期刊
BRIEFINGS IN BIOINFORMATICS
卷 22, 期 4, 页码 -出版社
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbaa246
关键词
Mycobacterium tuberculosis; whole genome sequencing; bioinformatics; Africa; capacity building
资金
- Vlaamse Interuniversitaire Raad-secretariaat voor universitaire ontwikkelingssamenwerking [ET2018JOI008A10]
- Research Foundation Flanders under FWO Odysseus [G0F8316N]
- South African Research Chairs Initiative of the Department of Science and Technology and National Research Foundation of South Africa [64751]
- South African Medical Research Council
Asia and Africa are underrepresented in Mtb WGS research compared to their TB burden, leading to adaptations in training, mentoring, and infrastructure building. Utilizing case studies created a safe space for students to voice and defend their opinions. Ensuring quality DNA extraction, biosafety level 3 and general laboratory skill training, commercial DNA extraction kits, and a combination of training in a highly equipped laboratory and local setting were added to the program.
Background: 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.
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