A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions
Arnold Bainomugisa, Tania Duarte, Evelyn Lavu, Sushil Pandey, Chris Coulter, Ben J Marais, Lachlan M Coin
MICROBIAL GENOMICS | MICROBIOLOGY SOC | Published : 2018
A better understanding of the genomic changes that facilitate the emergence and spread of drug-resistant Mycobacterium tuberculosis strains is currently required. Here, we report the use of the MinION nanopore sequencer (Oxford Nanopore Technologies) to sequence and assemble an extensively drug-resistant (XDR) isolate, which is part of a modern Beijing sub-lineage strain, prevalent in Western Province, Papua New Guinea. Using 238-fold coverage obtained from a single flow-cell, de novo assembly of nanopore reads resulted into one contiguous assembly with 99.92 % assembly accuracy. Incorporation of complementary short read sequences (Illumina) as part of consensus error correction resulted in ..View full abstract
Awarded by Centre for Superbugs Solutions, Institute for Molecular Bioscience
This study was supported by funding from the Centre for Superbugs Solutions (610246), Institute for Molecular Bioscience.