{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T01:11:36Z","timestamp":1789002696537,"version":"build-2803163510"},"reference-count":62,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,12,7]],"date-time":"2025-12-07T00:00:00Z","timestamp":1765065600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,12,13]],"date-time":"2025-12-13T00:00:00Z","timestamp":1765584000000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Forschungszentrum Borstel - Leibniz Lungenzentrum"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Microbiol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Non-tuberculous mycobacteria (NTM) are ubiquitous environmental organisms that can cause severe infections in vulnerable individuals. However, the environmental reservoirs and transmission routes of clinically relevant NTM remain insufficiently understood. Given the rising incidence of NTM infections, understanding where these bacteria thrive can inform public health measures and reduce infection risk. In this study, we analysed the prevalence and genetic diversity of mycobacteria in indoor water samples from private residences and a hospital in Frankfurt am Main, Germany, and characterised them using whole genome sequencing and phenotypic drug susceptibility testing. Core genome multi-locus sequence typing (cgMLST) was employed to compare environmental isolates with nearly 3,000 clinical and environmental NTM isolates from around the world, aiming to identify potential epidemiological connections and global lineages. NTM were isolated from 9 of 41 households (22.0%) and 15 of 102 water samples (14.7%). Eight different NTM-species were identified, including one novel species. For\n                    <jats:italic>Mycobacterium abscessus<\/jats:italic>\n                    and\n                    <jats:italic>Mycobacterium chimaera<\/jats:italic>\n                    , strains belonging to globally distributed lineages were detected. Notably,\n                    <jats:italic>M. abscessus<\/jats:italic>\n                    dominant circulating clone 3 (DCC3) was present in shower water and we report, for the first time, global lineages of\n                    <jats:italic>M. chelonae<\/jats:italic>\n                    in both environmental and clinical samples. While NTM from different households were genetically distinct, isolates from five households (\n                    <jats:italic>M. chimaera<\/jats:italic>\n                    ,\n                    <jats:italic>M. abscessus<\/jats:italic>\n                    , and\n                    <jats:italic>M. chelonae<\/jats:italic>\n                    ) were closely related to clinical isolates from Germany and abroad. In conclusion, our findings highlight indoor water systems as reservoirs for some clinically significant NTM, including globally relevant clones such as\n                    <jats:italic>M. abscessus<\/jats:italic>\n                    DCC3, and underscore the potential for targeted public health interventions to reduce exposure risks, especially for vulnerable populations.\n                  <\/jats:p>","DOI":"10.1186\/s12866-025-04563-7","type":"journal-article","created":{"date-parts":[[2025,12,7]],"date-time":"2025-12-07T02:35:34Z","timestamp":1765074934000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Global lineages of non-tuberculous mycobacteria in residential water samples from Germany"],"prefix":"10.1186","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5428-1456","authenticated-orcid":false,"given":"Margo","family":"Diricks","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Denia","family":"Frank","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Inna","family":"Friesen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Niemann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas A.","family":"Wichelhaus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nils","family":"Wetzstein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"the NTMscope-Eco study group","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Theresa","family":"Alisch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tobias","family":"Appel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tobias","family":"Burbach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerrit","family":"Burger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela","family":"Cirillo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie","family":"Faber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara