{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["11(11)"],"submitter":["Conceicao EC"],"funding":["Research Foundation Flanders (FWO) through the TORCH consortium FWO TBM","Key Digital Technologies Joint Undertaking","South African Medical Research Council"],"pubmed_abstract":["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-ana"],"journal":["Microbial genomics"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12645293"],"repository":["biostudies-literature"],"pubmed_title":["&lt;i&gt;Mycobacterium tuberculosis&lt;/i&gt; cultured in MGIT media for whole-genome sequencing application: a systematic literature review and meta-analysis."],"pmcid":["PMC12645293"],"funding_grant_id":["101103171","T001018N"],"pubmed_authors":["Ngom JT","de Oliveira T","Dippenaar A","Van der Spuy G","Heupink T","Haffejee M","Warren RM","Rennie V","Loubser J","Sharma A","Wells F","Conceicao EC","Mann B","Omar S","Van Rie A","Fuertes MD"],"additional_accession":[]},"is_claimable":false,"name":"&lt;i&gt;Mycobacterium tuberculosis&lt;/i&gt; cultured in MGIT media for whole-genome sequencing application: a systematic literature review and meta-analysis.","description":"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-ana","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Nov","modification":"2026-06-05T19:04:35.257Z","creation":"2026-05-20T03:14:57.946Z"},"accession":"S-EPMC12645293","cross_references":{"pubmed":["41277813"],"doi":["10.1099/mgen.0.001565"]}}