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

Journal of Biomedical Science

Chun-Kai Huang¹  Ming-Chih Yu²  Ching-Sheng Hung³  Yu-Chih Liang⁴  Cheng-Hui Wang⁵  Jung-Chun Lin⁶ 

[1] Department of Laboratory Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan;School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, 11031, Taipei, Taiwan;Division of Pulmonary Medicine, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan;School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan;Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan;Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan;Department of Laboratory Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan;Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan;School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, 11031, Taipei, Taiwan;Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan;Department of Laboratory Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan;School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, 11031, Taipei, Taiwan;Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan;Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan;School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, 11031, Taipei, Taiwan;

关键词: InhA;    Isoniazid;    KatG;    MinION;    Mycobacterium tuberculosis;   

DOI  :  10.1186/s12929-021-00783-x

来源: Springer

【 摘 要 】

BackgroundWith 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.MethodsIn 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.ResultsIn 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).ConclusionsTaken 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.

【 授权许可】

CC BY