ArticleMicrobial genomics2018
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.
Article in Microbial genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 2 of them syntheses that pooled it.
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Who cites it
33 citing papers in PubMed, 2 syntheses or guidelines pooled it, 61 citations in OpenAlex.
- Nanopore Sequencing for Mycobacterium tuberculosis: a Critical Review of the Literature, New Developments, and Future Opportunities.Journal of clinical microbiology · 2022Pooled it
- Systematic Review of Mutations Associated with Isoniazid Resistance Points to Continuing Evolution and Subsequent Evasion of Molecular Detection, and Potential for Emergence of Multidrug Resistance in Clinical Strains of Mycobacterium tuberculosis.Antimicrobial agents and chemotherapy · 2021Pooled it
- Complete genomes reveal a refined map of Mycobacterium tuberculosis genetic diversity across evolutionary scales.Nature communications · 2026Article
- First Confirmed Case of Zoonotic Transmission of RR-TB from a Dog to a Human, a Neglected Mode ofPathogens (Basel, Switzerland) · 2025Review
- Interred mechanisms of resistance and host immune evasion revealed through network-connectivity analysis ofmSystems · 2025Article
- A pragmatic pipeline for drug resistance and lineage identification in Mycobacterium tuberculosis using whole genome sequencing.PLOS global public health · 2025Article
- High-Accuracy Long-Read Sequencing ofThe Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale · 2025Article
- Article
- A practical comparison of the next-generation sequencing platform and assemblers using yeast genome.Life science alliance · 2023Article
- A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome.Nature communications · 2022Article
- Accuracy of an amplicon-sequencing nanopore approach to identify variants in tuberculosis drug-resistance-associated genes.Microbial genomics · 2021Article
- Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing ofMicrobial genomics · 2021Article
- Whole Genome Sequencing in the Management of Non-Tuberculous Mycobacterial Infections.Microorganisms · 2021Review
- The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis.FEMS microbiology reviews · 2021Review
- Genomic epidemiology of tuberculosis in eastern Malaysia: insights for strengthening public health responses.Microbial genomics · 2021Article
- High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings.Small methods · 2021Review
- Characterization of Fecal Microbiota with Clinical Specimen Using Long-Read and Short-Read Sequencing Platform.International journal of molecular sciences · 2020Article
- Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples.Journal of clinical microbiology · 2020Article
- Genetic Identification and Drug-Resistance Characterization ofAntibiotics (Basel, Switzerland) · 2020Article
- Comparison of two molecular diagnostic methods for identifying Beijing genotype ofIranian journal of microbiology · 2020Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 a 4 404 064 bp genome with 99.98 % assembly accuracy. This assembly had an average nucleotide identity of 99.7 % relative to the reference genome, H37Rv. We assembled nearly all GC-rich repetitive PE/PPE family genes (166/168) and identified variants within these genes. With an estimated genotypic error rate of 5.3 % from MinION data, we demonstrated identification of variants to include the conventional drug resistance mutations, and those that contribute to the resistance phenotype (efflux pumps/transporter) and virulence. Reference-based alignment of the assembly allowed detection of deletions and insertions. MinION sequencing provided a fully annotated assembly of a transmissible XDR strain from an endemic setting and showed its utility to provide further understanding of genomic processes within Mycobacterium tuberculosis.
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