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Advancing TB Diagnosis in Sub-Saharan Africa: A Roadmap for Next-Generation Sequencing Implementation

L de Araujo(1) C Utpatel(1) V Dreyer(1) A Cabibbe(2) T Niemann(1) V Mohr(1) C Gerlach(1) T Kohl(1) D Sinbandze(5) M Ziyane(5) T Fernando(6) C Abujate(6) L Mhuulu(7) A Diergaardt(7) A Kay(5) S Dlamini(3) T Dlamini(3) G Günther(8) M Claassens(7) E Nepolo(7) N Ismael(6) S Viegas(6) D Cirillo(2) S Niemann(1)

1:Molecular Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, 23845, Germany; 2:Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy; 3:National TB Reference Laboratory, Eswatini Health Laboratory Services, Eswatini.; 4:– Department of Global Health, Amsterdam UMC, University of Amsterdam, The Netherlands; 5:Baylor College of Medicine Children’s Foundation, Eswatini; 6:Instituto Nacional de Saúde, Marracuene, Mozambique.; 7:Department of Human, Biological & Translational Medical Sciences, School of Medicine, University of Namibia, Windhoek, Namibia; 8:Department of Pulmonology and Allergology, Inselspital, Bern University Hospital, University of Bern, Bern,3010, Switzerland

Targeted next-generation sequencing (tNGS) from clinical specimens has the potential to become a comprehensive tool for a broader, routine drug-resistance prediction of Mycobacterium tuberculosis complex (MTBC) strains, the causative agent of tuberculosis (TB). However, TB mainly affects low- and middle-income countries (LMIC) , which have specific needs and challenges for implementing new technologies.

Within the framework of the German Global Health Protection Programme, we share our experience on using a model for programmatic implementation of tNGS in three LMIC: Eswatini, Namibia and Mozambique. A roadmap of the implementation process will be herein described, this includes the budget/costs, strategic plan, list of equipment and other materials, trainings, and a SWOT analysis.

After successful capacity building of wet and dry lab infrastructure, the local team received hands-on on-site and on-line trainings on all needed steps from DNA extraction to sequencing on the iSeq100 sequencer. Multiplex PCR was based on a commercial test, the Deeplex®-Myc-TB, which was selected because of its capacity to deep sequence 18 MTBC gene targets that are associated with 13 first- and second-line drugs and includes mycobacterial species identification. Upon completion of the practical trainings, strains from clinical culture samples from TB patients were sequenced in pilot runs.

tNGS was successfully implemented in Eswatini, Namibia and Mozambique and is capable of providing additional clinically-relevant information, such as genotypic resistance profiles, lineage, and mixed infection information. Our next step is to proceed with the programmatic adoption of tNGS data in clinical practice and national guidelines.

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