Integrative utility of long read sequencing-based whole genome analysis and phenotypic assay on differentiating isoniazid-resistant signature of Mycobacterium tuberculosis

• Published in: Journal of biomedical science Vol. 28; no. 1; p. 86
• Main Authors: Yu, Ming-Chih, Hung, Ching-Sheng, Huang, Chun-Kai, Wang, Cheng-Hui, Liang, Yu-Chih, Lin, Jung-Chun
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 18.12.2021; BioMed Central; BMC
• Subjects: Algorithms; Analysis; Antibiotics; Antitubercular agents; Antitubercular Agents - pharmacology; Cloning; Disease resistance; Disease transmission; DNA sequencing; Drug resistance; Drug resistance in microorganisms; Drug Resistance, Bacterial - genetics; Gene sequencing; Genes; Genetic aspects; Genome, Bacterial; Genomes; Genomics; InhA; INHA gene; Isoniazid; Isoniazid - pharmacology; KatG; KatG gene; Laboratories; Medical research; Medicine, Experimental; MinION; Mutation; Mycobacterium tuberculosis; Mycobacterium tuberculosis - drug effects; Mycobacterium tuberculosis - genetics; Next-generation sequencing; Nucleotide sequencing; Nucleotides; Phenotype; Statistical analysis; Tuberculosis; Variance analysis; Whole Genome Sequencing; Workflow; Taiwan; United Kingdom > UK; Denmark; United States > US; MinION; KatG; Mycobacterium tuberculosis; InhA; Isoniazid
• ISSN: 1423-0127; 1021-7770; 1423-0127
• DOI: 10.1186/s12929-021-00783-x

With the advancement of next generation sequencing technologies (NGS), whole-genome sequencing (WGS) has been deployed to a wide range of clinical scenarios. Rapid and accurate classification of drug-resistant Mycobacterium tuberculosis (MTB) would be advantageous in reducing the amplification of additional drug resistance and disease transmission. In this study, a long-read sequencing approach was subjected to the whole-genome sequencing of clinical MTB clones with susceptibility test profiles, including isoniazid (INH) susceptible clones (n = 10) and INH resistant clones (n = 42) isolated from clinical specimens. Non-synonymous variants within the katG or inhA gene associated with INH resistance was identified using Nanopore sequencing coupled with a corresponding analytical workflow. In total, 54 nucleotide variants within the katG gene and 39 variants within the inhA gene associated with INH resistance were identified. Consistency among the results of genotypic profiles, susceptibility test, and minimal inhibitory concentration, the high-INH resistance signature was estimated using the area under the receiver operating characteristic curve with the existence of Ser315Thr (AUC = 0.822) or Thr579Asn (AUC = 0.875). Taken together, we curated lists of coding variants associated with differential INH resistance using Nanopore sequencing, which may constitute an emerging platform for rapid and accurate identification of drug-resistant MTB clones.