalmers University of Technology.
    Lagerstedt, Erik
    Department of Astronomy and Theoretical Physics, Lund University.
    Noble, C.
    Department of Astronomy and Theoretical Physics, Lund University.
    Fritzsche, J.
    Department of Applied Physics, Chalmers University of Technology.
    Karami, N.
    Department of Clinical Microbiology, Sahlgrenska University Hospital and Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg.
    Ambjörnsson, T.
    Department of Astronomy and Theoretical Physics, Lund University.
    Sandegren, L.
    Department of Medical Biochemistry and Microbiology, Uppsala University.
    Westerlund, F.
    Department of Biology and Biological Engineering, Chalmers University of Technology.
    Fast size-determination of intact bacterial plasmids using nanofluidic channels2015In: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 15, no 13, p. 2739-2743Article in journal (Refereed)
    Abstract [en]

    We demonstrate how nanofluidic channels can be used as a tool to rapidly determine the number and sizes of plasmids in bacterial isolates. Each step can be automated at low cost, opening up opportunities for general use in microbiology labs.

  • 2.
    Nyberg, Lena K.
    et al.
    Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    Quaderi, Saair
    Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden / Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
    Emilsson, Gustav
    Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden / Department of Applied Physics, Chalmers University of Technology, Gothenburg, Sweden.
    Karami, Nahid
    Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
    Lagerstedt, Erik
    Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
    Müller, Vilhelm
    Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    Noble, Charleston
    Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
    Hammarberg, Susanna
    Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
    Nilsson, Adam N.
    Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
    Sjöberg, Fei
    Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
    Fritzsche, Joachim
    Department of Applied Physics, Chalmers University of Technology, Gothenburg, Sweden.
    Kristiansson, Erik
    Department of Mathematical Sciences, Chalmers University of Technology, University of Gothenburg, Gothenburg, Sweden.
    Sandegren, Linus
    Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
    Ambjörnsson, Tobias
    Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
    Westerlund, Fredrik
    Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 30410Article in journal (Refereed)
    Abstract [en]

    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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