{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:44:53Z","timestamp":1785426293568,"version":"3.56.0"},"reference-count":42,"publisher":"American Society for Microbiology","issue":"7","license":[{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"Development Fund of Zhongshan Hospital, Fudan University","award":["2024ZSFZ39"],"award-info":[{"award-number":["2024ZSFZ39"]}]},{"name":"Development Fund of Zhongshan Hospital, Fudan University","award":["XK-079-4"],"award-info":[{"award-number":["XK-079-4"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Tuberculosis (TB) returns to be the leading infectious killer globally after coronavirus disease 2019. The World Health Organization (WHO) formally included targeted next-generation sequencing (tNGS) in its list of recommendations for\n                      <jats:italic toggle=\"yes\">Mycobacterium tuberculosis<\/jats:italic>\n                      (MTB) and drug resistance (DR). In this study, we explored the application of various clinical sample types for TB diagnosis and DR profiles. In comparison to the composite reference standard, the overall sensitivity values of culture, Xpert, metagenomic next-generation sequencing (mNGS), and tNGS were 0.458, 0.614, 0.772, and 0.760, respectively. tNGS had sensitivity similar to mNGS, which had advantages over culture and Xpert, respectively, despite different classification of sample types. In comparison to the microbiological reference standard, the overall sensitivity values of culture, Xpert, mNGS, and tNGS were 0.606, 0.811, 0.856, and 0.884, respectively. Suprisingly, in extrapulmonary tissue and serous effusion, mNGS and tNGS had advantages over Xpert. DR-related mutations were detected in 15 cases (13.2%). There were 51 (44.7%) applicable for all DR genes, with 22 (19.3%) not applicable for DR genes. DR genes were partially applicable in 41 (36.0%) samples. However, in culture-negative TB cases, tNGS can additionally provide 52.7% first-line DR profiles. Sanger sequencing was performed on 14 samples to confirm gene mutation identified by tNGS, and the results were entirely consistent. It was concluded that the tNGS assay was a promising approach in the initial diagnostic test of MTB and DR-related genes in different clinical samples, even for the smear- and culture-negative paucibacillary samples.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>tNGS combines gene-specific amplification with next-generation sequencing to detect MTB and drug-resistant genes by amplifying numerous loci directly from clinical samples. The WHO implemented tNGS for the purpose of monitoring respiratory specimens for MTB detection and DR-TB due to its high sensitivity and specificity, culture independence, and ability to report heterogeneous\/silent mutations. The sensitivity outperformed both culture and Xpert, and the turnaround time was significantly less than that of culture-based assays. The tNGS assay used in this study costs USD 96 and has a 12 hour turnaround time. Nonetheless, tNGS has a great deal of promise for enhancing TB detection while also addressing DR strains.<\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.03127-24","type":"journal-article","created":{"date-parts":[[2025,6,10]],"date-time":"2025-06-10T09:02:53Z","timestamp":1749546173000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":7,"title":["Targeted next-generation sequencing: a promising approach for\n                    <i>Mycobacterium tuberculosis<\/i>\n                    detection and drug resistance when applied in paucibacillary clinical samples"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3333-8721","authenticated-orcid":false,"given":"Wenting","family":"Jin","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013q1eq08","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Infectious Diseases, Zhongshan Hospital, Fudan University","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meixia","family":"Wang","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013q1eq08","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Infection Management, Zhongshan Hospital (Xiamen), Fudan University","place":["Xiamen, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Wang","sequence":"additional","affiliation":[{"name":"Guangzhou KingCreate Biotechnology Co., Ltd.","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beidi","family":"Zhu","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013q1eq08","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Infectious Diseases, Zhongshan Hospital, Fudan University","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-8846-0071","authenticated-orcid":true,"given":"Qingqing","family":"Wang","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013q1eq08","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Infectious Diseases, Zhongshan Hospital, Fudan University","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunmei","family":"Zhou","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013q1eq08","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology, Zhongshan Hospital, Fudan University","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pei","family":"Li","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02d0gmv36","id-type":"ROR","asserted-by":"publisher"}],"name":"KingMed Diagnostics","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chaohui","family":"Hu","sequence":"additional","affiliation":[{"name":"Guangzhou KingCreate Biotechnology Co., Ltd.","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Liu","sequence":"additional","affiliation":[{"name":"Guangzhou KingCreate Biotechnology Co., Ltd.","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jue","family":"Pan","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013q1eq08","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Infectious