{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T18:39:30Z","timestamp":1785436770806,"version":"3.56.0"},"reference-count":26,"publisher":"American Society for Microbiology","issue":"7","license":[{"start":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T00:00:00Z","timestamp":1783468800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T00:00:00Z","timestamp":1783468800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100012308","name":"National Jewish Health","doi-asserted-by":"publisher","award":["Internal funding"],"award-info":[{"award-number":["Internal funding"]}],"id":[{"id":"10.13039\/100012308","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Preclinical Design and Clinical Translation of TB Regimens (PReDicTR) Consortium","award":["UM1AI179699"],"award-info":[{"award-number":["UM1AI179699"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2026,7,8]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Accurate identification and genotypic drug resistance prediction in mycobacteria are essential for early diagnosis and appropriate clinical management. Targeted next-generation sequencing (tNGS) detects multiple genetic targets and enables direct testing from primary specimens. We evaluated identification using the Deeplex Myc-TB assay for\n                      <jats:italic toggle=\"yes\">Mycobacterium tuberculosis<\/jats:italic>\n                      complex (MTBC) and nontuberculous mycobacteria (NTM) as well as MTBC drug-resistance prediction from 78 isolates and 102 sputum samples. DNA libraries were sequenced (Illumina MiSeq), and results were analyzed using defined acceptability criteria. Performance was compared against reference phenotypic and genotypic methods. Testing for MTBC was invalid in &lt;2.5% of cases, but NTM testing was invalid more frequently, especially in sputum (&gt;50%). Of the evaluable isolates\/sputum, specificity was 100% for negative\/nontarget organisms. Among isolates, sensitivity for organism identification was 92.7% (38\/41) for MTBC, 100% (5\/5) for rapidly growing mycobacteria (RGM), and 87.5% (14\/16) for slowly growing mycobacteria (SGM). For sputum, sensitivity was 97.6% (41\/42) for MTBC, 70% (7\/10) for SGM, and 66% (2\/3) for RGM. Categorical agreement of MTBC resistotypes against reference susceptibility methods was 91.9% (489\/532) for isolates and 90.8% (472\/520) for sputum, increasing to 96.8% (489\/505) and 97.3% (472\/485), respectively, when variants of unknown significance were excluded. Limit-of-detection studies confirmed published thresholds of 100\u20131,000 genomes\/PCR in both isolates and sputum. Deeplex Myc-TB provides highly specific identification and reliable genotypic resistance profiling from isolates and sputum, especially for MTBC. While identification of rare NTM species and mixed infections remain challenging, tNGS demonstrates substantial promise for rapid mycobacterial diagnostics.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        Rapid and accurate diagnosis of mycobacterial infections is essential for initiating effective treatment, interrupting transmission, and improving patient outcomes. Traditional phenotypic methods for organism identification and antibiotic susceptibility testing are slow and may be unreliable for certain drugs. This study evaluates the Deeplex Myc-TB targeted next-generation sequencing assay to identify mycobacteria and resistance-associated mutations from the\n                        <jats:italic toggle=\"yes\">Mycobacterium tuberculosis<\/jats:italic>\n                        complex (MTBC) for both isolates and clinical sputum. Our findings show strong correlation of MTBC identification and resistance markers compared with reference methods.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/jcm.00106-26","type":"journal-article","created":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T13:03:21Z","timestamp":1781269401000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Performance of a targeted next generation sequencing assay for mycobacterial identification and drug resistance from sputum and isolates"],"prefix":"10.1128","volume":"64","author":[{"given":"Sharon K.","family":"Kuss-Duerkop","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/016z2bp30","id-type":"ROR","asserted-by":"publisher"}],"name":"Advanced Diagnostic Laboratories, National Jewish Health","place":["Denver, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Godo","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/016z2bp30","id-type":"ROR","asserted-by":"publisher"}],"name":"Advanced Diagnostic Laboratories, National Jewish Health","place":["Denver, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily K.","family":"DeCurtis","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03wmf1y16","id-type":"ROR","asserted-by":"publisher"}],"name":"University of Colorado Anschutz Medical Campus","place":["Aurora, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Van","family":"Pham","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/016z2bp30","id-type":"ROR","asserted-by":"publisher"}],"name":"Advanced Diagnostic Laboratories, National Jewish Health","place":["Denver, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorraine","family":"Abushanab","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/016z2bp30","id-type":"ROR","asserted-by":"publisher"}],"name":"Advanced Diagnostic Laboratories, National Jewish Health","place":["Denver, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valerie","family":"Archuleta","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/016z2bp30","id-type":"ROR","asserted-by":"publisher"}],"name":"Advanced Diagnostic Laboratories, National Jewish Health","place":["Denver, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7157-4034","authenticated-orcid":true,"given":"Gregory T.","family":"Robertson","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03k1gpj17","id-type":"ROR","asserted-by":"publisher"}],"name":"Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University","place":["Fort Collins, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongbao","family":"Wang","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/016z2bp30","id-type":"ROR","asserted-by":"publisher"}],"name":"Advanced Diagnostic Laboratories, National Jewish Health","place":["Denver, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6686-8545","authenticated-orcid":true,"given":"Reeti","family":"Khare","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/016z2bp30","id-type":"ROR","asserted-by":"publisher"}],"name":"Advanced Diagnostic Laboratories, National Jewish Health","place":["Denver, USA"]},{"id":[{"id":"https:\/\/ror.org\/016z2bp30","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Medicine, National Jewish Health","place":["Denver, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciae421"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa241"},{"key":"e_1_3_4_4_2","volume-title":"Module 3: diagnosis \u2013 rapid diagnostics for tuberculosis detection","author":"WHO","year":"2024","unstructured":"WHO. 2024. WHO consolidated guidelines on tuberculosis. In Module 3: diagnosis \u2013 rapid diagnostics for tuberculosis detection, 3rd ed","edition":"3"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01638-24"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.02338-2020"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2020.04.049"},{"key":"e_1_3_4_8_2","unstructured":"Anonymous. 2020. Deeplex Myc-TB User Manual RUO Genoscreen Lille France"},{"key":"e_1_3_4_9_2","volume-title":"Clinical microbiology procedures handbook","author":"Wengenack NL","year":"2023","unstructured":"Wengenack NL. 2023. General mycobacteriology procedures. In Leber AL, Burnham CD (ed), Clinical microbiology procedures handbook, 5th ed. ASM Press, Washington D.C.","edition":"5"},{"key":"e_1_3_4_10_2","volume-title":"Technical manual for drug susceptibility testing of medicines used in the treatment of tuberculosis","author":"World Health Organization","year":"2018","unstructured":"World Health Organization. 2018. Technical manual for drug susceptibility testing of medicines used in the treatment of tuberculosis. World Health Organization."},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.5588\/ijtld.18.0417"},{"key":"e_1_3_4_12_2","volume-title":"M24","author":"CLSI","year":"2018","unstructured":"CLSI. 2018. Susceptibility testing of mycobacteria, Nocardia spp., and other aerobic actinomycetes. In M24, 3rd ed. Institute CLS, Wayne, PA.","edition":"3"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","unstructured":"Percy C Memelis I Edwards T Roberts AP Biagini G Cantillon D. 2024. 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Preparation of mycobacteria-containing artificial sputum for TB panel testing and microscopy of sputum smears. 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