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  • Müller, Vilhelm,1990Chalmers University of Technology,Chalmers Univ Technol, Dept Biol & Biol Engn, S-41296 Gothenburg, Sweden. (author)

Cultivation-Free Typing of Bacteria Using Optical DNA Mapping

  • Article/chapterEnglish2020

Publisher, publication year, extent ...

  • 2020-04-15
  • American Chemical Society (ACS),2020

Numbers

  • LIBRIS-ID:oai:gup.ub.gu.se/294086
  • https://gup.ub.gu.se/publication/294086URI
  • https://doi.org/10.1021/acsinfecdis.9b00464DOI
  • https://research.chalmers.se/publication/517383URI
  • https://lup.lub.lu.se/record/29cd63bc-8505-4b61-9465-11fa5a9e92e1URI
  • http://kipublications.ki.se/Default.aspx?queryparsed=id:143730085URI
  • https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-414316URI

Supplementary language notes

  • Language:English

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  • Subject category:ref swepub-contenttype
  • Subject category:art swepub-publicationtype

Notes

  • A variety of pathogenic bacteria can infect humans, and rapid species identification is crucial for the correct treatment. However, the identification process can often be time-consuming and depend on the cultivation of the bacterial pathogen(s). Here, we present a stand-alone, enzyme-free, optical DNA mapping assay capable of species identification by matching the intensity profiles of large DNA molecules to a database of fully assembled bacterial genomes (>10 000). The assay includes a new data analysis strategy as well as a general DNA extraction protocol for both Gram-negative and Gram-positive bacteria. We demonstrate that the assay is capable of identifying bacteria directly from uncultured clinical urine samples, as well as in mixtures, with the potential to be discriminative even at the subspecies level. We foresee that the assay has applications both within research laboratories and in clinical settings, where the time-consuming step of cultivation can be minimized or even completely avoided.

Subject headings and genre

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  • Nyblom, My,1995Chalmers University of Technology,Chalmers Univ Technol, Dept Biol & Biol Engn, S-41296 Gothenburg, Sweden.(Swepub:cth)myny (author)
  • Johnning, Anna,1985Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,CARe - Centrum för antibiotikaresistensforskning,Department of Mathematical Sciences,Centre for antibiotic resistance research, CARe,University of Gothenburg,Chalmers tekniska högskola,Chalmers University of Technology,Stiftelsen Fraunhofer-Chalmers Centrum för Industrimatematik (FCC),Fraunhofer-Chalmers Research Centre for Industrial Mathematics (FCC),Chalmers Univ Technol, Dept Math Sci, S-41296 Gothenburg, Sweden.;Univ Gothenburg, S-41296 Gothenburg, Sweden.;Fraunhofer Chalmers Ctr, Syst & Data Anal, S-41288 Gothenburg, Sweden.;Univ Gothenburg, Ctr Antibiot Resistance Res, CARe, S-40530 Gothenburg, Sweden.(Swepub:cth)johnning (author)
  • Wrande, MarieUppsala universitet,Uppsala University,Institutionen för medicinsk biokemi och mikrobiologi(Swepub:uu)masve204 (author)
  • Dvirnas, AlbertasLund University,Lunds universitet,Beräkningsbiologi och biologisk fysik - Genomgår omorganisation,Institutionen för astronomi och teoretisk fysik - Genomgår omorganisation,Naturvetenskapliga fakulteten,Computational Biology and Biological Physics - Undergoing reorganization,Department of Astronomy and Theoretical Physics - Undergoing reorganization,Faculty of Science,Lund Univ, Dept Astron & Theoret Phys, S-22362 Lund, Sweden.(Swepub:lu)al6377dv (author)
  • Kesarimangalam, Sriram,1983Chalmers tekniska högskola,Chalmers University of Technology,Chalmers Univ Technol, Dept Biol & Biol Engn, S-41296 Gothenburg, Sweden.(Swepub:cth)sriramk (author)
  • Giske, C. G.Karolinska Institutet,Karolinska University Hospital,Karolinska Inst, Dept Lab Med, S-14186 Stockholm, Sweden.;Karolinska Univ Hosp, Dept Clin Microbiol, S-17176 Stockholm, Sweden. (author)
  • Ambjörnsson, Tobias,1974Lund University,Lunds universitet,Beräkningsbiologi och biologisk fysik - Genomgår omorganisation,Institutionen för astronomi och teoretisk fysik - Genomgår omorganisation,Naturvetenskapliga fakulteten,Computational Biology and Biological Physics - Undergoing reorganization,Department of Astronomy and Theoretical Physics - Undergoing reorganization,Faculty of Science,Lund Univ, Dept Astron & Theoret Phys, S-22362 Lund, Sweden.(Swepub:lu)thep-tar (author)
  • Sandegren, LinusUppsala universitet,Uppsala University,Institutionen för medicinsk biokemi och mikrobiologi(Swepub:uu)lisan839 (author)
  • Kristiansson, Erik,1978Gothenburg University,Göteborgs universitet,CARe - Centrum för antibiotikaresistensforskning,Institutionen för matematiska vetenskaper,Centre for antibiotic resistance research, CARe,Department of Mathematical Sciences,Chalmers tekniska högskola,Chalmers University of Technology,University of Gothenburg,Chalmers Univ Technol, Dept Math Sci, S-41296 Gothenburg, Sweden.;Univ Gothenburg, Ctr Antibiot Resistance Res, CARe, S-40530 Gothenburg, Sweden.(Swepub:cth)erikkr (author)
  • Westerlund, Fredrik,1978Chalmers University of Technology,Chalmers Univ Technol, Dept Biol & Biol Engn, S-41296 Gothenburg, Sweden.(Swepub:cth)fredrikw (author)
  • Kk, SriramChalmers University of Technology (author)
  • Chalmers University of TechnologyChalmers Univ Technol, Dept Biol & Biol Engn, S-41296 Gothenburg, Sweden. (creator_code:org_t)

Related titles

  • In:Acs Infectious Diseases: American Chemical Society (ACS)6:5, s. 1076-10842373-8227

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