Garcia","family":"Torres","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arash","family":"Ghodousi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katharina","family":"Giesbrecht","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia","family":"Hafner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Doris","family":"Heidmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ludwig","family":"Hofbauer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisabeth","family":"Holt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raja","family":"Idris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Kuhns","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lena","family":"Iliewski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johanna","family":"Kessel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Kraiczy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastian","family":"Maffiold","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lina","family":"Meyer-Heinemann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sophie","family":"Mielke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9","family":"Mohr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martyna","family":"Olesiuk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Flavia","family":"Reyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Riedel-Christ","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph","family":"Stephan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carsten","family":"Szagunn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria J. G. T.","family":"Vehreschild","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tobias","family":"Weirauch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia","family":"W\u00fcrstle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ann-Sophie","family":"Zielbauer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,12,7]]},"reference":[{"key":"4563_CR1","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1164\/rccm.200604-571ST","volume":"175","author":"DE Griffith","year":"2007","unstructured":"Griffith DE, Aksamit T, Brown-Elliott BA, Catanzaro A, Daley C, Gordin F, et al. An official ATS\/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am J Respir Crit Care Med. 2007;175:367\u2013416. https:\/\/doi.org\/10.1164\/rccm.200604-571ST.","journal-title":"Am J Respir Crit Care Med"},{"key":"4563_CR2","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1016\/S0025-7125(16)34193-1","volume":"43","author":"EH Runyon","year":"1959","unstructured":"Runyon EH. Anonymous mycobacteria in pulmonary disease. Med Clin North Am. 1959;43:273\u201390. https:\/\/doi.org\/10.1016\/S0025-7125(16)34193-1.","journal-title":"Med Clin North Am"},{"key":"4563_CR3","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.00535-2020","author":"CL Daley","year":"2020","unstructured":"Daley CL, Iaccarino JM, Lange C, Cambau E, Wallace RJ, Andrejak C, et al. Treatment of nontuberculous mycobacterial pulmonary disease: an official ATS\/ERS\/ESCMID\/IDSA clinical practice guideline. Eur Respir J. 2020. https:\/\/doi.org\/10.1183\/13993003.00535-2020.","journal-title":"Eur Respir J"},{"key":"4563_CR4","doi-asserted-by":"publisher","unstructured":"Marras TK, Mirsaeidi M, Vinnard C, Chan ED, Eagle G, Zhang R, et al. Guidelines-based treatment associated with improved economic outcomes in nontuberculous mycobacterial lung disease. J Med Econ. 2019:1\u20131. https:\/\/doi.org\/10.1080\/13696998.2019.1620243.","DOI":"10.1080\/13696998.2019.1620243"},{"key":"4563_CR5","doi-asserted-by":"publisher","first-page":"1900250","DOI":"10.1183\/13993003.00250-2019","volume":"54","author":"S Cowman","year":"2019","unstructured":"Cowman S, van Ingen J, Griffith DE, Loebinger MR. Non-tuberculous mycobacterial pulmonary disease. Eur Respir J. 2019;54:1900250. https:\/\/doi.org\/10.1183\/13993003.00250-2019.","journal-title":"Eur Respir J"},{"key":"4563_CR6","doi-asserted-by":"publisher","first-page":"6696","DOI":"10.1038\/s41598-017-06931-4","volume":"7","author":"TS Hermansen","year":"2017","unstructured":"Hermansen TS, Ravn P, Svensson E, Lillebaek T. Nontuberculous mycobacteria in Denmark, incidence and clinical importance during the last quarter-century. Sci Rep. 2017;7:6696. https:\/\/doi.org\/10.1038\/s41598-017-06931-4.","journal-title":"Sci Rep"},{"key":"4563_CR7","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2022.10.013","author":"VN