<i>Mycobacterium tuberculosis</i> cultured in MGIT media for whole-genome sequencing application: a systematic literature review and meta-analysis.

ABSTRACT: Whole-genome sequencing (WGS) holds promise for accurate and comprehensive diagnosis of drug resistance in Mycobacterium tuberculosis and identification of transmission events. 'Early positive cultures' (EPC) are increasingly used when WGS is implemented to guide clinical care to reduce the turnaround time. We performed a systematic literature review to compare methods used for EPC-based WGS and performed an individual sample data meta-analysis to identify variables associated with bioinformatic quality measures. Of 423 studies identified, 15 met eligibility criteria. We analysed 1,065 FASTQ files from 11 studies using Illumina sequencing; 96.1% passed all quality control thresholds. Median genome coverage was 65× (IQR, 63-82), with a pooled mapping percentage of 91.2%. The meta-ana

SUBMITTER: Conceicao EC 

PROVIDER: S-EPMC12645293 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature