Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak

Santosh K. Bikkarolla, Viveka Nordberg, Fredrika Rajer, Vilhelm Müller, Muhammad Humaun Kabir, K. K. Sriram, Albertas Dvirnas, Tobias Ambjörnsson, Christian G. Giske, Lars Navér, Linus Sandegren, Fredrik Westerlund

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22 Citations (Scopus)
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The global spread of antibiotic resistance among Enterobacteriaceae is
largely due to multidrug resistance plasmids that can transfer between different bacterial strains and species. Horizontal gene transfer of resistance plasmids can complicate hospital outbreaks and cause problems in epidemiological tracing, since tracing is usually based on bacterial clonality. We have developed a method, based on optical DNA mapping combined with Cas9-assisted identification of resistance genes, which is used here to characterize plasmids during an extended-spectrum -lactamase (ESBL)-producing Enterobacteriaceae outbreak at a Swedish neonatal intensive care unit. The outbreak included 17 neonates initially colonized with ESBLproducing Klebsiella pneumoniae (ESBL-KP), some of which were found to carry additional ESBL-producing Escherichia coli (ESBL-EC) in follow-up samples. We demonstrate that all ESBL-KP isolates contained two plasmids with the blaCTX-M-15 gene located on the smaller one (~80 kbp). The same ESBL-KP clone was present in follow-up samples for up to 2 years in some patients, and the plasmid carrying the blaCTX-M-15 gene was stable throughout this time period. However, extensive genetic rearrangements within the second plasmid were observed in the optical DNA maps for several of the ESBL-KP isolates. Optical mapping also demonstrated that even though other bacterial clones and species carrying blaCTX-M group 1 genes were
found in some neonates, no transfer of resistance plasmids had occurred. The data instead pointed toward unrelated acquisition of ESBL-producing Enterobacteriaceae (EPE). In addition to revealing important information about the specific outbreak, the method presented is a promising tool for surveillance and infection control in clinical settings.
Original languageEnglish
Article numbere00347-19
Pages (from-to)1-12
Number of pages12
Issue number4
Publication statusPublished (in print/issue) - 9 Jul 2019

Bibliographical note

Funding Information:
This project was funded by grants to F.W. from Torsten Söderbergs Stiftelse, Åke Wibergs Stiftelse and the EU Horizon 2020 program BeyondSeq (634890), to L.S. from the Swedish Research Council (K2013-99X-22208-01-5), and to F.W., L.S., T.A., and C.G. from Familjen Erling Perssons Stiftelse. Santosh K. Bikkarolla has a personal stipend from the Wenner-Gren Foundation.

Publisher Copyright:
© 2019 Bikkarolla et al.

Copyright 2019 Elsevier B.V., All rights reserved.


  • Antibiotic resistance
  • CRISPR/Cas9
  • Intensive care unit
  • Optical DNA mapping
  • Plasmids


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