Browsing by Author "Göller PC"

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    Field evaluation of nanopore targeted next-generation sequencing to predict drug-resistant tuberculosis from native sputum in South Africa and Zambia.
    (2025-Mar-12) Schwab TC; Joseph L; Moono A; Göller PC; Motsei M; Muula G; Evans D; Neuenschwander S; Günther G; Bolton C; Keller PM; Ramette A; Egger M; Omar SV; Fenner L; Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.; Population Health Sciences, University of Bristol, Bristol, United Kingdom.; Center for Infectious Disease Research in Zambia, Lusaka, Zambia.; Department of Pulmonology and Allergology, Inselspital Universitatsspital Bern, Bern, Switzerland.; Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland.; Department of Medical Science, Faculty of Health Sciences, University of Namibia, Windhoek, Namibia.; Institute for Infectious Diseases, University of Bern Institute for Infectious Diseases, Bern, Switzerland.; Clinical Bacteriology/Mycology, University Hospital Basel, Basel, Switzerland.; Centre for Infectious Disease Epidemiology & Research, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa.; Centre for Tuberculosis, National & WHO Supranational TB Reference Laboratory, a division of the National Health Laboratory Services, National Institute for Communicable Diseases, Johannesburg, South Africa.; Health Economics and Epidemiology Research Office, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.; CIDRZ; Centre for Infectious Disease Research in Zambia (CIDRZ)
    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 "low" 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 (