title: Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules.
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.
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
authors.forename: Lena K
authors.initials: LK
authors.lastname: Nyberg
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.|Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
authors.forename: Saair
authors.initials: S
authors.lastname: Quaderi
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.|Department of Applied Physics, Chalmers University of Technology, Gothenburg, Sweden.
authors.forename: Gustav
authors.initials: G
authors.lastname: Emilsson
authors.affiliation: Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
authors.forename: Nahid
authors.initials: N
authors.lastname: Karami
authors.affiliation: Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Lagerstedt
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
authors.forename: Vilhelm
authors.initials: V
authors.lastname: Müller
authors.affiliation: Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
authors.forename: Charleston
authors.initials: C
authors.lastname: Noble
authors.affiliation: Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
authors.forename: Susanna
authors.initials: S
authors.lastname: Hammarberg
authors.affiliation: Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
authors.forename: Adam N
authors.initials: AN
authors.lastname: Nilsson
authors.affiliation: Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
authors.forename: Fei
authors.initials: F
authors.lastname: Sjöberg
authors.affiliation: Department of Applied Physics, Chalmers University of Technology, Gothenburg, Sweden.
authors.forename: Joachim
authors.initials: J
authors.lastname: Fritzsche
authors.affiliation: Department of Mathematical Sciences, Chalmers University of Technology/University of Gothenburg, Gothenburg, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Kristiansson
authors.affiliation: Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Linus
authors.initials: L
authors.lastname: Sandegren
authors.affiliation: Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
authors.forename: Tobias
authors.initials: T
authors.lastname: Ambjörnsson
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Westerlund
mesh_terms: D001419:Bacteria / Q000235:genetics; D004247:DNA / Q000737:chemistry*; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D005456:Fluorescent Dyes; D044085:Microfluidics / Q000379:methods*; D061848:Optical Imaging / Q000379:methods*; D010957:Plasmids / Q000235:genetics*
chemical_list: D005456:Fluorescent Dyes; D004247:DNA