{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T10:56:37Z","timestamp":1781607397422,"version":"3.54.5"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T00:00:00Z","timestamp":1779753600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Purpose<\/jats:title>\n                    <jats:p>To evaluate the diagnostic performance of nanopore-targeted sequencing (NTS) for sputum smear-negative pulmonary tuberculosis (PTB).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>In this retrospective study, bronchoalveolar lavage fluid from patients with suspected PTB and negative sputum smears was tested with NTS, Xpert MTB\/RIF, and MGIT 960 culture at Shanghai Pulmonary Hospital (August 2022\u2013March 2024). Sensitivity and specificity were evaluated against both microbiological and composite reference standards. Receiver operating characteristic curves were generated and Youden's index was employed to determine the optimal NTS cutoff.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Among the 249 participants enrolled, 100 were microbiologically confirmed PTB, 33 were probable PTB, and 116 were tuberculosis-negative. Under microbiological reference standard, the sensitivity of NTS was 0.940 (95% confidence interval [CI], 0.869\u20130.975), higher than Xpert MTB\/RIF (0.840 [95% CI, 0.750\u20130.903]; P = .041) and MGIT 960 culture (0.640 [95% CI, 0.537\u20130.732]; both P &amp;lt; .001). The specificity of NTS was 0.776 (95% CI 0.687\u20130.846), compared to 0.974 (95% CI 0.921\u20130.993) for Xpert MTB\/RIF and 1.000 (95% CI 0.960\u20131.000) for MGIT 960 culture. Excluding patients with prior PTB history, NTS specificity increased to 0.856 (95% CI, 0.766\u20130.916). According to Youden's index, when 4 Mycobacterium tuberculosis\u2013specific sequence reads was defined as the optimal NTS cutoff for positive NTS result, the specificity of NTS rose to 0.907 (95% CI, 0.827\u20130.954).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>NTS offers rapid, highly sensitive detection of PTB in patients with low bacillary burden. Applying an optimal read-count cutoff and accounting for prior PTB history can enhance clinical utility.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/ofid\/ofag323","type":"journal-article","created":{"date-parts":[[2026,5,24]],"date-time":"2026-05-24T11:35:11Z","timestamp":1779622511000},"source":"Crossref","is-referenced-by-count":0,"title":["Diagnostic Performance of Nanopore-targeted Sequencing for Sputum Smear-negative Pulmonary Tuberculosis: A Retrospective Study"],"prefix":"10.1093","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-3199-8662","authenticated-orcid":false,"given":"Wei","family":"Wei","sequence":"first","affiliation":[{"name":"Clinic and Research Centre of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University , Shanghai ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xubin","family":"Zheng","sequence":"additional","affiliation":[{"name":"Clinic and Research Centre of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University , Shanghai ,","place":["China"]},{"name":"Division of Infectious Diseases, Department of Medicine, Karolinska Institute , Stockholm ,","place":["Sweden"]},{"name":"Department of Infectious Diseases, Karolinska University Hospital , Stockholm ,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lan","family":"Yao","sequence":"additional","affiliation":[{"name":"Clinic and Research Centre of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University , Shanghai ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3445-920X","authenticated-orcid":false,"given":"Qin","family":"Sun","sequence":"additional","affiliation":[{"name":"Clinic and Research Centre of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University , Shanghai ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2099-8205","authenticated-orcid":false,"given":"Wei","family":"Sha","sequence":"additional","affiliation":[{"name":"Clinic and Research Centre of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University , Shanghai ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,5,26]]},"reference":[{"key":"2026061606390681100_ofag323-B1","volume-title":"Global tuberculosis report","author":"World Health Organization","year":"2023"},{"key":"2026061606390681100_ofag323-B2","doi-asserted-by":"crossref","first-page":"1799","DOI":"10.1016\/S0140-6736(15)60570-0","article-title":"WHO's new end TB strategy","volume":"385","author":"Uplekar","year":"2015","journal-title":"Lancet"},{"key":"2026061606390681100_ofag323-B3","first-page":"Cd009593","article-title":"Xpert\u00ae MTB\/RIF assay for pulmonary tuberculosis and rifampicin resistance in adults","volume":"2014","author":"Steingart","year":"2014","journal-title":"Cochrane Database Syst Rev"},{"key":"2026061606390681100_ofag323-B4","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/S1473-3099(17)30691-6","article-title":"Xpert MTB\/RIF Ultra for detection of Mycobacterium tuberculosis and rifampicin resistance: a prospective multicentre diagnostic accuracy study","volume":"18","author":"Dorman","year":"2018","journal-title":"Lancet Infect Dis"},{"key":"2026061606390681100_ofag323-B5","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1093\/cid\/ciu022","article-title":"Xpert MTB\/RIF testing in a low tuberculosis incidence, high-resource setting: limitations in accuracy and clinical impact","volume":"58","author":"Sohn","year":"2014","journal-title":"Clin