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

Dataset type: Workflow
Data released on December 11, 2017

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. http://dx.doi.org/10.5524/100387

DOI10.5524/100387

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.

Additional details

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





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
RB01562E. coli Escherichia coli Description:NA
Alternative accession-BioSample:SAMN07508944
Strain:LZ135
...
+
RB02562E. coli Escherichia coli Description:NA
Alternative accession-BioSample:SAMN07508945
Strain:JN105
...
+
RB03562E. coli Escherichia coli Description:NA
Alternative accession-BioSample:SAMN07508946
Strain:WH96T
...
+
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
Strain:C267
...
+
RB06562E. coli Escherichia coli Description:NA
Alternative accession-BioSample:SAMN07508949
Strain:C499
...
+
RB07670  Vibrio parahaemolyticus Description:NA
Alternative accession-BioSample:SAMN07508950
Strain:Vb0506
...
+
RB0890371  Salmonella enterica subsp. enterica serovar Typhimurium Description:NA
Alternative accession-BioSample:SAMN07508951
Strain:QJ18
...
+
RB09562E. coli Escherichia coli Description:NA
Alternative accession-BioSample:SAMN07508952
Strain:5T-KPC
...
+
RB10562E. coli Escherichia coli Description:NA
Alternative accession-BioSample:SAMN07508953
Strain:29-KPC
...
+
Displaying 1-10 of 12 Sample(s).




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).
Funding body Awardee Award ID Comments
Ministry of Science and Technology S Chen 2013CB127200 Chinese National Key Basic Research and Development (973) Program
Research Grants Council S Chen C7038-15G University Grants Committee
Date Action
December 11, 2017 Dataset publish
March 27, 2018 File readme.txt updated
March 30, 2018 Manuscript Link added : 10.1093/gigascience/gix132