Series 1: The Use of <i>hsp</i>65- and <i>erm</i>(41)-Targeted Amplicon Sequencing in the Diagnostic Workflow for Non-Tuberculous Mycobacteria

Series 1: The Use of <i>hsp</i>65- and <i>erm</i>(41)-Targeted Amplicon Sequencing in the Diagnostic Workflow for Non-Tuberculous Mycobacteria

Evolving technologies available to clinical laboratories and laboratory-related updates to clinical guidelines both drive the need for clinical laboratories to keep their test menu updated and in line with current technological and clinical developments. Our laboratory has developed a targeted Illum...

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Main Authors: Tracy Lee, Adriana Cabrera, Kathleen Kolehmainen, Trevor Hird, Danielle Jorgensen, Alan O’Dwyer, Dan Fornika, Rupinder Kaur KhunKhun, Mabel Rodrigues, Natalie Prystajecky, John Tyson, Inna Sekirov, James E. A. Zlosnik
Format: Article
Language:English
Published: MDPI AG 2025-07-01
Series:Tropical Medicine and Infectious Disease
Subjects:
non-tuberculous mycobacteria
identification
speciation
next-generation sequencing
molecular resistance
Online Access:https://www.mdpi.com/2414-6366/10/7/192
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Summary:Evolving technologies available to clinical laboratories and laboratory-related updates to clinical guidelines both drive the need for clinical laboratories to keep their test menu updated and in line with current technological and clinical developments. Our laboratory has developed a targeted Illumina-based amplicon next-generation sequencing (NGS) assay to interrogate the <i>hsp</i>65 and <i>erm(</i>41) genes of <i>Mycobacterium</i> spp. for the purposes of providing species-level ± subspecies-level identification of <i>Mycobacterium</i> spp. organisms in clinical samples and genotypic predictions for inducible macrolide resistance (in the case of <i>M. abscessus</i> complex members). The developed assay demonstrated 100% sensitivity and specificity for <i>M. tuberculosis</i> and <i>M. abscessus</i> complex cultured organisms, 98% ID overall concordance relative to the available reference identification, and a nearly 60% “rescue” rate for primary samples that could not be identified using our previous method. There was 94.6% concordance between genotypic and phenotypic results for inducible macrolide resistance. The developed assay was successfully implemented in our clinical laboratory and has been accredited for clinical use.
ISSN:2414-6366

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