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

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.
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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.
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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.