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Collaborative implementation of targeted next-generation sequencing for the diagnosis of drug-resistant tuberculosis in Eswatini.

L de Araujo(1) T Niemann(1) V Dreyer(1) C Gerlach(1) C Utpatel(1) V Mohr(1) D Sibandze(2,3,4) M Ziyane(2,3,4) A Cabibbe(5) T Kohl(1) D Vambe(6) A Kay(4,7) S Dlamini(2) T Dlamini(6) D Cirillo(5) S Niemann(1)

1:Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel Germany; 2:National TB Reference Laboratory, Eswatini Health Laboratory Services, Eswatini.; 3:Department of Global Health, Amsterdam UMC, University of Amsterdam, The Netherlands; 4:Baylor College of Medicine Children’s Foundation, Eswatini; 5:Emerging Bacterial Pathogens Unit, San Raffaele Scientific Institute, Italy.; 6:National TB Control Program, Ministry of Health, Eswatini; 7:Baylor College of Medicine, USA

The Kingdom of Eswatini, a landlocked country in Southern Africa, is classified among the tuberculosis (TB) highly endemic and high TB-HIV countries. Furthermore, data from surveys performed in 2009 and 2017 showed local outbreaks and transmission of rifampicin-resistant TB strains harboring the mutation RpoB I491F that is not interrogated by any of the endorsed molecular drug susceptibility testing (DST) and can be also missed by phenotypic tests.

Within the framework of the Global Health Protection Program (Germany), our objective was to implement targeted next-generation sequencing (tNGS) technology to close the current gaps in the prediction of drug-resistant TB in Eswatini. The implementation model is based on developing competencies distributed in 5 work packages: i. recognition of needs and cooperation; ii. coordination and networking; iii. technology transfer, adaptation of procedures, and human capacity building; iv. communication, integration, and sustainability.

The implementation officially started in Jan/2020 with an investment of ~270,000 euros/year. The budget was distributed as follows: out- and in-country personnel (49%), consumables (20%), devices (18%), workshops (11%), and others (2%). The local team was offered hands-on online, on-site, and regional trainings and conferences. On 29/09/2021 the first successful tNGS was run locally, since then >50 TB samples were sequenced. A Clinical Advisory Committee was created to educate and translate tNGS data into clinical practice.

Despite the challenges caused by the current pandemic and geopolitical events, tNGS for TB DST is successfully implemented in Eswatini with the potential for research/clinical applications and to interrogate other emergent pathogens.

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