Diseases, Zhongshan Hospital, Fudan University","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-5331-6442","authenticated-orcid":false,"given":"Jiachang","family":"Chen","sequence":"additional","affiliation":[{"name":"Guangzhou KingCreate Biotechnology Co., Ltd.","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8687-992X","authenticated-orcid":true,"given":"Bijie","family":"Hu","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013q1eq08","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Infectious Diseases, Zhongshan Hospital, Fudan University","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","unstructured":"WHO. 2024. Global tuberculosis report 2024"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2020.12.031"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2019.01.019"},{"key":"e_1_3_4_5_2","volume-title":"Xpert MTB\/RIF implementation manual: technical and operational \u2018how-to\u2019; practical considerations","author":"WHO","year":"2014","unstructured":"WHO. 2014. Xpert MTB\/RIF implementation manual: technical and operational \u2018how-to\u2019; practical considerations."},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.01354-2017"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1800474"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(21)00452-7"},{"key":"e_1_3_4_9_2","unstructured":"WHO. 2022. WHO consolidated guidelines on tuberculosis. Module 4: treatment\u2014drug-resistant tuberculosis treatment 2022 update."},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(24)00263-9"},{"key":"e_1_3_4_11_2","unstructured":"WHO. 2023. Use of targeted next-generation sequencing to detect drug-resistant tuberculosis: rapid communication July 2023."},{"key":"e_1_3_4_12_2","first-page":"86","volume-title":"Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance","author":"WHO","year":"2021","unstructured":"WHO. 2021. Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance, p 86."},{"key":"e_1_3_4_13_2","volume-title":"Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance","author":"WHO","year":"2023","unstructured":"WHO. 2023. Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance. 2nd ed.","edition":"2"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.04098-23"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jinf.2023.10.018"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2023.1206056"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.5588\/ijtld.22.0138"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.21037\/atm-20-2274"},{"key":"e_1_3_4_19_2","first-page":"S231","article-title":"Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice","author":"Qing M","year":"2018","unstructured":"Qing M, Yuyan M, Qingqing W, Jue P, Yao Z, Wenting J, Yumeng Y, Yi S, Yingnan H, Mengran W. 2018. Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice. Clin Infect Dis:S231\u2013S240.","journal-title":"Clin Infect Dis"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty560"},{"key":"e_1_3_4_21_2","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li H","year":"2013","unstructured":"Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv e-prints","journal-title":"arXiv e-prints"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2023.1059433"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.924410"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-55112-y"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1080\/23744235.2023.2241550"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00026-24"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jfp.2024.100256"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2024.105307"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.heliyon.2023.e23217"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-022-01054-6"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.01287-23"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01358-21"},{"key":"e_1_3_4_33_2","unstructured":"WHO. 2024. Global tuberculosis report 2023."},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.1002794"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2021.04.027"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.1007\/s15010-024-02411-w:1-13"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2024.1349715"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2024.1403619"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jinf.2023.01.031"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1128\/Spectrum.00610-21"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(24)00586-3"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.4046\/trd.2015.78.2.47"},{"key":"e_1_3_4_43_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0237753"}],"container-title":["Microbiology Spectrum"],"original-title":[],"contributor":[{"given":"Fangyou","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"reviewer"}]},{"given":"Bo","family":"Yan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"reviewer"}]}],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.03127-24","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.03127-24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T09:04:43Z","timestamp":1751360683000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.03127-24"}},"subtitle":[],"editor":[{"given":"Sadjia","family":"Bekal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,7]]},"references-count":42,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2025,7]]}},"alternative-id":["10.1128\/spectrum.03127-24"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.03127-24","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7]]},"assertion":[{"value":"2024-12-13","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-03-31","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-06-10","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e03127-24"}}