{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T06:02:09Z","timestamp":1792735329828,"version":"4.5.0"},"reference-count":26,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2025,3,12]],"date-time":"2025-03-12T00:00:00Z","timestamp":1741737600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,3,12]],"date-time":"2025-03-12T00:00:00Z","timestamp":1741737600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000060","name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"crossref","award":["U01AI069924"],"award-info":[{"award-number":["U01AI069924"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2025,3,12]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:sec>\n            <jats:title\/>\n            <jats:p>\n              Rapid and comprehensive drug susceptibility testing (DST) is essential for diagnosing and treating drug-resistant tuberculosis effectively, and next-generation sequencing can be an effective genotypic DST method. We implemented and evaluated the performance of a nanopore targeted sequencing assay, called the Tuberculosis Drug Resistance Test (TBDR, Oxford Nanopore Diagnostics, Ltd., United Kingdom), which predicts drug resistance to 16 TB drugs, at a South African reference laboratory and a district diagnostic laboratory in Zambia. We compared the sequencing success rates between unprocessed and decontaminated sputum samples and determined the diagnostic accuracy against local DST (Xpert MTB\/RIF Ultra, Xpert MTB\/XDR, and BD BACTEC MGIT phenotypic DST). We prospectively sequenced 236 samples and have 148 samples with sequencing results from unprocessed and decontaminated sputum. We obtained successful sequencing results from 66.4% (94\/148) unprocessed sputum samples and 75% (111\/148) decontaminated samples. Sequencing success rates at the two sites differed, with 50.7% (36\/71) successful sequencing results from unprocessed sputum in Zambia and 75.3% (58\/77) in South Africa. Samples with \u201clow\u201d bacterial load, measured by Xpert MTB\/RIF Ultra, tended to produce fewer successful sequencing results. TBDR sequencing predicted resistances in 48 samples, detecting resistance for rifampicin (\n              <jats:italic>n<\/jats:italic>\n              = 41) and isoniazid (\n              <jats:italic>n<\/jats:italic>\n              = 20), as well as 10 second-line drugs (\n              <jats:italic>n<\/jats:italic>\n              = 15). Sensitivity was variable compared to phenotypic DST, ranging from 33 (ethionamide) to 94% (rifampicin), while specificity remained above 90% for all drugs, except clofazimine. The TBDR assay can provide rapid, comprehensive genotypic DST. Technical and operational challenges need to be addressed for its broader implementation in high tuberculosis-burden settings.\n            <\/jats:p>\n            <jats:sec>\n              <jats:title>IMPORTANCE<\/jats:title>\n              <jats:p>This study illustrates the use of the Tuberculosis Drug Resistance Test (TBDR, Oxford Nanopore Diagnostics, Ltd., United Kingdom) as a rapid drug susceptibility testing (DST) approach for diagnosing drug-resistant TB in the high TB-burden countries of South Africa and Zambia. The TBDR assay predicts resistance to 16 TB drugs, including first- and second-line treatments. By implementing the TBDR assay in a national reference laboratory in South Africa and a district diagnostic laboratory in Zambia, we demonstrate how this technology can provide faster diagnostic results (days) compared to traditional phenotypic DST methods (~2 months), with adequate sensitivity. Missed resistances compared to phenotypic DST indicate that technical improvements are needed. Successful sequencing from unprocessed and decontaminated sputum samples at different sites suggests feasibility in diverse settings, though operational challenges remain. Implementing this rapid, comprehensive DST approach could enhance drug-resistant tuberculosis diagnosis and treatment, ultimately improving patient outcomes and helping to combat tuberculosis in high-burden regions.<\/jats:p>\n            <\/jats:sec>\n          <\/jats:sec>","DOI":"10.1128\/jcm.01390-24","type":"journal-article","created":{"date-parts":[[2025,2,12]],"date-time":"2025-02-12T14:01:21Z","timestamp":1739368881000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":17,"title":["Field evaluation of nanopore targeted next-generation sequencing to predict drug-resistant tuberculosis from native sputum in South Africa and Zambia"],"prefix":"10.1128","volume":"63","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1863-2722","authenticated-orcid":false,"given":"Tiana C.","family":"Schwab","sequence":"first","affiliation":[{"name":"Institute of Social and Preventive Medicine, University of Bern","place":["Bern, Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lavania","family":"Joseph","sequence":"additional","affiliation":[{"name":"Centre