{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,15]],"date-time":"2026-08-15T10:41:36Z","timestamp":1786790496049,"version":"build-2736575974"},"reference-count":21,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T00:00:00Z","timestamp":1781481600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Capital\u2019s Funds for Health Improvement and Research","award":["2024-2G-3017"],"award-info":[{"award-number":["2024-2G-3017"]}]},{"name":"Beijing Natural Science Foundation of China","award":["7242078"],"award-info":[{"award-number":["7242078"]}]},{"name":"Beijing Center for Disease Prevention and Control","award":["BJCDC\/2023-KYJH-06"],"award-info":[{"award-number":["BJCDC\/2023-KYJH-06"]}]},{"award":["BJCDC\/2023-KYJH-06"],"award-info":[{"award-number":["BJCDC\/2023-KYJH-06"]}],"id":[{"id":"https:\/\/ror.org\/058dc0w16","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Direct sputum targeted next-generation sequencing (tNGS) offers rapid resistance profiling without culture, but its concordance with isolate-based whole-genome sequencing (WGS) and phenotypic drug susceptibility testing (pDST) remains unclear. We compared tNGS (direct sputum) and WGS (cultured isolates) for 14 drugs\u2019 resistance prediction in 68 culture-positive tuberculosis specimens, using pDST as reference. Performance for lineage concordance was also assessed. tNGS showed the highest rifampicin (RIF) sensitivity (90.9%) but the lowest specificity (65.2%); WGS achieved the best overall agreement (86.8%). For isoniazid, tNGS sensitivity was 82.6% vs. WGS 78.3%, but WGS specificity was higher (91.1% vs. 75.6%). tNGS outperformed WGS for ethambutol (EMB) sensitivity (80.0% vs. 40.0%). Both methods performed poorly for pyrazinamide (PZA) (agreement ~40%). Among 68 specimens, 51.5% had fully concordant resistance profiles; tNGS-only variants outnumbered WGS-only variants 2:1. Crucially, tNGS and WGS on the same 24 cultured isolates yielded identical results, proving that discrepancies arise from culture-driven clonal selection, not technical differences. Direct sputum tNGS suggests broader within-host resistance diversity that may be missed by culture, whereas WGS offers superior specificity. The two methods are complementary, with culture bias being the primary source of discordance.<\/jats:p>","DOI":"10.3390\/ijms27125392","type":"journal-article","created":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T00:49:01Z","timestamp":1781570941000},"page":"5392","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Evaluating the Performance of Sputum-Based Targeted Sequencing Against Mycobacterial Whole-Genome Sequencing in Predicting Tuberculosis Drug Resistance"],"prefix":"10.3390","volume":"27","author":[{"given":"Lili","family":"Tian","sequence":"first","affiliation":[{"name":"Beijing Center for Disease Prevention and Control, Beijing 100035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nenhan","family":"Wang","sequence":"additional","affiliation":[{"name":"Beijing Center for Disease Prevention and Control, Beijing 100035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-4021-6215","authenticated-orcid":false,"given":"Xiaowei","family":"Dai","sequence":"additional","affiliation":[{"name":"Beijing Center for Disease Prevention and Control, Beijing 100035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuangshuang","family":"Chen","sequence":"additional","affiliation":[{"name":"Beijing Center for Disease Prevention and Control, Beijing 100035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Chen","sequence":"additional","affiliation":[{"name":"Beijing Center for Disease Prevention and Control, Beijing 100035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Li","sequence":"additional","affiliation":[{"name":"Beijing Center for Disease Prevention and Control, Beijing 100035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chuanyou","family":"Li","sequence":"additional","affiliation":[{"name":"Beijing Center for Disease Prevention and Control, Beijing 100035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongtai","family":"Zhang","sequence":"additional","affiliation":[{"name":"Beijing Center for Disease Prevention and Control, Beijing 100035, China"},{"name":"School of Public Health, Capital Medical University, Beijing 100069, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,15]]},"reference":[{"key":"ref_1","unstructured":"(2023, November 07). Global Tuberculosis Report 2023. Available online: https:\/\/www.who.int\/publications\/i\/item\/9789240083851."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/S2213-2600(17)30079-6","article-title":"The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis","volume":"5","author":"Dheda","year":"2017","journal-title":"Lancet Respir. Med."},{"key":"ref_3","unstructured":"World Health Organization (2014). Xpert MTB\/RIF Implementation Manual: Technical and Operational \u2018How-To\u2019, World Health Organization."