Please use this identifier to cite or link to this item: http://hdl.handle.net/10397/79687
Title: Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data
Authors: Li, RC 
Xie, MM 
Dong, N 
Lin, DC 
Yang, XM 
Wong, MHY 
Chan, EWC 
Chen, S 
Keywords: Multidrug resistance (MDR) plasmids
De novo assembly
Nanopore sequencing
Long reads
Issue Date: 2018
Publisher: Oxford University Press
Source: Gigascience, 9 Jan. 2018, v. 7, no. 3, p. 1-9 How to cite?
Journal: Gigascience 
Abstract: Background: Multidrug resistance (MDR)-encoding plasmids are considered major molecular vehicles responsible for transmission of antibiotic resistance genes among bacteria of the same or different species. Delineating the complete sequences of such plasmids could provide valuable insight into the evolution and transmission mechanisms underlying bacterial antibiotic resistance development. However, due to the presence of multiple repeats of mobile elements, complete sequencing of MDR plasmids remains technically complicated, expensive, and time-consuming.
Results: Here, we demonstrate a rapid and efficient approach to obtaining multiple MDR plasmid sequences through the use of the MinION nanopore sequencing platform, which is incorporated in a portable device. By assembling the long sequencing reads generated by a single MinION run according to a rapid barcoding sequencing protocol, we obtained the complete sequences of 20 plasmids harbored by multiple bacterial strains. Importantly, single long reads covering a plasmid end-to-end were recorded, indicating that de novo assembly may be unnecessary if the single reads exhibit high accuracy.
Conclusions: This workflow represents a convenient and cost-effective approach for systematic assessment of MDR plasmids responsible for treatment failure of bacterial infections, offering the opportunity to perform detailed molecular epidemiological studies to probe the evolutionary and transmission mechanisms of MDR-encoding elements.
URI: http://hdl.handle.net/10397/79687
EISSN: 2047-217X
DOI: 10.1093/gigascience/gix132
Rights: ©The Author(s) 2018. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative CommonsAttribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in anymedium,provided the original work is properly cited.
The following publication Li, R. C., Xie, M. M., Dong, N., Lin, D. C., Yang, X. M., Wong, M. H. Y., … & Chen, S. (2018). Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data. Gigascience, 7(3), 1-9 is available at https://dx.doi.org/10.1093/gigascience/gix132
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