Infect Dis"},{"key":"2026061606390681100_ofag323-B6","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1146\/annurev-pathmechdis-012418-012751","article-title":"Clinical metagenomic next-generation sequencing for pathogen detection","volume":"14","author":"Gu","year":"2019","journal-title":"Annu Rev Pathol"},{"key":"2026061606390681100_ofag323-B7","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1007\/s15010-022-01890-z","article-title":"Diagnostic performance of metagenomic next-generation sequencing in non-tuberculous mycobacterial pulmonary disease when applied to clinical practice","volume":"51","author":"Wei","year":"2023","journal-title":"Infection"},{"key":"2026061606390681100_ofag323-B8","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1016\/j.jinf.2020.08.004","article-title":"Clinical metagenomic sequencing for diagnosis of pulmonary tuberculosis","volume":"81","author":"Shi","year":"2020","journal-title":"J Infect"},{"key":"2026061606390681100_ofag323-B9","doi-asserted-by":"crossref","first-page":"S231","DOI":"10.1093\/cid\/ciy693","article-title":"Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice","volume":"67","author":"Miao","year":"2018","journal-title":"Clin Infect Dis"},{"key":"2026061606390681100_ofag323-B10","doi-asserted-by":"crossref","first-page":"102051","DOI":"10.1016\/j.tube.2021.102051","article-title":"Targeted next generation sequencing directly from sputum for comprehensive genetic information on drug resistant Mycobacterium tuberculosis","volume":"127","author":"Kambli","year":"2021","journal-title":"Tuberculosis (Edinb)"},{"key":"2026061606390681100_ofag323-B11","doi-asserted-by":"crossref","first-page":"1206","DOI":"10.1038\/s41431-024-01564-4","article-title":"Overcoming barriers to single-cell RNA sequencing adoption in low- and middle-income countries","volume":"32","author":"Boakye Serebour","year":"2024","journal-title":"Eur J Hum Genet"},{"key":"2026061606390681100_ofag323-B12","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1016\/j.tig.2018.05.008","article-title":"The third revolution in sequencing technology","volume":"34","author":"van Dijk","year":"2018","journal-title":"Trends Genet"},{"key":"2026061606390681100_ofag323-B13","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1038\/nbt.3423","article-title":"Three decades of nanopore sequencing","volume":"34","author":"Deamer","year":"2016","journal-title":"Nat Biotechnol"},{"key":"2026061606390681100_ofag323-B14","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.01315-19","article-title":"Third-generation sequencing in the clinical laboratory: exploring the advantages and challenges of nanopore sequencing","volume":"58","author":"Petersen","year":"2019","journal-title":"J Clin Microbiol"},{"key":"2026061606390681100_ofag323-B15","doi-asserted-by":"crossref","first-page":"1800228","DOI":"10.2807\/1560-7917.ES.2018.23.50.1800228","article-title":"Assessment of metagenomic nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples","volume":"23","author":"Kafetzopoulou","year":"2018","journal-title":"Euro Surveill"},{"key":"2026061606390681100_ofag323-B16","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.02127-19","article-title":"Nanopore sequencing reveals novel targets for detection and surveillance of human and avian influenza A viruses","volume":"58","author":"Yip","year":"2020","journal-title":"J Clin Microbiol"},{"key":"2026061606390681100_ofag323-B17","doi-asserted-by":"crossref","first-page":"1354","DOI":"10.1101\/gr.262865.120","article-title":"High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic nanopore sequencing","volume":"30","author":"Sanderson","year":"2020","journal-title":"Genome Res"},{"key":"2026061606390681100_ofag323-B18","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1080\/23744235.2023.2276785","article-title":"The application of nanopore targeted sequencing for pathogen diagnosis in bronchoalveolar lavage fluid of patients with pneumonia: a prospective multicenter study","volume":"56","author":"Lin","year":"2024","journal-title":"Infect Dis (Lond)"},{"key":"2026061606390681100_ofag323-B19","doi-asserted-by":"crossref","first-page":"1107990","DOI":"10.3389\/fcimb.2023.1107990","article-title":"A preliminary evaluation of targeted nanopore sequencing technology for the detection of Mycobacterium tuberculosis in bronchoalveolar lavage fluid specimens","volume":"13","author":"Sun","year":"2023","journal-title":"Front Cell Infect Microbiol"},{"key":"2026061606390681100_ofag323-B20","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/j.ijid.2022.06.001","article-title":"Diagnostic accuracy of nanopore sequencing using respiratory specimens in the diagnosis of pulmonary tuberculosis","volume":"122","author":"Yu","year":"2022","journal-title":"Int J Infect Dis"},{"key":"2026061606390681100_ofag323-B21","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/s12941-024-00714-2","article-title":"Nanopore sequencing for smear-negative pulmonary tuberculosis-a multicentre prospective study in China","volume":"23","author":"Yan","year":"2024","journal-title":"Ann Clin Microbiol Antimicrob"},{"key":"2026061606390681100_ofag323-B22","doi-asserted-by":"crossref","first-page":"104858","DOI":"10.1016\/j.ebiom.2023.104858","article-title":"A dual-process of targeted and unbiased nanopore sequencing enables accurate and rapid diagnosis of lower respiratory