for Tuberculosis, National & WHO Supranational TB Reference Laboratory, a division of the National Health Laboratory Services, National Institute for Communicable Diseases","place":["Johannesburg, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Moono","sequence":"additional","affiliation":[{"name":"Center for Infectious Disease Research in Zambia","place":["Lusaka, Zambia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pauline C.","family":"G\u00f6ller","sequence":"additional","affiliation":[{"name":"Institute of Medical Microbiology, University of Z\u00fcrich","place":["Z\u00fcrich, Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mamello","family":"Motsei","sequence":"additional","affiliation":[{"name":"Centre for Tuberculosis, National & WHO Supranational TB Reference Laboratory, a division of the National Health Laboratory Services, National Institute for Communicable Diseases","place":["Johannesburg, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guy","family":"Muula","sequence":"additional","affiliation":[{"name":"Center for Infectious Disease Research in Zambia","place":["Lusaka, Zambia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Denise","family":"Evans","sequence":"additional","affiliation":[{"name":"Health Economics and Epidemiology Research Office, Faculty of Health Sciences, University of the Witwatersrand","place":["Johannesburg, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Neuenschwander","sequence":"additional","affiliation":[{"name":"Institute for Infectious Diseases, University of Bern Institute for Infectious Diseases","place":["Bern, Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2217-4322","authenticated-orcid":true,"given":"Gunar","family":"G\u00fcnther","sequence":"additional","affiliation":[{"name":"Department of Pulmonology and Allergology, Inselspital Universitatsspital Bern","place":["Bern, Switzerland"]},{"name":"Department of Medical Science, Faculty of Health Sciences, University of Namibia","place":["Windhoek, Namibia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolyn","family":"Bolton","sequence":"additional","affiliation":[{"name":"Center for Infectious Disease Research in Zambia","place":["Lusaka, Zambia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter M.","family":"Keller","sequence":"additional","affiliation":[{"name":"Clinical Bacteriology\/Mycology, University Hospital Basel","place":["Basel, Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alban","family":"Ramette","sequence":"additional","affiliation":[{"name":"Institute for Infectious Diseases, University of Bern Institute for Infectious Diseases","place":["Bern, Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7462-5132","authenticated-orcid":false,"given":"Matthias","family":"Egger","sequence":"additional","affiliation":[{"name":"Institute of Social and Preventive Medicine, University of Bern","place":["Bern, Switzerland"]},{"name":"Centre for Infectious Disease Epidemiology & Research, School of Public Health & Family Medicine, University of Cape Town","place":["Cape Town, South Africa"]},{"name":"Population Health Sciences, University of Bristol","place":["Bristol, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaheed V.","family":"Omar","sequence":"additional","affiliation":[{"name":"Centre for Tuberculosis, National & WHO Supranational TB Reference Laboratory, a division of the National Health Laboratory Services, National Institute for Communicable Diseases","place":["Johannesburg, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3309-4835","authenticated-orcid":true,"given":"Lukas","family":"Fenner","sequence":"additional","affiliation":[{"name":"Institute of Social and Preventive Medicine, University of Bern","place":["Bern, Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"on behalf of IeDEA Southern Africa (IeDEA-SA)","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","unstructured":"World Health Organization. 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Technical report on critical concentrations for drug susceptibility testing of isoniazid and the rifamycins (rifampicin rifabutin and rifapentine). Available from: https:\/\/www.who.int\/publications\/i\/item\/9789240017283. Retrieved 11 Sep 2024."},{"key":"e_1_3_5_17_2","unstructured":"World Health Organization. 2018. Technical report on critical concentrations for drug susceptibility testing of medicines used in the treatment of drug-resistant tuberculosis. Available from: https:\/\/www.who.int\/publications\/i\/item\/WHO-CDS-TB-2018.5. Retrieved 11 Sep 2024."},{"key":"e_1_3_5_18_2","unstructured":"World Health Organization. 2023. Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance. Available from: https:\/\/www.who.int\/publications\/i\/item\/9789240082410. 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