Tuberculosis sequencing pipeline resources (2023) Further to the item below (Workshop and resources: Oxford Nanopore sequencing for tuberculosis, 2022), Linzy Elton has developed webpages and videos designed to help people build a pragmatic pipeline for whole genome sequencing (WGS) for sites with little/no access to larger scale Illumina sequencing platforms. The pipeline is primarily designed to identify antimicrobial resistances (e.g. for hard to treat cases) and lineages (e.g. to identify relapse vs reinfection or non-tuberculous mycobacteria. This is likely to be small-scale (at least at first), to be used in house as an alternative to the potentially expensive or logistically difficult Illumina platform. The information is available on the PANDORA website (https://pandora.tghn.org/sequencing/tuberculosis-sequencing-pipeline/)
Report of the technical consultation on innovative clinical trial designs for evaluating new TB preventive treatments. (2022) Virtual meeting, 15-17 September 2021 (published 2022). https://www.who.int/publications/i/item/9789240047150. The World Health Organization (WHO) Global Tuberculosis Programme, in collaboration with University College London and other partners, convened a virtual technical consultation from 15 to 17 September 2021 that focused on innovative clinical trial designs that could be used for evaluating new tuberculosis (TB) preventive treatments (TPTs). The objectives of the meeting were to identify and summarize challenges in designing future TPT trials and to explore innovative designs that could facilitate advances in biomedical TB preventive interventions and would complement similar developments in other fields relevant to TB prevention. Discussions were organized in four main sessions: Session 1: Models of delivery; Session 2: Estimating the benefits and harms of TPT; Session 3: Trial design and analytical approaches; Session 4: Trial populations. Yohhei Hamada and Molebogeng (Lele) Rangaka, both from the Institute for Global Health and the Medical Research Council (MRC) Clinical Trials Unit at University College London (UCL), drafted the concept note and helped organize the meeting. Elena Pallari and Genevieve Wills, both also from the MRC Clinical Trials Unit at UCL, served as meeting rapporteurs. Others involved from UCL included Angela Crook, David Dunn, Becky Turner and Ian White (MRC Clinical Trials Unit at UCL).
WHO consolidated guidelines on tuberculosis: module 3: diagnosis: tests for TB infection. (2022) Yohhei Hamada and Lele Rangaka, with colleagues, led a series of systematic reviews that informed the development of the World Health Organization guidelines on the use of Mycobacterium tuberculosis antigen-based skin tests. The four reviews each addressed the accuracy, safety, costs and cost-effectiveness of, and feasibility, acceptability, and patient preferences for the use of the new skin tests. The guidelines and the systematic review reports are available on the WHO website.
Workshop and resources: Oxford Nanopore sequencing for tuberculosis. (2022) https://pandora.tghn.org/training/oxford-nanopore-sequencing-tuberculosis/. This workshop took place 22-25th August 2022 at the National Institute for Medical Research (NIMR) at Muhimbili, Dar es Salaam, Tanzania. It was jointly run by UCL and NIMR. The aim of the workshop was to provide theoretical and practical training for all of the steps in the tuberculosis Oxford Nanopore Technologies (ONT) sequencing pipeline, from CTAB DNA extraction, DNA quantification best practice, library preparation and setting up a sequencing run, and analysing sequencing data. The workshop was run using a combination of theoretical, laboratory and bioinformatic sessions, with discussion and Q&A sessions throughout the workshop. The website includes links to the presentations and workshop handbook, how to set up a sequencing laboratory (aimed at resource constrained laboratories), how to learn sequencing bioinformatics, and tutorial videos on ONT sequencing. The UCL team were Linzy Elton and Sylvia Rofael from the UCL Centre for Clinical Microbiology.
TB and COVID-19 discussion (2020) (https://www.ucl.ac.uk/tb/how-will-covid-19-affect-tb-patients-and-control)
- Video (YouTube https://www.youtube.com/watch?v=XS5LQc0rlzU)
- Audio (Soundcloud https://soundcloud.com/ucl-tb/tb-and-covid-19-discussion)
The IMPACT study - Voices from the Front Line (2020) (https://www.ucl.ac.uk/tb/impact-study)
- Presentation (Slideshare)
Blog: JoiHok!: New UCL graduate sets up TB initiative in Kolkata (2020) (https://blogs.ucl.ac.uk/tb/2020/03/30/joihok/)