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/s41579-019-0214-5","article-title":"Whole genome sequencing of Mycobacterium tuberculosis: Current standards and open issues","volume":"17","author":"Meehan","year":"2019","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Dookie, N., Khan, A., Padayatchi, N., and Naidoo, K. (2022). Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.775030"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"e00888-17","DOI":"10.1128\/AAC.00888-17","article-title":"Mycobacterium tuberculosis Subculture Results in Loss of Potentially Clinically Relevant Heteroresistance","volume":"61","author":"Metcalfe","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"fuaa071","DOI":"10.1093\/femsre\/fuaa071","article-title":"The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis","volume":"45","author":"Castro","year":"2021","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Murphy, S.G., Smith, C., Lapierre, P., Shea, J., Patel, K., Halse, T.A., Dickinson, M., Escuyer, V., Rowlinson, M.C., and Musser, K.A. (2023). Direct detection of drug-resistant Mycobacterium tuberculosis using targeted next generation sequencing. Front. Public Health, 11.","DOI":"10.3389\/fpubh.2023.1206056"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"S152","DOI":"10.1016\/j.ijtb.2025.02.019","article-title":"Direct targeted next-generation sequencing for diagnosis of drug-resistant tuberculosis from clinical samples\u2014An update","volume":"72","author":"Gopalaswamy","year":"2025","journal-title":"Indian J. Tuberc."},{"key":"ref_10","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."},{"key":"ref_11","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"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"7114","DOI":"10.1038\/s41467-024-51266-0","article-title":"Genetic diversity within diagnostic sputum samples is mirrored in the culture of Mycobacterium tuberculosis across different settings","volume":"15","author":"Goig","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_13","unstructured":"World Health Organization (2022). WHO Operational Handbook on Tuberculosis. Module 4: Treatment-Drug-Resistant Tuberculosis Treatment, World Health Organization."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"de Diego Fuertes, M., Costa Conceicao, E., Wells, F., Rennie, V., Heupink, T., Churchyard, G., Ndebele, F., Van der Spoel Van Dijk, A., Fanampe, B., and Charalombous, S. (2026). Targeted and whole-genome sequencing for drug resistance and genetic relatedness inference of rifampicin-resistant Mycobacterium tuberculosis: An in-depth comparison. ERJ Open Res., 12.","DOI":"10.1183\/23120541.00630-2025"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2627072","DOI":"10.1080\/22221751.2026.2627072","article-title":"Rapid drug resistance prediction in positive Mycobacterium tuberculosis clinical samples using an extensive targeted next-generation sequencing panel","volume":"15","author":"Rosendal","year":"2026","journal-title":"Emerg. Microbes Infect."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"qzae046","DOI":"10.1093\/gpbjnl\/qzae046","article-title":"Deep Amplicon Sequencing Reveals Culture-dependent Clonal Selection of Mycobacterium tuberculosis in Clinical Samples","volume":"22","author":"Qu","year":"2025","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1021\/acs.analchem.4c04166","article-title":"Development and Comprehensive Evaluation of Culture-Independent, Long Amplicon-Based Targeted Next-Generation Sequencing Methods for Predicting Antimicrobial Resistance in Tuberculosis","volume":"97","author":"Zhang","year":"2025","journal-title":"Anal. Chem."},{"key":"ref_18","unstructured":"World Health Organization (2023). Use of Targeted Next-Generation Sequencing to Detect Drug-Resistant Tuberculosis: Rapid Communication, July 2023, World Health Organizatio."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1128\/jcm.31.2.406-409.1993","article-title":"Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: Recommendations for a standardized methodology","volume":"31","author":"Cave","year":"1993","journal-title":"J. Clin. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"qzaf072","DOI":"10.1093\/gpbjnl\/qzaf072","article-title":"The GSA Family in 2025: A Broadened Sharing Platform for Multi-omics and Multimodal Data","volume":"23","author":"Zhang","year":"2025","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"D28","DOI":"10.1093\/nar\/gkaf1172","article-title":"Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2026","volume":"54","author":"Bao","year":"2026","journal-title":"Nucleic Acids Res."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/12\/5392\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T03:10:59Z","timestamp":1782270659000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/12\/5392"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,15]]},"references-count":21,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2026,6]]}},"alternative-id":["ijms27125392"],"URL":"https:\/\/doi.org\/10.3390\/ijms27125392","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,15]]}}}