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Data released on December 11, 2017

Supporting data for "Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data"

Li, R; Xie, M; Dong, N; Lin, D; Yang, X; Wong, M; Chan, E; CHEN, S (2017): Supporting data for "Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data" GigaScience Database. RIS BibTeX Text

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 sequence 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 IS elements, complete sequencing of MDR plasmids remains technically complicated, expensive and time consuming.
Here, we demonstrate a rapid and efficient approach to obtain multiple MDR plasmid sequences through the use of the MinION nanopore sequencing platform, which is incorporated in a portable MinION device. By assembling the long sequencing reads generated by a single MinION run according to a rapid barcoding sequencing protocol, we obtained the complete sequence of 20 plasmids harbored by bacterial strains recovered from multiple samples. 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.
This workflow represents a novel, convenient and cost effective approach for systematic assessment of the full range of MDR plasmids responsible for causing failure in antimicrobial treatment of bacterial infections, offering for the first time the opportunity to perform detailed molecular epidemiological studies to probe the evolutionary and transmission routes / mechanisms of MDR-encoding elements.

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Read the peer-reviewed publication(s):

Li, R., Xie, M., Dong, N., Lin, D., Yang, X., 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). doi:10.1093/gigascience/gix132

Accessions (data included in GigaDB):

BioProject: PRJNA398365


multidrug resistance (mdr) plasmids de novo assembly nanopore sequencing long reads 




  • Funding body - Ministry of Science and Technology
  • Award ID - 2013CB127200
  • Comment - Chinese National Key Basic Research and Development (973) Program
  • Awardee - S Chen
  • Funding body - Research Grants Council
  • Award ID - C7038-15G
  • Comment - University Grants Committee
  • Awardee - S Chen

Samples: Table Settings


Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
RB01562E. coli Escherichia coli Description:NA
Alternative accession-BioSample:SAMN07508944
RB02562E. coli Escherichia coli Description:NA
Alternative accession-BioSample:SAMN07508945
RB03562E. coli Escherichia coli Description:NA
Alternative accession-BioSample:SAMN07508946
RB04562E. coli Escherichia coli Description:NA
Alternative accession-BioSample:SAMN07508947
Strain:SZM584-1-T NDM TC
RB05562E. coli Escherichia coli Description:NA
Alternative accession-BioSample:SAMN07508948
RB06562E. coli Escherichia coli Description:NA
Alternative accession-BioSample:SAMN07508949
RB07670  Vibrio parahaemolyticus Description:NA
Alternative accession-BioSample:SAMN07508950
RB0890371  Salmonella enterica subsp. enterica serovar Typhimurium Description:NA
Alternative accession-BioSample:SAMN07508951
RB09562E. coli Escherichia coli Description:NA
Alternative accession-BioSample:SAMN07508952
RB10562E. coli Escherichia coli Description:NA
Alternative accession-BioSample:SAMN07508953
Displaying 1-10 of 12 Sample(s).

Files: (FTP site) Table Settings


File Description
Sample ID
Data Type
File Format
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
Sequence readsFASTA306.88 KB2017-11-29
Sequence readsUNKNOWN157.88 MB2017-11-29
file_typeUNKNOWN252.66 KB2017-11-29
file_typeUNKNOWN179.94 KB2017-11-29
Sequence assemblyFASTA209.86 KB2017-11-29
ReadmeTEXT2.1 KB2017-11-29
Sequence assemblyFASTA2.41 MB2017-11-29
Displaying 1-7 of 7 File(s).



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