{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T13:11:07Z","timestamp":1788959467761,"version":"build-2803163510"},"reference-count":35,"publisher":"American Society for Microbiology","issue":"9","license":[{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100005762","name":"National Taiwan University Hospital","doi-asserted-by":"publisher","award":["112N0008"],"award-info":[{"award-number":["112N0008"]}],"id":[{"id":"10.13039\/501100005762","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005762","name":"National Taiwan University Hospital","doi-asserted-by":"publisher","award":["NTUH113-A172"],"award-info":[{"award-number":["NTUH113-A172"]}],"id":[{"id":"10.13039\/501100005762","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2026,9,9]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Nontuberculous mycobacteria (NTM) are diverse, and species-level identification remains challenging in routine diagnostics. We analyzed NTM isolates collected at three regional centers of the National Taiwan University Hospital (NTUH) from 2019 to 2024 to assess geographic variation and identification performance after implementation of matrix-assisted laser desorption\/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Among 3,188 cases meeting the microbiological criteria for probable pulmonary NTM disease, the species distribution differed by region:\n                      <jats:italic toggle=\"yes\">Mycobacterium avium<\/jats:italic>\n                      complex predominated in central Taiwan (Yunlin, 47.3%), whereas\n                      <jats:italic toggle=\"yes\">M. abscessus<\/jats:italic>\n                      complex (Taipei, 26.5%) and\n                      <jats:italic toggle=\"yes\">M. kansasii<\/jats:italic>\n                      (Hsinchu, 12.4%) were more common in northern Taiwan. In 2019, 14.5% of isolates were reported to be unidentified by MALDI-TOF MS; with workflow optimization and database updates, this percentage decreased but plateaued at 4.5\u20134.8%. Whole-genome sequencing (WGS) of 61 randomly selected persistently unidentified isolates revealed eight average nucleotide identity (ANI)-defined clusters; 55 isolates (90.2%) could not be assigned to known species using current reference databases. Two clusters detected only in Hsinchu were phylogenetically closest to\n                      <jats:italic toggle=\"yes\">M. kyorinense<\/jats:italic>\n                      , with ANI values below the species demarcation threshold. Overall, we observed marked regional heterogeneity of NTM in Taiwan and a persistent identification gap that remained after MALDI-TOF MS optimization and follow-up WGS.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>This study characterized regional differences in the NTM species distribution across Taiwan, and the results highlight the limitations of current identification approaches. MALDI-TOF MS identifies most isolates, but locally circulating lineages represent a persistent gap in global reference libraries. Even with whole-genome sequencing (WGS), 90.2% (55\/61) of persistently unresolved isolates could not be assigned to known species in the current reference databases despite the formation of clear ANI- and phylogeny-defined clusters. These findings show that both proteomic and genomic reference resources for clinical NTM remain incomplete. Expanding regionally representative databases and performing WGS for isolates that remain unresolved by MALDI-TOF MS will be necessary to improve species-level resolution for surveillance and clinical interpretation.<\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/jcm.00622-26","type":"journal-article","created":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T14:04:56Z","timestamp":1786716296000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Effectiveness of mass spectrometry and genomic analysis in the surveillance of nontuberculous\n                    <i>Mycobacterium<\/i>\n                    in Taiwan"],"prefix":"10.1128","volume":"64","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-5879-2006","authenticated-orcid":false,"given":"Hsueh-Wei","family":"Chu","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03nteze27","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Laboratory Medicine, National Taiwan University Hospital","place":["Taipei, Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hsin-Ni","family":"Huang","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03nteze27","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Laboratory Medicine, National Taiwan University Hospital","place":["Taipei, Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chin-Chung","family":"Shu","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03nteze27","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Internal Medicine, National Taiwan University Hospital","place":["Taipei, Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tai-Fen","family":"Lee","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03nteze27","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Laboratory Medicine, National Taiwan University Hospital","place":["Taipei, Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7805-4178","authenticated-orcid":true,"given":"Yu-Tsung","family":"Huang","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03nteze27","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Laboratory Medicine, National Taiwan University Hospital","place":["Taipei, Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccm.2014.11.002"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jctube.2021.100244"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2008.131673"},{"key":"e_1_3_4_5_2","first-page":"1186","article-title":"Non-tuberculous mycobacteria: patterns of isolation. 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