ReviewBriefings in bioinformatics2021
Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries.
Review in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 24 citations in OpenAlex.
- Reference-free clustering as an epidemiological tool forMicrobial genomics · 2026Article
- Harnessing genomic and bioinformatics for surveillance of pathogens in Africa: a scoping review of existing training and gaps in training.BMC infectious diseases · 2026Article
- The Impact of Adopting Whole-Genome Sequencing for Tuberculosis Diagnosis in China: A Cost-Effectiveness Analysis.Open forum infectious diseases · 2026Article
- Whole genome sequencing for Mycobacterium tuberculosis in public health responses: a review of current practice and enablers in select low-incidence jurisdictions.BMC public health · 2026Review
- Capacity building for zoonosis control in China: Assessing needs and gaps by the one health lens.One health (Amsterdam, Netherlands) · 2025Article
- Article
- Empowering tuberculosis genomic surveillance in Limpopo, South Africa through capacity building.Frontiers in public health · 2025Article
- Strategies to Enhance Diagnostic Capabilities for the New Drug-Resistant Tuberculosis (DR-TB) Drugs.Pathogens (Basel, Switzerland) · 2024Review
- aXonica: A support package for MRI based Neuroimaging.Biotechnology notes (Amsterdam, Netherlands) · 2024Article
- Advancing pathogen genomics in resource-limited settings.Cell genomics · 2023Review
- Lineage classification and antitubercular drug resistance surveillance ofMicrobiology spectrum · 2023Article
- Genomic Sequencing Profiles ofTropical medicine and infectious disease · 2023Article
- Whole Genomic Analysis Revealed High Genetic Diversity and Drug-Resistant Characteristics ofInfection and drug resistance · 2023Article
- Implementing molecular tuberculosis diagnostic methods in limited-resource and high-burden countries.Breathe (Sheffield, England) · 2022Review
- Bedaquiline resistance probability to guide treatment decision making for rifampicin-resistant tuberculosis: insights from a qualitative study.BMC infectious diseases · 2022Article
- Article
- Whole genome characterization, and geographical distribution of M. tuberculosis in central region of Veracruz, Mexico.The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious DiseasesArticle
Corrections and comments
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Authors and funding
10 authors at 5 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhole 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.
methodsWe 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.
findingsCompared 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.
interpretationBy 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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.