Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries

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dc.contributor.authorVan Heusden, Peter
dc.date.accessioned2021-09-23T13:29:19Z
dc.date.available2021-09-23T13:29:19Z
dc.date.issued2020
dc.description.abstractBackground Whole-genome sequencing (WGS) is increasingly used for Mycobacterium tuberculosis (Mtb) research. Countries with the highest tuberculosis (TB) burden face important challenges to integrate WGS into surveillance and research. Methods We assessed the global status of Mtb WGS and developed a 3-week training course coupled with long-term mentoring and WGS infrastructure building. Training focused on genome sequencing, bioinformatics and development of a locally relevant WGS research project. The aim of the long-term mentoring was to support trainees in project implementation and funding acquisition. The focus of WGS infrastructure building was on the DNA extraction process and bioinformatics. Findings Compared to their TB burden, Asia and Africa are grossly underrepresented in Mtb WGS research. Challenges faced resulted in adaptations to the training, mentoring and infrastructure building. Out-of-date laptop hardware and operating systems were overcome by using online tools and a Galaxy WGS analysis pipeline. A case studies approach created a safe atmosphere for students to formulate and defend opinions. Because quality DNA extraction is paramount for WGS, a biosafety level 3 and general laboratory skill training session were added, use of commercial DNA extraction kits was introduced and a 2-week training in a highly equipped laboratory was combined with a 1-week training in the local setting. Interpretation By developing and sharing the components of and experiences with a sequencing and bioinformatics training program, we hope to stimulate capacity building programs for Mtb WGS and empower high-burden countries to play an important role in WGS-based TB surveillance and research.en_US
dc.identifier.citationEmmanuel Rivière, Tim H Heupink, Nabila Ismail, Anzaan Dippenaar, Charlene Clarke, Gemeda Abebe, Peter Heusden, Rob Warren, Conor J Meehan, Annelies Van Rie, Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries, Briefings in Bioinformatics, Volume 22, Issue 4, July 2021, bbaa246, https://doi.org/10.1093/bib/bbaa246en_US
dc.identifier.issn1467-5463
dc.identifier.issn1477-4054
dc.identifier.uri10.1093/bib/bbaa246
dc.identifier.urihttp://hdl.handle.net/10566/6809
dc.language.isoenen_US
dc.publisherOxford University Pressen_US
dc.subjectMycobacterium tuberculosisen_US
dc.subjectWhole-genome sequencingen_US
dc.subjectBioinformaticsen_US
dc.subjectAfricaen_US
dc.subjectCapacity buildingen_US
dc.subjectMtben_US
dc.subjectWGSen_US
dc.subjectTBen_US
dc.subjectTuberculosisen_US
dc.subjectTraining courseen_US
dc.subjectLong-term mentoringen_US
dc.subjectTrainingen_US
dc.subjectProject implementationen_US
dc.subjectFunding acquisitionen_US
dc.subjectOnline toolsen_US
dc.subjectGalaxy WGSen_US
dc.subjectDNA extractionen_US
dc.subjectBiosafetyen_US
dc.subjectGenome sequencingen_US
dc.titleCapacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countriesen_US
dc.typeArticleen_US

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