Publication Highlight: Mycobacterium tuberculosis cultured in MGIT media for whole-genome sequencing application: a systematic literature review and meta-analysis
A new study by GenPath Africa consortium members Emilyn Costa Conceição, Felicia Wells, Abhinav Sharma, Túlio de Oliveira, Gian Van der Spuy, and Rob Warren at Stellenbosch University, and Miguel de Diego Fuertes, Vincent Rennie, Anzaan Dippenaar and Annelies Van Rie at University of Antwerp, provides the evidence and guidance needed to help countries adopt genomic surveillance of tuberculosis (TB) more confidently.
What is this publication about?
In this study, researchers analysed 15 scientific papers and over 1,000 sequencing datasets to assess how well whole-genome sequencing (WGS) performs when applied directly to Mycobacterium tuberculosis liquid MGIT cultures. By comparing laboratory methods and sequencing results across multiple countries, the researchers identified the key factors that influence data quality. The study also recommends replacing the ambiguous term “early positive culture (EPC)” with the more accurate clinical primary culture (CPC) to better reflect real laboratory practices.
Why is this important?
WGS can greatly improve drug-resistant TB (DR-TB) diagnosis, as it is more accurate than traditional methods, yet laboratories currently use widely varying MGIT-based workflows. Despite this variability, the study found that over 96% of samples met quality standards, showing that CPC-based WGS is robust and feasible. Notably, the number of sequencing cycles, rather than extraction or heat-inactivation methods, was the key factor influencing success. By highlighting which steps truly matter, the study supports simpler, more consistent and cost-effective workflows that can be implemented even in resource-limited settings.
How can this make a difference?
A standardised CPC workflow and reporting checklist can speed up the adoption of WGS in routine TB diagnostics and surveillance and can thus enable faster detection of DR-TB, better outbreak investigation and transmission tracking, more equitable access to genomic tools in high-burden settings, and can improve use of data to guide treatment and control strategies. The study also points to the future potential of portable nanopore sequencing, which could enable rapid, decentralised TB genomic testing and strengthen tuberculosis control efforts worldwide.
Emilyn C. Conceição, Felicia Wells, Abhinav Sharma, Mishka Haffejee, Brendon Mann, Justice T. Ngom, Shatha Omar, Johannes Loubser, Miguel de Diego Fuertes, Vincent Rennie, Anzaan Dippenaar, Tim Heupink, Túlio de Oliveira, Gian Van der Spuy, Annelies Van Rie and Robin M. Warren, "Mycobacterium tuberculosis cultured in MGIT media for whole-genome sequencing application: a systematic literature review and meta-analysis", Microbial Genomics, Volume 11, Issue 11, 24 November 2025. doi.org:10.1099/mgen.0.001565.
