Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak
Journal article, 2019

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 β-lactamase (ESBL)-producing Enterobacteriaceae outbreak at a Swedish neonatal intensive care unit. The outbreak included 17 neonates initially colonized with ESBL-producing 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.

intensive care unit

plasmids

CRISPR/Cas9

Antibiotic resistance

optical dna mapping

Author

Santosh Kumar Bikarolla

Chalmers, Biology and Biological Engineering, Chemical Biology

Viveka Nordberg

Karolinska University Hospital

Karolinska Institutet

Fredrika Rajer

Uppsala University

Vilhelm Müller

Chalmers, Biology and Biological Engineering, Chemical Biology

Muhammad Humaun Kabir

Karolinska Institutet

Sriram Kesarimangalam

Chalmers, Biology and Biological Engineering, Chemical Biology

Albertas Dvirnas

Lund University

Tobias Ambjornsson

Lund University

Christian G. Giske

Karolinska Institutet

Karolinska University Hospital

Lars Navér

Karolinska Institutet

Linus Sandegren

Uppsala University

Fredrik Westerlund

Chalmers, Biology and Biological Engineering, Chemical Biology

mBio

2161-2129 (ISSN) 2150-7511 (eISSN)

Vol. 10 4 e00347-19

Areas of Advance

Nanoscience and Nanotechnology (2010-2017)

Subject Categories

Infectious Medicine

Nano Technology

DOI

10.1128/mBio.00347-19

PubMed

31289171

More information

Latest update

6/28/2020