A pragmatic pipeline for drug resistance and lineage identification in Mycobacterium tuberculosis using whole genome sequencing.

ABSTRACT: Delays in accurate diagnosis of drug resistant tuberculosis (DR-TB) can hinder treatment. Whole genome sequencing (WGS) provides more information than standard molecular and phenotypic testing, but commonly used platforms are expensive to implement, and data interpretation requires significant expertise. We aimed to optimise a TB WGS diagnostic pipeline balancing user-friendliness, cost-effectiveness and time to results, whilst ensuring accuracy. Growth conditions, DNA extraction protocols and Oxford Nanopore Technologies (ONT) library preparation kits were compared. ONT was compared with Illumina protocols. Software for basecalling and analysis were evaluated to find the most accurate resistance SNP and lineage predictor. Optimally, a spin-column CTAB DNA extraction method was combined wi

SUBMITTER: Elton L 

PROVIDER: S-EPMC11809915 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature