A complete nanopore-only assembly of an XDR Mycobacterium tuberculosis Beijing lineage strain identifies novel genetic variation in repetitive PE/PPE gene regions
30th January 2018 - BioRxiv
A better understanding of the genomic changes that facilitate the emergence and spread of drug resistant M. tuberculosis strains is required. We sequenced an extensively drug resistant (XDR) Beijing sub-lineage 220.127.116.11 strain from the Western Province of Papua New Guinea using long-read sequencing (Oxford Nanopore MinION). We assembled a 4404947bp circular genome with 3670 coding sequences including highly repetitive PE/PPE genes. Comparison with Illumina reads indicated a base-level accuracy of 99.52%. Mutations known to confer drug resistance to first and second line drugs were identified and concurred with phenotypic resistance assays. We identified mutations in efflux pump genes (Rv0194), transporters (secA1, glnQ, uspA), cell wall biosynthesis genes (pdk, mmpL, fadD) and virulence genes (mce-gene family, mycp1) that may contribute to the drug resistance phenotype and successful transmission of this strain. Using the newly assembled genome as reference to map raw Illumina reads from representative M. tuberculosis lineages, we detect large insertions relative to the reference genome. We provide a fully annotated genome of a transmissible XDR M. tuberculosis strain from Papua New Guinea using Oxford Nanopore MinION sequencing and provide insight into genomic mechanisms of resistance and virulence.