{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T18:59:49Z","timestamp":1785437989140,"version":"3.56.0"},"reference-count":29,"publisher":"American Society for Microbiology","issue":"4","license":[{"start":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T00:00:00Z","timestamp":1775606400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T00:00:00Z","timestamp":1775606400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100007449","name":"Takeda Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007449","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009098","name":"Japanese Respiratory Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100009098","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020148","name":"Foundation of Kinoshita Memorial Enterprise","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100020148","id-type":"DOI","asserted-by":"publisher"}]},{"name":"MSD Life Science Foundation"},{"DOI":"10.13039\/501100008665","name":"Osaka Medical Research Foundation for Intractable Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008732","name":"Uehara Memorial Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008732","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["24fk0108673h0702"],"award-info":[{"award-number":["24fk0108673h0702"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP21lm02007, JP223fa627002"],"award-info":[{"award-number":["JP21lm02007, JP223fa627002"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Japan Intractable Diseases (Nanbyo) Research Foundation","award":["2020B02"],"award-info":[{"award-number":["2020B02"]}]},{"name":"JSPS KAKENHI","award":["24K11378"],"award-info":[{"award-number":["24K11378"]}]},{"name":"JSPS KAKENHI","award":["24K18468"],"award-info":[{"award-number":["24K18468"]}]},{"DOI":"10.13039\/501100003844","name":"Inamori Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003844","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100008801","name":"Senri Life Science Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100008801","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2026,4,8]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      The genus\n                      <jats:italic toggle=\"yes\">Mycobacterium<\/jats:italic>\n                      , including\n                      <jats:italic toggle=\"yes\">Mycobacterium tuberculosis<\/jats:italic>\n                      and over 200 nontuberculous mycobacteria (NTM), shows wide variability in clinical outcomes and drug susceptibility. Although culture-based identification remains the gold standard, slow mycobacterial growth delays diagnosis and treatment. In this study, we evaluated a novel culture-free method for subspecies-level identification directly from sputum. In this single-center prospective cohort study at Osaka Toneyama Medical Center, we analyzed 125 sputum samples from 115 patients with NTM pulmonary disease and 10 with non-NTM respiratory conditions. Samples were decontaminated using N-acetyl-L-cysteine\u2013sodium hydroxide (NALC-NaOH) or succinic acid. We compared the reference culture method (mycobacterial culture plus whole-genome sequencing) and a culture-free direct target capture sequencing method. Core genome multi-locus sequence typing identified subspecies in both workflows, covering 186 mycobacterial species, including\n                      <jats:italic toggle=\"yes\">M. tuberculosis<\/jats:italic>\n                      . The 115 NTM cohort specimens yielded 57 smear-positive and 93 culture-positive results. The identified subspecies included 48\n                      <jats:italic toggle=\"yes\">Mycobacterium avium<\/jats:italic>\n                      subsp.\n                      <jats:italic toggle=\"yes\">hominissuis<\/jats:italic>\n                      , 22\n                      <jats:italic toggle=\"yes\">Mycobacterium intracellulare<\/jats:italic>\n                      subsp.\n                      <jats:italic toggle=\"yes\">intracellulare<\/jats:italic>\n                      , 5 subsp.\n                      <jats:italic toggle=\"yes\">chimaera<\/jats:italic>\n                      , 7\n                      <jats:italic toggle=\"yes\">Mycobacterium abscessus<\/jats:italic>\n                      subsp.\n                      <jats:italic toggle=\"yes\">abscessus<\/jats:italic>\n                      , 5 subsp.\n                      <jats:italic toggle=\"yes\">massiliense<\/jats:italic>\n                      , 1\n                      <jats:italic toggle=\"yes\">M. tuberculosis<\/jats:italic>\n                      , and 5 other NTM species. The culture-free method showed a high identification rate for smear-positive specimens (75.4%) but a low identification rate for smear-negative specimens (13.9%). NALC-NaOH pretreatment resulted in higher accuracy (90.5%) than did succinic acid pretreatment (66.7%). Thus, our culture-free subspecies-level identification method achieved high accuracy, especially in alkaline-treated smear-positive sputum samples, achieving rates above 90%. This method is recommended in clinical practice for patients who require rapid diagnosis and timely initiation of appropriate treatment, bypassing time-consuming culture steps.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        Accurate identification of\n                        <jats:italic toggle=\"yes\">Mycobacterium<\/jats:italic>\n                        species and subspecies is crucial for effective treatment, as drug susceptibility and clinical outcomes vary significantly among them. However, conventional diagnosis relies on culture-based methods that can take several weeks, critically delaying appropriate therapy. This study validates a novel culture-free method using target capture sequencing for the comprehensive, subspecies-level identification of over 186 mycobacterial species directly from sputum specimens. Our findings revealed the high accuracy of this approach for smear-positive specimens, especially with alkaline pretreatment. This rapid method is applicable in clinical settings and enables timely and precise treatment decisions, greatly benefiting patients who require urgent intervention.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/jcm.01128-25","type":"journal-article","created":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T14:03:43Z","timestamp":1772201023000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":2,"title":["Comparison of culture and culture-free methods for comprehensive identification of mycobacteria: a single-center prospective study"],"prefix":"10.1128","volume":"64","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-8838-6674","authenticated-orcid":false,"given":"Kazuki","family":"Hashimoto","sequence":"first","affiliation":[{"name":"Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka 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