{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T19:23:28Z","timestamp":1764617008023,"version":"3.46.0"},"reference-count":40,"publisher":"Microbiology Society","issue":"12","license":[{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,12,1]]},"abstract":"<jats:p>\n                    Non-tuberculous mycobacteria are emerging respiratory pathogens that can persist in treated water systems. In 2018, a cluster of\n                    <jats:italic>Mycobacterium intracellulare<\/jats:italic>\n                    lung infections was linked to a pool facility in Australia, prompting an epidemiological and genomic investigation.\n                    <jats:italic>M. intracellulare<\/jats:italic>\n                    was isolated from five sputum samples across four clinical cases and from fourteen pool water samples across a total of five collection time points. All cases were resolved following exclusion from the pool facility, with only one patient requiring short-term steroids; none of the patients required anti-mycobacterial treatment. To test if this was a point-source outbreak, whole-genome sequencing of mycobacteria recovered from patients and the pool was implemented. Initial analysis confirmed all patient and water isolates were\n                    <jats:italic>M. intracellulare<\/jats:italic>\n                    with sequence type 210. A complete, circular genome was constructed from one of the isolates linked to this cluster and was used as a reference genome for high-resolution core genome SNP analysis. This analysis showed tight clustering of\n                    <jats:italic>M. intracellulare<\/jats:italic>\n                    genomes from patient and pool water isolates that were distinct from other\n                    <jats:italic>M. intracellulare<\/jats:italic>\n                    . Thus, epidemiological and comparative genome analysis strongly implicated the pool as the origin of these infections.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001577","type":"journal-article","created":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T18:17:32Z","timestamp":1764613052000},"source":"Crossref","is-referenced-by-count":0,"title":["Genomic characterization and SNP analysis connect respiratory infections caused by Mycobacterium intracellulare with a pool facility"],"prefix":"10.1099","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4726-5527","authenticated-orcid":false,"given":"Caitlin A.","family":"Selway","sequence":"first","affiliation":[{"name":"Microbiology and Infectious Disease, SA Pathology, Adelaide, SA 5000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lisa","family":"Shephard","sequence":"additional","affiliation":[{"name":"Microbiology and Infectious Disease, SA Pathology, Adelaide, SA 5000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michaela","family":"Hobby","sequence":"additional","affiliation":[{"name":"Health and Regulation Protection, SA Health, Adelaide, SA 5000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Koen","family":"Vandelannoote","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, VIC 3000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris","family":"Lease","sequence":"additional","affiliation":[{"name":"Health and Regulation Protection, SA Health, Adelaide, SA 5000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Cunliffe","sequence":"additional","affiliation":[{"name":"Health and Regulation Protection, SA Health, Adelaide, SA 5000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jamie","family":"Woodward","sequence":"additional","affiliation":[{"name":"Health and Regulation Protection, SA Health, Adelaide, SA 5000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Timothy P.","family":"Stinear","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, VIC 3000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Turra","sequence":"additional","affiliation":[{"name":"Microbiology and Infectious Disease, SA Pathology, Adelaide, SA 5000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simone","family":"Barry","sequence":"additional","affiliation":[{"name":"University of Adelaide, Adelaide, SA 5000, Australia"},{"name":"SA TB Services, Central Adelaide Health Network, Adelaide, SA 5000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James","family":"Geake","sequence":"additional","affiliation":[{"name":"University of Adelaide, Adelaide, SA 5000, Australia"},{"name":"SA TB Services, Central Adelaide Health Network, Adelaide, SA 5000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard","family":"Stapledon","sequence":"additional","affiliation":[{"name":"Royal Adelaide Hospital, SA Health, Adelaide, SA 5000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lito","family":"Papanicolas","sequence":"additional","affiliation":[{"name":"Microbiology and Infectious Disease, SA Pathology, Adelaide, SA 5000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lex E. X.","family":"Leong","sequence":"additional","affiliation":[{"name":"University of South Australia, Adelaide, SA 5000, Australia"},{"name":"Microbiology and Infectious Disease, SA Pathology, Adelaide, SA 5000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.17.1.98-106.2004"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00899-13"},{"article-title":"Australian drinking water guidelines paper 6 national water quality management strategy","year":"2011","author":"NHMRC","key":"R3"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.68.3.1025-1032.2002"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-6-63"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1111\/jam.12272"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1183\/09031936.00149212"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-015-1140-4"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1378\/chest.111.3.813"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.4046\/trd.2012.72.5.452"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(08)70100-2"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.3201\/eid1703.101510"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2012.03929.x"},{"article-title":"seqtk [Internet]","year":"2024","author":"Li","key":"R14"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0997-x"},{"article-title":"mlst [Internet]","year":"2024","author":"Seemann","key":"R17"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-595"},{"year":"2024","key":"R19","article-title":"dorado [Internet]"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.001244"},{"article-title":"snippy: fast bacterial variant calling from NGS reads","year":"2024","author":"Seemann","key":"R21"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaa015"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4285"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msx281"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000056"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1111\/2041-210X.12628"},{"article-title":"snp-dists [Internet]","year":"2024","author":"Seemann","key":"R27"},{"year":"2013","key":"R28"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.200604-571ST"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1378\/chest.11-0089"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201111-2016OC"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.1086\/318136"},{"key":"R34","article-title":"Incidence of nontuberculous mycobacterial disease in New Zealand, 2004","volume":"120","author":"Freeman","year":"2007","journal-title":"N Z Med J"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.67.3.1225-1231.2001"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1001\/jama.260.11.1599"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(94)90239-9"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.4.1702-1705.2000"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.69.9.5685-5689.2003"},{"key":"R40","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2018.07.451"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001577?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T18:17:33Z","timestamp":1764613053000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001577"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,1]]},"references-count":40,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2025,12,1]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.001577","relation":{},"ISSN":["2057-5858"],"issn-type":[{"type":"electronic","value":"2057-5858"}],"subject":[],"published":{"date-parts":[[2025,12,1]]}}}