Dahl","year":"2022","unstructured":"Dahl VN, M\u00f8lhave M, Fl\u00f8e A, van Ingen J, Sch\u00f6n T, Lillebaek T, et al. Global trends of pulmonary infections with nontuberculous mycobacteria: a systematic review. Int J Infect Dis. 2022. https:\/\/doi.org\/10.1016\/j.ijid.2022.10.013.","journal-title":"Int J Infect Dis"},{"key":"4563_CR8","doi-asserted-by":"publisher","DOI":"10.3201\/EID2206.160045","volume":"22","author":"R Sommerstein","year":"2016","unstructured":"Sommerstein R, R\u00fcegg C, Kohler P, Bloemberg G, Kuster SP, Sax H. Transmission of Mycobacterium chimaera from heater-cooler units during cardiac surgery despite an ultraclean air ventilation system. Emerg Infect Dis. 2016;22:1008. https:\/\/doi.org\/10.3201\/EID2206.160045.","journal-title":"Emerg Infect Dis"},{"key":"4563_CR9","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1016\/j.femsec.2004.04.016","volume":"49","author":"MF Thorel","year":"2004","unstructured":"Thorel MF, Falkinham JO, Moreau RG. Environmental mycobacteria from alpine and subalpine habitats. FEMS Microbiol Ecol. 2004;49:343\u20137. https:\/\/doi.org\/10.1016\/j.femsec.2004.04.016.","journal-title":"FEMS Microbiol Ecol"},{"key":"4563_CR10","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PNTD.0005068","author":"JR Honda","year":"2016","unstructured":"Honda JR, Hasan NA, Davidson RM, Williams MD, Epperson LE, Reynolds PR, et al. Environmental nontuberculous mycobacteria in the Hawaiian Islands. PLoS Negl Trop Dis. 2016. https:\/\/doi.org\/10.1371\/JOURNAL.PNTD.0005068.","journal-title":"PLoS Negl Trop Dis"},{"key":"4563_CR11","doi-asserted-by":"publisher","first-page":"1747","DOI":"10.1128\/JCM.00186-13","volume":"51","author":"RJ Wallace","year":"2013","unstructured":"Wallace RJ, Iakhiaeva E, Williams MD, Brown-Elliott BA, Vasireddy S, Vasireddy R, et al. Absence of Mycobacterium intracellulare and presence of Mycobacterium chimaera in household water and biofilm samples of patients in the United States with Mycobacterium avium complex respiratory disease. J Clin Microbiol. 2013;51:1747. https:\/\/doi.org\/10.1128\/JCM.00186-13.","journal-title":"J Clin Microbiol"},{"key":"4563_CR12","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1111\/lam.12243","volume":"59","author":"A Lahiri","year":"2014","unstructured":"Lahiri A, Kneisel J, Kloster I, Kamal E, Lewin A. Abundance of Mycobacterium avium ssp. hominissuis in soil and dust in Germany - implications for the infection route. Lett Appl Microbiol. 2014;59:65\u201370. https:\/\/doi.org\/10.1111\/lam.12243.","journal-title":"Lett Appl Microbiol"},{"key":"4563_CR13","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.02029","volume":"9","author":"J Honda","year":"2018","unstructured":"Honda J, Virdi R, Chan ED. Global environmental nontuberculous mycobacteria and their contemporaneous man-made and natural niches. Front Microbiol. 2018;9:2029. https:\/\/doi.org\/10.3389\/fmicb.2018.02029.","journal-title":"Front Microbiol"},{"key":"4563_CR14","doi-asserted-by":"publisher","first-page":"3006","DOI":"10.1128\/JCM.00899-13","volume":"51","author":"R Thomson","year":"2013","unstructured":"Thomson R, Tolson C, Carter R, Coulter C, Huygens F, Hargreaves M. Isolation of nontuberculous mycobacteria (NTM) from household water and shower aerosols in patients with pulmonary disease caused by NTM. J Clin Microbiol. 2013;51:3006\u201311. https:\/\/doi.org\/10.1128\/JCM.00899-13.","journal-title":"J Clin Microbiol"},{"key":"4563_CR15","doi-asserted-by":"publisher","first-page":"473","DOI":"10.3201\/eid2503.180336","volume":"25","author":"L Lande","year":"2019","unstructured":"Lande L, Alexander DC, Wallace RJ, Kwait R, Iakhiaeva E, Williams M, et al. Mycobacterium avium in community and household water, suburban Philadelphia, Pennsylvania, USA, 2010\u20132012. Emerg Infect Dis. 2019;25:473\u201381. https:\/\/doi.org\/10.3201\/eid2503.180336.","journal-title":"Emerg Infect Dis"},{"key":"4563_CR16","doi-asserted-by":"publisher","DOI":"10.1093\/LAMBIO\/OVAD090","author":"JJX Song","year":"2023","unstructured":"Song JJX, Oguma K. Mycobacterial contamination in tap and shower waters in Thailand. Lett Appl Microbiol. 2023. https:\/\/doi.org\/10.1093\/LAMBIO\/OVAD090.","journal-title":"Lett Appl Microbiol"},{"key":"4563_CR17","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/S0163-4453(95)91333-5","volume":"31","author":"M Peters","year":"1995","unstructured":"Peters M, M\u00fcller C, R\u00fcsch-Gerdes S, Seidel C, G\u00f6bel U, Pohle HD, et al. Isolation of atypical mycobacteria from tap water in hospitals and homes: is this a possible source of disseminated MAC infection in AIDS patients? J Infect. 