Multi-clonal evolution of multi-drug-resistant/extensively drug-resistant Mycobacterium tuberculosis in a high-prevalence setting of Papua New Guinea for over three decades

Abstract

An outbreak of multi-drug resistant (MDR) tuberculosis (TB) has been reported on Daru Island, Papua New Guinea. Mycobacterium tuberculosis strains driving this outbreak and the temporal accrual of drug resistance mutations have not been described. Whole genome sequencing of 100 of 165 clinical isolates referred from Daru General Hospital to the Supranational reference laboratory, Brisbane, during 2012–2015 revealed that 95 belonged to a single modern Beijing sub-lineage strain. Molecular dating suggested acquisition of streptomycin and isoniazid resistance in the 1960s, with potentially enhanced virulence mediated by an mycP1 mutation. The Beijing sub-lineage strain demonstrated a high degree of co-resistance between isoniazid and ethionamide (80/95; 84.2 %) attributed to an inhA promoter mutation combined with inhA and ndh coding mutations. Multi-drug resistance, observed in 78/95 samples, emerged with the acquisition of a typical rpoB mutation together with a compensatory rpoC mutation in the 1980s. There was independent acquisition of fluoroquinolone and aminoglycoside resistance, and evidence of local transmission of extensively drug resistant (XDR) strains from 2009. These findings underline the importance of whole genome sequencing in informing an effective public health response to MDR/XDR TB.

A complete high quality nanopore-only assembly of an XDR Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions

“…In this study, we utilized Oxford Nanopore MinION sequencing to assemble a comprehensive genome of a strain that is responsible for a drug resistant outbreaks in the Western Province of Papua New Guinea (24). The complete circular genome of this modern Beijing sub-lineage 2.2.1.1 strain revealed genetic determinants of drug resistance against first and second line TB drugs.…”

“…We assessed single nucleotide polymorphisms (SNPs) within PE/PPE genes from nanopore and Illumina reads. In addition, representative raw Illumina reads from four M. tuberculosis lineages; Indo-Oceanic, East-Asian (including Beijing lineage), East-African-Indian and Euro-American lineage (including H37Rv) from previous studies (24, 25, 39, 40) were mapped to the draft genome and assessed for large deletions that differentiate the draft genome from other lineages.…”

“…Papua New Guinea (PNG) has a high rate of drug resistant TB in its Western Province (22, 23). We recently characterized a drug resistant tuberculosis outbreak on Daru island, which is driven by a modern Beijing sub-lineage 2.2.1.1 strain (24). Whilst some genetic markers within the strain have been identified (24), the molecular mechanisms responsible for pathogenesis and virulence are not fully elucidated.…”

“…We recently characterized a drug resistant tuberculosis outbreak on Daru island, which is driven by a modern Beijing sub-lineage 2.2.1.1 strain (24). Whilst some genetic markers within the strain have been identified (24), the molecular mechanisms responsible for pathogenesis and virulence are not fully elucidated. Genomic regions like proline-glutamate (PE, 99 loci) and proline-proline-glutamate (PPE, 69) genes are routinely excluded in genomic analysis of M. tuberculosis due to their repetitive nature and high GC content (10, 24, 25).…”

“…Whilst some genetic markers within the strain have been identified (24), the molecular mechanisms responsible for pathogenesis and virulence are not fully elucidated. Genomic regions like proline-glutamate (PE, 99 loci) and proline-proline-glutamate (PPE, 69) genes are routinely excluded in genomic analysis of M. tuberculosis due to their repetitive nature and high GC content (10, 24, 25). A recent multinational study utilized 518 sample to study PE/PPE family genes and was able to assemble at least 120 out of the 168 genes for each sample (26).…”