The Next Frontier in Tuberculosis Investigation: Automated Whole Genome Sequencing for Mycobacterium tuberculosis Analysis-Reference-Cited by-同舟云学术

The Next Frontier in Tuberculosis Investigation: Automated Whole Genome Sequencing for Mycobacterium tuberculosis Analysis

Published:2024-07-19 Issue:14 Volume:25 Page:7909
ISSN:1422-0067
Container-title:International Journal of Molecular Sciences
language:en
Short-container-title:IJMS

Author:

Ng Justin H. J.¹^ORCID,Castro Lina²,Gorzalski Andrew³,Allred Adam¹,Siao Danielle³,Wong Edwina²,Lin Andrew¹,Shokralla Shadi¹,Pandori Mark³,Masinde Godfred²,Khaksar Ramin¹

Affiliation:

1. Clear Labs, Inc., 1559 Industrial Road, San Carlos, CA 94070, USA

2. San Francisco Public Health Laboratories, 101 Grove Street, Room 419, San Francisco, CA 94102, USA

3. Nevada State Public Health Laboratory, 1664 North Virginia Street, Reno, NV 89557, USA

Abstract

A fully automated bacteria whole genome sequencing (WGS) assay was evaluated to characterize Mycobacterium tuberculosis (MTB) and non-tuberculosis Mycobacterium (NTM) clinical isolates. The results generated were highly reproducible, with 100% concordance in species and sub-lineage classification and 92% concordance between antimicrobial resistance (AMR) genotypic and phenotypic profiles. Using extracted deoxyribonucleic acid (DNA) from MTB clinical isolates as starting material, these findings demonstrate that a fully automated WGS assay, with a short turnaround time of 24.5 hours, provides timely and valuable insights into MTB outbreak investigation while providing reliable genotypic AMR profiling consistent with traditional antimicrobial susceptibility tests (AST). This study establishes a favorable proposition for the adoption of end-to-end fully automated WGS solutions for decentralized MTB diagnostics, thereby aiding in World Health Organization’s (WHO) vision of tuberculosis eradication.

Publisher

MDPI AG

Link

https://www.mdpi.com/1422-0067/25/14/7909/pdf

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