infections","volume":"98","author":"Guo","year":"2023","journal-title":"EBioMedicine"},{"key":"2026061606390681100_ofag323-B23","first-page":"22","volume-title":"Definitions and reporting framework for tuberculosis-2013 revision","author":"World Health Organization","year":"2013"},{"key":"2026061606390681100_ofag323-B24","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1093\/cid\/civ1223","article-title":"Xpert MTB\/RIF results in patients with previous tuberculosis: can we distinguish true from false positive results?","volume":"62","author":"Theron","year":"2016","journal-title":"Clin Infect Dis"},{"key":"2026061606390681100_ofag323-B25","doi-asserted-by":"crossref","first-page":"1504","DOI":"10.1183\/09031936.00214114","article-title":"Suboptimal specificity of Xpert MTB\/RIF among treatment-experienced patients","volume":"45","author":"Metcalfe","year":"2015","journal-title":"Eur Respir J"},{"key":"2026061606390681100_ofag323-B26","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.01696-17","article-title":"False-positive Xpert MTB\/RIF results in retested patients with previous tuberculosis: frequency, profile, and prospective clinical outcomes","volume":"56","author":"Theron","year":"2018","journal-title":"J Clin Microbiol"},{"key":"2026061606390681100_ofag323-B27","doi-asserted-by":"crossref","first-page":"351","DOI":"10.3389\/fcimb.2019.00351","article-title":"Clinical evaluation of diagnosis efficacy of active Mycobacterium tuberculosis complex infection via metagenomic next-generation sequencing of direct clinical samples","volume":"9","author":"Zhou","year":"2019","journal-title":"Front Cell Infect Microbiol"},{"key":"2026061606390681100_ofag323-B28","doi-asserted-by":"crossref","first-page":"211","DOI":"10.4046\/trd.2019.0087","article-title":"False-positive Mycobacterium tuberculosis detection: ways to prevent cross-contamination","volume":"83","author":"Asgharzadeh","year":"2020","journal-title":"Tuberc Respir Dis (Seoul)"},{"key":"2026061606390681100_ofag323-B29","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1007\/s00408-019-00241-4","article-title":"Laboratory cross-contamination of Mycobacterium tuberculosis: a systematic review and meta-analysis","volume":"197","author":"Barac","year":"2019","journal-title":"Lung"},{"key":"2026061606390681100_ofag323-B30","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1164\/rccm.200208-797CC","article-title":"Infection control in the bronchoscopy suite: a review of outbreaks and guidelines for prevention","volume":"167","author":"Culver","year":"2003","journal-title":"Am J Respir Crit Care Med"},{"key":"2026061606390681100_ofag323-B31","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1093\/cid\/cix881","article-title":"Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases","volume":"66","author":"Simner","year":"2018","journal-title":"Clin Infect Dis"},{"key":"2026061606390681100_ofag323-B32","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1007\/s00408-023-00612-y","article-title":"Nanopore-based metagenomic sequencing in respiratory tract infection: a developing diagnostic platform","volume":"201","author":"Chapman","year":"2023","journal-title":"Lung"},{"key":"2026061606390681100_ofag323-B33","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1186\/s12890-023-02337-3","article-title":"Diagnostic value of a nanopore sequencing assay of bronchoalveolar lavage fluid in pulmonary tuberculosis","volume":"23","author":"Liu","year":"2023","journal-title":"BMC Pulm Med"},{"key":"2026061606390681100_ofag323-B34","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.ijid.2021.04.040","article-title":"Efficacy of the Xpert Mycobacterium tuberculosis\/rifampicin assay for diagnosing sputum-smear negative or sputum-scarce pulmonary tuberculosis in bronchoalveolar lavage fluid","volume":"107","author":"Yang","year":"2021","journal-title":"Int J Infect Dis"},{"key":"2026061606390681100_ofag323-B35","doi-asserted-by":"crossref","first-page":"17596","DOI":"10.1038\/s41598-018-35750-4","article-title":"Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford nanopore MinION sequencer","volume":"8","author":"Golparian","year":"2018","journal-title":"Sci Rep"},{"key":"2026061606390681100_ofag323-B36","doi-asserted-by":"crossref","first-page":"760","DOI":"10.12688\/f1000research.11354.1","article-title":"MinION analysis and reference consortium: phase 2 data release and analysis of R9.0 chemistry","volume":"6","author":"Jain","year":"2017","journal-title":"F1000Res"}],"container-title":["Open Forum Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ofid\/advance-article-pdf\/doi\/10.1093\/ofid\/ofag323\/68386139\/ofag323.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ofid\/article-pdf\/13\/6\/ofag323\/68386139\/ofag323.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ofid\/article-pdf\/13\/6\/ofag323\/68386139\/ofag323.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T10:39:19Z","timestamp":1781606359000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ofid\/article\/doi\/10.1093\/ofid\/ofag323\/8692878"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,26]]},"references-count":36,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2026,6,2]]}},"URL":"https:\/\/doi.org\/10.1093\/ofid\/ofag323","relation":{},"ISSN":["2328-8957"],"issn-type":[{"value":"2328-8957","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,6]]},"published":{"date-parts":[[2026,5,26]]},"article-number":"ofag323"}}