A parallelized nanofluidic device for high-throughput optical dna mapping of bacterial plasmids
Journal article, 2021

Optical DNA mapping (ODM) has developed into an important technique for DNA anal-ysis, where single DNA molecules are sequence-specifically labeled and stretched, for example, in nanofluidic channels. We have developed an ODM assay to analyze bacterial plasmids—circular extrachromosomal DNA that often carry genes that make bacteria resistant to antibiotics. As for most techniques, the next important step is to increase throughput and automation. In this work, we designed and fabricated a nanofluidic device that, together with a simple automation routine, allows parallel analysis of up to 10 samples at the same time. Using plasmids encoding extended-spectrum beta-lactamases (ESBL), isolated from Escherichia coli and Klebsiella pneumoniae, we demon-strate the multiplexing capabilities of the device when it comes to both many samples in parallel and different resistance genes. As a final example, we combined the device with a novel protocol for rapid cultivation and extraction of plasmids from fecal samples collected from patients. This combined protocol will make it possible to analyze many patient samples in one device already on the day the sample is collected, which is an important step forward for the ODM analysis of plas-mids in clinical diagnostics.

Antibiotic resistance

Multiplexing

Plasmids

Optical DNA mapping

nanofluidics

Author

Sriram Kesarimangalam

Chalmers, Biology and Biological Engineering, Chemical Biology

Yii Lih Lin

Chalmers, Biology and Biological Engineering, Chemical Biology

Tsegaye Sewunet

Karolinska Institutet

Marie Wrande

Uppsala University

L. Sandegren

Uppsala University

Christian G. Giske

Karolinska Institutet

Karolinska University Hospital

Fredrik Westerlund

Chalmers, Biology and Biological Engineering, Chemical Biology

Micromachines

2072-666X (ISSN)

Vol. 12 10 1234

Subject Categories

Infectious Medicine

Microbiology

Microbiology in the medical area

DOI

10.3390/mi12101234

PubMed

34683285

More information

Latest update

11/5/2021