Optical maps of plasmids as a proxy for clonal spread of MDR bacteria: A case study of an outbreak in a rural Ethiopian hospital
Journal article, 2020

Objectives: MDR bacteria have become a prevailing health threat worldwide. We here aimed to use optical DNA mapping (ODM) as a rapid method to trace nosocomial spread of bacterial clones and gene elements.We believe that this method has the potential to be a tool of pivotal importance for MDR control.
Methods: Twenty-four Escherichia coli samples of ST410 from three different wards were collected at an Ethiopian hospital and their plasmids were analysed by ODM. Plasmids were specifically digested with Cas9 targeting the antibiotic resistance genes, stained by competitive binding and confined in nanochannels for imaging. The resulting intensity profiles (barcodes) for each plasmid were compared to identify potential clonal spread of resistant bacteria.
Results: ODM demonstrated that a large fraction of the patients carried bacteria with a plasmid of the same origin, carrying the ESBL gene blaCTX-M-15, suggesting clonal spread. The results correlate perfectly with core genome (cg)MLST data, where bacteria with the same plasmid also had very similar cgMLST profiles.
Conclusions: ODM is a rapid discriminatory method for identifying plasmids and antibiotic resistance genes. Long-range deletions/insertions, which are challenging for short-read next-generation sequencing, can be easily identified and used to trace bacterial clonal spread. We propose that plasmid typing can be a useful tool to identify clonal spread of MDR bacteria. Furthermore, the simplicity of the method enables possible future application in low-and middle-income countries.


Yii Lih Lin

Chalmers, Biology and Biological Engineering, Chemical Biology

Tsegaye Sewunet

Jimma University

Karolinska Institutet

Sriram Kesarimangalam

Chalmers, Biology and Biological Engineering, Chemical Biology

Christian G. Giske

Karolinska Institutet

Karolinska University Hospital

Fredrik Westerlund

Chalmers, Biology and Biological Engineering, Chemical Biology

Journal of Antimicrobial Chemotherapy

0305-7453 (ISSN) 1460-2091 (eISSN)

Vol. 75 10 2804-2811

Driving Forces

Sustainable development

Areas of Advance

Health Engineering

Subject Categories


Bioinformatics and Systems Biology






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