{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T02:21:28Z","timestamp":1772245288899,"version":"3.50.1"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,6,13]],"date-time":"2024-06-13T00:00:00Z","timestamp":1718236800000},"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":[[2025,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The commonly-used drug susceptibility testing (DST) relies on bacterial culture and faces shortcomings such as long turnaround time and clonal\/subclonal selection biases. Here, we developed a targeted deep amplicon sequencing (DAS) method directly applied to clinical specimens. In this DAS panel, we examined 941 drug-resistant mutations (DRMs) associated with 20 anti-tuberculosis drugs with only 4 pg of initial DNA input, and reduced the clinical testing time from 20 days to 2 days. A prospective study was conducted using 115 clinical specimens, predominantly positive for the Xpert\u00ae \u00a0Mycobacterium tuberculosis\/rifampicin (Xpert MTB\/RIF) assay, to evaluate DRM detection. DAS was performed on culture-free specimens, while culture-dependent isolates were used for phenotypic DST, DAS, and whole-genome sequencing (WGS). For in silico molecular DST, our result based on DAS panel revealed the similar accuracy to three published reports based on WGS. For 82 isolates, application of DAS using the resistance-determining mutation method showed better accuracy (93.03% vs. 92.16%), sensitivity (96.10% vs. 95.02%), and specificity (91.33% vs. 90.62%) than WGS using the Mykrobe software. Compared to culture-dependent WGS, culture-free DAS provides a full picture of sequence variation at the population level, exhibiting in detail the gain-and-loss variants caused by bacterial culture. Our study performs a systematic verification of the advantages of DAS in clinical applications and comprehensively illustrates the discrepancies in Mycobacterium tuberculosis before and after culture.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzae046","type":"journal-article","created":{"date-parts":[[2024,6,14]],"date-time":"2024-06-14T11:51:51Z","timestamp":1718365911000},"source":"Crossref","is-referenced-by-count":5,"title":["Deep Amplicon Sequencing Reveals Culture-dependent Clonal Selection of <i>Mycobacterium tuberculosis<\/i> in Clinical Samples"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1061-2353","authenticated-orcid":false,"given":"Jiuxin","family":"Qu","sequence":"first","affiliation":[{"name":"Department of Clinical Laboratory, Shenzhen Third People\u2019s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology , Shenzhen 518114,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6637-6807","authenticated-orcid":false,"given":"Wanfei","family":"Liu","sequence":"additional","affiliation":[{"name":"Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen 518120,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4148-8703","authenticated-orcid":false,"given":"Shuyan","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Shenzhen Third People\u2019s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology , Shenzhen 518114,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-8841-1796","authenticated-orcid":false,"given":"Chi","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Shenzhen Third People\u2019s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology , Shenzhen 518114,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-4735-9970","authenticated-orcid":false,"given":"Wenjie","family":"Lai","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Shenzhen Third People\u2019s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology , Shenzhen 518114,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9370-4290","authenticated-orcid":false,"given":"Rui","family":"Qin","sequence":"additional","affiliation":[{"name":"Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen 518120,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-5889-5935","authenticated-orcid":false,"given":"Feidi","family":"Ye","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Shenzhen Third People\u2019s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology , Shenzhen 518114,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7143-8884","authenticated-orcid":false,"given":"Yuanchun","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Shenzhen Third People\u2019s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology , Shenzhen 518114,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1112-8010","authenticated-orcid":false,"given":"Liang","family":"Fu","sequence":"additional","affiliation":[{"name":"Division Two of Pulmonary Diseases Department, Shenzhen Third People\u2019s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology , Shenzhen 518114,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2479-3327","authenticated-orcid":false,"given":"Guofang","family":"Deng","sequence":"additional","affiliation":[{"name":"Division Two of Pulmonary Diseases Department, Shenzhen Third People\u2019s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology , Shenzhen 518114,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-5132-7093","authenticated-orcid":false,"given":"Lei","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Shenzhen Third People\u2019s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology , Shenzhen 518114,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2882-7758","authenticated-orcid":false,"given":"Qiang","family":"Lin","sequence":"additional","affiliation":[{"name":"Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen 518120,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2989-571X","authenticated-orcid":false,"given":"Peng","family":"Cui","sequence":"additional","affiliation":[{"name":"Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen 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