biostudies-literatureUnknown11(11)Conceicao ECResearch Foundation Flanders (FWO) through the TORCH consortium FWO TBMKey Digital Technologies Joint UndertakingSouth African Medical Research CouncilWhole-genome sequencing (WGS) holds promise for accurate and comprehensive diagnosis of drug resistance in <i>Mycobacterium tuberculosis</i> 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-anaMicrobial genomicshttps://www.ebi.ac.uk/biostudies/studies/S-EPMC12645293biostudies-literature&lt;i&gt;Mycobacterium tuberculosis&lt;/i&gt; cultured in MGIT media for whole-genome sequencing application: a systematic literature review and meta-analysis.PMC12645293101103171T001018NNgom JTde Oliveira TDippenaar AVan der Spuy GHeupink THaffejee MWarren RMRennie VLoubser JSharma AWells FConceicao ECMann BOmar SVan Rie AFuertes MDfalse&lt;i&gt;Mycobacterium tuberculosis&lt;/i&gt; cultured in MGIT media for whole-genome sequencing application: a systematic literature review and meta-analysis.Whole-genome sequencing (WGS) holds promise for accurate and comprehensive diagnosis of drug resistance in <i>Mycobacterium tuberculosis</i> 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-ana2025-01-01T00:00:00Z2025 Nov2026-06-05T19:04:35.257Z2026-05-20T03:14:57.946ZS-EPMC126452934127781310.1099/mgen.0.001565