{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T09:58:34Z","timestamp":1790935114392,"version":"4.1.0"},"reference-count":30,"publisher":"American Society for Microbiology","issue":"12","license":[{"start":{"date-parts":[[2012,12,1]],"date-time":"2012-12-01T00:00:00Z","timestamp":1354320000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2012,12]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            A novel protocol for full-length\n            <jats:named-content content-type=\"genus-species\">Mycobacterium tuberculosis<\/jats:named-content>\n            gene analysis of first- and second-line drug resistance was developed using the Ion Torrent Personal Genome Machine (PGM). Five genes\u2014\n            <jats:italic>rpoB<\/jats:italic>\n            (rifampin),\n            <jats:italic>katG<\/jats:italic>\n            (isoniazid),\n            <jats:italic>pncA<\/jats:italic>\n            (pyrazinamide),\n            <jats:italic>gyrA<\/jats:italic>\n            (ofloxacin\/fluoroquinolone), and\n            <jats:italic>rrs<\/jats:italic>\n            (aminoglycosides)\u2014were amplified and sequenced, and results were compared to those obtained by genotypic Hain line probe assay (LPA) and phenotypic Bactec MGIT 960 analysis using 26 geographically diverse South African clinical isolates collected between July and November 2011. Ion Torrent sequencing exhibited 100% (26\/26) concordance to phenotypic resistance obtained by MGIT 960 culture and genotypic\n            <jats:italic>rpoB<\/jats:italic>\n            and\n            <jats:italic>katG<\/jats:italic>\n            results by LPA. In several rifampin-resistant isolates, Ion Torrent sequencing revealed uncommon substitutions (H526R and D516G) that did not have a defined mutation by LPA. Importantly, previously uncharacterized mutations in\n            <jats:italic>rpoB<\/jats:italic>\n            (V194I),\n            <jats:italic>rrs<\/jats:italic>\n            (G878A), and\n            <jats:italic>pncA<\/jats:italic>\n            (Q122Stop) genes were observed. Ion Torrent sequencing may facilitate tracking and monitoring geographically diverse multidrug-resistant and extensively drug-resistant strains and could potentially be integrated into selected regional and reference settings throughout Africa, India, and China.\n          <\/jats:p>","DOI":"10.1128\/jcm.01893-12","type":"journal-article","created":{"date-parts":[[2012,9,13]],"date-time":"2012-09-13T02:32:10Z","timestamp":1347503530000},"page":"3831-3837","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":69,"title":["Next-Generation Ion Torrent Sequencing of Drug Resistance Mutations in Mycobacterium tuberculosis Strains"],"prefix":"10.1128","volume":"50","author":[{"given":"Luke T.","family":"Daum","sequence":"first","affiliation":[{"name":"Longhorn Vaccines &amp; Diagnostics, San Antonio, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John D.","family":"Rodriguez","sequence":"additional","affiliation":[{"name":"Longhorn Vaccines &amp; Diagnostics, San Antonio, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sue A.","family":"Worthy","sequence":"additional","affiliation":[{"name":"Longhorn Vaccines &amp; Diagnostics, San Antonio, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nazir A.","family":"Ismail","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa"},{"name":"Centre for Tuberculosis, National Institute of Communicable Diseases (NICD), Sandringham, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaheed V.","family":"Omar","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa"},{"name":"Centre for Tuberculosis, National Institute of Communicable Diseases (NICD), Sandringham, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andries W.","family":"Dreyer","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P. Bernard","family":"Fourie","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anwar A.","family":"Hoosen","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James P.","family":"Chambers","sequence":"additional","affiliation":[{"name":"Longhorn Vaccines &amp; Diagnostics, San Antonio, Texas, USA"},{"name":"University of Texas at San Antonio, San Antonio, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerald W.","family":"Fischer","sequence":"additional","affiliation":[{"name":"Longhorn Vaccines &amp; Diagnostics, San Antonio, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.41.3.1235-1239.2003"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.48.4.1281-1288.2004"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2334-11-78"},{"key":"e_1_3_2_5_2","volume-title":"30th Annu. 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Life Technologies Incorporated Foster City CA."},{"issue":"1","key":"e_1_3_2_12_2","first-page":"27","article-title":"Extensively drug resistant tuberculosis (XDR-TB): a potential threat","volume":"2","author":"Marwar A","year":"2011","unstructured":"MarwarA. 2011. Extensively drug resistant tuberculosis (XDR-TB): a potential threat. J. Basic Clin. Pharm. 2(1):27\u201332.","journal-title":"J. Basic Clin. 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