{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T02:59:19Z","timestamp":1768532359753,"version":"3.49.0"},"reference-count":19,"publisher":"International Union Against Tuberculosis and Lung Disease","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJTLD Open"],"accepted":{"date-parts":[[2025,8,4]]},"published-print":{"date-parts":[[2025,11]]},"abstract":"<jats:title>SUMMARY<\/jats:title>\n                  <jats:sec>\n                    <jats:title>BACKGROUND<\/jats:title>\n                    <jats:p>Targeted next-generation sequencing has emerged as a rapid solution for diagnosing drug-resistant TB (DR-TB) directly from clinical specimens. Updating the bioinformatics software component can lead to rapid improvements in diagnostic performance. We compared the diagnostic performance of an updated bioinformatic pipeline output to the original pipeline output for the Oxford Nanopore Technology (ONT) TB Drug Resistance Test.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>METHODS<\/jats:title>\n                    <jats:p>A total of 721 sediment samples were evaluated for 13 anti-TB drugs using phenotypic drug susceptibility testing and whole genome sequencing. Sequencing data outputs previously analysed using the original pipeline were re-analysed using an updated pipeline and compared.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>RESULTS<\/jats:title>\n                    <jats:p>\n                      There were no significant differences in successful sequencing results, and direct comparison of DR-TB call agreement was substantial (\u03ba &gt; 0.7) between the original and updated pipeline outputs. Diagnostic accuracy relative to the composite reference standard was compared, and significant (\n                      <jats:italic>P<\/jats:italic>\n                      value &lt; 0.05) increases in sensitivity and diagnostic yield, using the updated pipeline, were identified for streptomycin, pyrazinamide, bedaquiline, and clofazimine.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>CONCLUSION<\/jats:title>\n                    <jats:p>Comparison of the updated pipeline to the original pipeline revealed significant improvements in diagnostic performance, demonstrating that bioinformatic enhancements alone \u2013 without wet-lab modifications \u2013 can substantially boost sensitivity and diagnostic yield for DR-TB. These findings underscore the critical role of continuous pipeline optimisation in the evolving resistance landscape to enhance real-time clinical decision-making.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.5588\/ijtldopen.25.0245","type":"journal-article","created":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T04:34:41Z","timestamp":1763008481000},"page":"677-684","source":"Crossref","is-referenced-by-count":0,"title":["Comparing end-user diagnostic outputs from a commercial tNGS pipeline for\n                    <i>Mycobacterium tuberculosis<\/i>\n                    drug resistance detection"],"prefix":"10.5588","volume":"2","author":[{"given":"M.","family":"Seifert","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"R.E.","family":"Colman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S.","family":"Laurent","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A.","family":"De la 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Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance. 2nd ed. Geneva: WHO, 2023. https:\/\/public.ebookcentral.proquest.com\/choice\/PublicFullRecord.aspx?p=31202946."},{"issue":"3","key":"2026011502265825000_2.11.677.13","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/S1473-3099(24)00586-3","article-title":"Evaluating culture-free targeted next-generation sequencing for diagnosing drug-resistant tuberculosis: a multicentre clinical study of two end-to-end commercial workflows","volume":"25","author":"Colman","year":"2025","journal-title":"Lancet Infect Dis"},{"key":"2026011502265825000_2.11.677.14","unstructured":"World Health Organization . WHO operational handbook on tuberculosis module 3: diagnosis: web annex D: TB interferon gamma release assays and targeted next generation sequencing solutions: systematic review and technical advisory group reports. Geneva: WHO, 2025."},{"issue":"3","key":"2026011502265825000_2.11.677.15","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1007\/s15010-024-02411-w","article-title":"Targeted next-generation sequencing - a promising approach in the diagnosis of Mycobacterium tuberculosis and drug resistance","volume":"53","author":"Wu","year":"2024","journal-title":"Infection"},{"key":"2026011502265825000_2.11.677.16","doi-asserted-by":"crossref","first-page":"1206056","DOI":"10.3389\/fpubh.2023.1206056","article-title":"Direct detection of drug-resistant Mycobacterium tuberculosis using targeted next generation sequencing","volume":"11","author":"Murphy","year":"2023","journal-title":"Front Public Health"},{"issue":"10","key":"2026011502265825000_2.11.677.17","doi-asserted-by":"crossref","first-page":"1162","DOI":"10.1016\/S1473-3099(24)00263-9","article-title":"Targeted next-generation sequencing to diagnose drug-resistant tuberculosis: a systematic review and meta-analysis","volume":"24","author":"Schwab","year":"2024","journal-title":"Lancet Infect Dis"},{"issue":"7","key":"2026011502265825000_2.11.677.18","doi-asserted-by":"crossref","first-page":"e1184","DOI":"10.1016\/S2214-109X(24)00148-7","article-title":"Diagnostic yield as an important metric for the evaluation of novel tuberculosis tests: rationale and guidance for future research","volume":"12","author":"Broger","year":"2024","journal-title":"Lancet Glob Health"},{"key":"2026011502265825000_2.11.677.19","doi-asserted-by":"publisher","DOI":"10.1016\/j.jclinepi.2009.08.024"}],"container-title":["IJTLD Open"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.5588\/ijtldopen.25.0245","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T10:27:43Z","timestamp":1768472863000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.theunion.org\/lookup\/doi\/10.5588\/ijtldopen.25.0245"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11]]},"references-count":19,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2025,11,1]]},"published-print":{"date-parts":[[2025,11]]}},"alternative-id":["10.5588\/ijtldopen.25.0245"],"URL":"https:\/\/doi.org\/10.5588\/ijtldopen.25.0245","relation":{},"ISSN":["3005-7590"],"issn-type":[{"value":"3005-7590","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11]]}}}