TY - JOUR
T1 - Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data
AU - Li, Ruichao
AU - Xie, Miaomiao
AU - Dong, Ning
AU - Lin, Dachuan
AU - Yang, Xuemei
AU - Wong, Marcus Ho Yin
AU - Chan, Edward Wai Chi
AU - Chen, Sheng
PY - 2018/3/1
Y1 - 2018/3/1
N2 - 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.
AB - 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.
KW - De novo assembly
KW - Long reads
KW - Multidrug resistance (MDR) plasmids
KW - Nanopore sequencing
UR - http://www.scopus.com/inward/record.url?scp=85050721613&partnerID=8YFLogxK
U2 - 10.1093/gigascience/gix132
DO - 10.1093/gigascience/gix132
M3 - Journal article
C2 - 29325009
AN - SCOPUS:85050721613
VL - 7
SP - 1
EP - 9
JO - GigaScience
JF - GigaScience
SN - 2047-217X
IS - 3
ER -