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

Contact Submitter

Accessions (data included in GigaDB):

BioProject: PRJNA398365

Keywords:

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

Workflow

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Funding:

  • 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

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
RB01562E. coli Escherichia coli Description:NA
Alternative accessions-BioSample: SAMN07508944
Strain:LZ135
...
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RB02562E. coli Escherichia coli Description:NA
Alternative accessions-BioSample: SAMN07508945
Strain:JN105
...
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RB03562E. coli Escherichia coli Description:NA
Alternative accessions-BioSample: SAMN07508946
Strain:WH96T
...
+
RB04562E. coli Escherichia coli Description:NA
Alternative accessions-BioSample: SAMN07508947
Strain:SZM584-1-T NDM TC
...
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RB05562E. coli Escherichia coli Description:NA
Alternative accessions-BioSample: SAMN07508948
Strain:C267
...
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RB06562E. coli Escherichia coli Description:NA
Alternative accessions-BioSample: SAMN07508949
Strain:C499
...
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RB07670  Vibrio parahaemolyticus Description:NA
Alternative accessions-BioSample: SAMN07508950
Strain:Vb0506
...
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RB0890371  Salmonella enterica subsp. enterica serovar Typhimurium Description:NA
Alternative accessions-BioSample: SAMN07508951
Strain:QJ18
...
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RB09562E. coli Escherichia coli Description:NA
Alternative accessions-BioSample: SAMN07508952
Strain:5T-KPC
...
+
RB10562E. coli Escherichia coli Description:NA
Alternative accessions-BioSample: SAMN07508953
Strain:29-KPC
...
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Displaying 1-10 of 12 Sample(s).

Files: (FTP site) Table Settings

Columns:

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

File NameSample IDFile 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
ReadmeTEXT-0 KB2017-11-29
Sequence assemblyFASTA2.41 MB2017-11-29
Displaying 1-7 of 7 File(s).

History:

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