{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T07:38:03Z","timestamp":1767166683033,"version":"build-2238731810"},"reference-count":24,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2025,2,4]],"date-time":"2025-02-04T00:00:00Z","timestamp":1738627200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,2,4]],"date-time":"2025-02-04T00:00:00Z","timestamp":1738627200000},"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":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,2,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      The\n                      <jats:italic>Mycobacterium avium<\/jats:italic>\n                      complex (MAC) is a common causative agent causing nontuberculous mycobacterial (NTM) pulmonary disease worldwide. Whole-genome sequencing was performed on a total of 203 retrospective MAC isolates from respiratory specimens. Phylogenomic analysis identified eight subspecies and species.\n                      <jats:italic>M. avium<\/jats:italic>\n                      subspecies\n                      <jats:italic>hominissuis<\/jats:italic>\n                      (MAH) was the overwhelmingly dominant species (148\/203, 72.9%). The other seven identified species were\n                      <jats:italic>M. intracellulare<\/jats:italic>\n                      subsp.\n                      <jats:italic>yongonense<\/jats:italic>\n                      (18\/203, 8.9%),\n                      <jats:italic>M. intracellulare<\/jats:italic>\n                      subsp.\n                      <jats:italic>chimaera<\/jats:italic>\n                      (10\/203, 4.9%),\n                      <jats:italic>M. colombiense<\/jats:italic>\n                      (11\/203, 5.4%),\n                      <jats:italic>M. paraintracellulare<\/jats:italic>\n                      (6\/203, 3%),\n                      <jats:italic>M. marseillense<\/jats:italic>\n                      (5\/203, 2.5%),\n                      <jats:italic>M. intracellulare<\/jats:italic>\n                      (3\/203, 1.5%), and\n                      <jats:italic>M. avium<\/jats:italic>\n                      subspecies\n                      <jats:italic>paratuberculosis<\/jats:italic>\n                      (2\/203, 1%). Significant genetic clustering was observed among MAH isolates. Notably, a large cluster (&lt;12 SNPs) of 76 MAH isolates bearing the same sequence type was observed. The presence of closely related isolates within hospital settings raises concerns about transmission routes with environmental sources potentially playing a significant role. Based on susceptibility breakpoints that are available for clarithromycin, amikacin, linezolid, and moxifloxacin, low rates of clarithromycin (0.5%, 1\/203) and amikacin (1.5%, 3\/203) phenotypic resistance were observed. While linezolid and moxifloxacin resistance were 25.6% (52\/2030) and 46.3% (94\/203), respectively. Drug resistance-associated loci were searched for mutations linked to phenotypic drug resistance. Of the entire cohort, only one isolate was found to have a A2059G 23S rRNA (\n                      <jats:italic>rrl<\/jats:italic>\n                      ) gene mutation responsible for macrolide resistance.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Mycobacterium avium<\/jats:italic>\n                      complex (MAC) infections are increasingly challenging to manage due to their complex species diversity and varied resistance patterns. This study underscores the genetic diversity within MAC, identifying at least eight species and subspecies among 203 clinical isolates, with\n                      <jats:italic>M. avium<\/jats:italic>\n                      subsp.\n                      <jats:italic>hominissuis<\/jats:italic>\n                      (MAH) being most prevalent at 72.9%. Notably, genetic clustering was observed within MAH and\n                      <jats:italic>M. intracellulare<\/jats:italic>\n                      subsp.\n                      <jats:italic>chimaera<\/jats:italic>\n                      , suggesting potential transmission routes within healthcare settings. Clarithromycin and amikacin resistance was found to be uncommon, aligning with the rarity of resistance-associated genetic mutations. These findings emphasize the need for enhanced infection control measures and routine susceptibility testing to tailor antibiotic therapies effectively.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.01600-24","type":"journal-article","created":{"date-parts":[[2025,1,10]],"date-time":"2025-01-10T09:55:36Z","timestamp":1736502936000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":2,"title":["Whole-genome phylogenetic analysis of\n                    <i>Mycobacterium avium<\/i>\n                    complex from clinical respiratory samples"],"prefix":"10.1128","volume":"13","author":[{"given":"Chew","family":"Ka Lip","sequence":"first","affiliation":[{"name":"Department of Laboratory Medicine, National University Hospital","place":["Singapore, Singapore"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joelle","family":"Go","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, National University Hospital","place":["Singapore, Singapore"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nur Aisyah","family":"Binte Abu Bakar","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, National University Hospital","place":["Singapore, Singapore"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sophie","family":"Octavia","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales","place":["Sydney, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raymond Tzer","family":"Pin Lin","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, National University Hospital","place":["Singapore, Singapore"]},{"name":"National Public Health Laboratory, National Centre for Infectious Diseases","place":["Singapore, Singapore"]},{"name":"Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore","place":["Singapore, Singapore"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9321-3341","authenticated-orcid":true,"given":"Jeanette W. P.","family":"Teo","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, National University Hospital","place":["Singapore, Singapore"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12890-018-0637-1"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.00535-2020"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tube.2018.12.004"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.01237-2022"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2711.210124"},{"key":"e_1_3_5_7_2","series-title":"CLSI Supplement M24S","volume-title":"CLSI. Performance standards for susceptibility testing of mycobacteria, Nocardia spp., and other aerobic actinomycetes","author":"CLSI","year":"2023","unstructured":"CLSI. 2023. CLSI. Performance standards for susceptibility testing of mycobacteria, Nocardia spp., and other aerobic actinomycetes. 2nd ed. CLSI Supplement M24S. Clinical and Laboratory Standards Institute; CLSI standard document M24 Clinical and Laboratory Standards Institute, Wayne, PA.","edition":"2"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv351"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu033"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw290"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2403.171554"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1136\/bmjresp-2017-000242"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2020.02.059"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2018.06.010"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0294677"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-85721-5"},{"key":"e_1_3_5_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02281-12"},{"key":"e_1_3_5_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.diagmicrobio.2018.10.022"},{"key":"e_1_3_5_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00527-18"},{"key":"e_1_3_5_21_2","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics12010064"},{"key":"e_1_3_5_22_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2020.06.019"},{"key":"e_1_3_5_23_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaf8156"},{"key":"e_1_3_5_24_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2503.180336"},{"key":"e_1_3_5_25_2","doi-asserted-by":"publisher","DOI":"10.7883\/yoken.JJID.2009.182"}],"updated-by":[{"DOI":"10.1128\/spectrum.03233-25","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2025,11,14]],"date-time":"2025-11-14T00:00:00Z","timestamp":1763078400000}}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01600-24","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01600-24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,4]],"date-time":"2025-02-04T09:02:47Z","timestamp":1738659767000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.01600-24"}},"subtitle":[],"editor":[{"given":"Fei","family":"Long","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2025,2,4]]},"references-count":24,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2025,2,4]]}},"alternative-id":["10.1128\/spectrum.01600-24"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.01600-24","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,4]]},"assertion":[{"value":"2024-07-01","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-12-13","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-01-10","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01600-24"}}