1995;31:39\u201344. https:\/\/doi.org\/10.1016\/S0163-4453(95)91333-5.","journal-title":"J Infect"},{"key":"4563_CR18","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2023.03.005","author":"N Wetzstein","year":"2023","unstructured":"Wetzstein N, AKohl T, Diricks M, Mas-Peiro S, Holubec T, Kessel J, et al. Clinical characteristics and outcome of Mycobacterium chimaera infections after cardiac surgery: systematic review and meta-analysis of 180 heater-cooler unit associated cases. Clin Microbiol Infect. 2023. https:\/\/doi.org\/10.1016\/j.cmi.2023.03.005.","journal-title":"Clin Microbiol Infect"},{"key":"4563_CR19","doi-asserted-by":"publisher","first-page":"1033","DOI":"10.1016\/S1473-3099(17)30324-9","volume":"17","author":"J van Ingen","year":"2017","unstructured":"van Ingen J, Kohl TA, Kranzer K, Hasse B, Keller PM, Katarzyna Szafra\u0144ska A, et al. Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study. Lancet Infect Dis. 2017;17:1033\u201341. https:\/\/doi.org\/10.1016\/S1473-3099(17)30324-9.","journal-title":"Lancet Infect Dis"},{"key":"4563_CR20","doi-asserted-by":"publisher","first-page":"2201237","DOI":"10.1183\/13993003.01237-2022","volume":"61","author":"AJ van Tonder","year":"2022","unstructured":"van Tonder AJ, Ellis HC, Churchward CP, Kumar K, Ramadan N, Benson S, et al. Mycobacterium avium complex (MAC) genomics and transmission in a London hospital. Eur Respir J. 2022;61:2201237. https:\/\/doi.org\/10.1183\/13993003.01237-2022.","journal-title":"Eur Respir J"},{"key":"4563_CR21","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1111\/bjd.15481","volume":"177","author":"C Painsi","year":"2017","unstructured":"Painsi C, Lange-Asschenfeldt B. Image gallery: pink papules within a tattoo linked to Mycobacterium chelonae infection. Br J Dermatol. 2017;177:e1\u2013e1. https:\/\/doi.org\/10.1111\/bjd.15481.","journal-title":"Br J Dermatol"},{"key":"4563_CR22","doi-asserted-by":"publisher","first-page":"1644","DOI":"10.1097\/PRS.0000000000005014","volume":"142","author":"P Padilla","year":"2018","unstructured":"Padilla P, Ly P, Dillard R, Boukovalas S, Zapata-Sirvent R, Phillips LG. Medical tourism and postoperative infections: a systematic literature review of causative organisms and empiric treatment. Plast Reconstr Surg. 2018;142:1644\u201351. https:\/\/doi.org\/10.1097\/PRS.0000000000005014.","journal-title":"Plast Reconstr Surg"},{"key":"4563_CR23","doi-asserted-by":"publisher","first-page":"100934","DOI":"10.1016\/j.lanmic.2024.06.001","volume":"0","author":"J Kikhney","year":"2024","unstructured":"Kikhney J, Friesen I, Wiesener S, Kursawe L, Loddenkemper C, Z\u00fcndorf J, et al. Endocarditis associated with contamination of cardiovascular bioprostheses with Mycobacterium chelonae: a collaborative microbiological study. Lancet Microbe. 2024;0:100934. https:\/\/doi.org\/10.1016\/j.lanmic.2024.06.001.","journal-title":"Lancet Microbe"},{"key":"4563_CR24","doi-asserted-by":"publisher","unstructured":"Wetzstein N, Diricks M, Kohl TA, Wichelhaus TA, Andres S, Paulowski L, et al. Molecular epidemiology of mycobacterium abscessus isolates recovered from german cystic fibrosis patients. Microbiol Spectr. 2022:e0171422. https:\/\/doi.org\/10.1128\/SPECTRUM.01714-22.","DOI":"10.1128\/SPECTRUM.01714-22"},{"key":"4563_CR25","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-022-32122-5","volume":"13","author":"M Diricks","year":"2022","unstructured":"Diricks M, Merker M, Wetzstein N, Kohl TA, Niemann S, Maurer FP. Delineating Mycobacterium abscessus population structure and transmission employing high-resolution core genome multilocus sequence typing. Nat Commun. 2022;13:1\u201310. https:\/\/doi.org\/10.1038\/s41467-022-32122-5.","journal-title":"Nat Commun"},{"key":"4563_CR26","doi-asserted-by":"publisher","DOI":"10.1126\/science.abb8699","author":"JM Bryant","year":"2021","unstructured":"Bryant JM, Brown KP, Burbaud S, Everall I, Belardinelli JM, Rodriguez-Rincon D, et al. Stepwise pathogenic evolution of Mycobacterium abscessus. Science. 2021. https:\/\/doi.org\/10.1126\/science.abb8699.","journal-title":"Science"},{"key":"4563_CR27","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.202409-1824OC","author":"RM Thomson","year":"2025","unstructured":"Thomson RM, Wheeler N, Stockwell RE, Bryant J, Taylor SL, Leong LEX, et al. Infection by clonally related Mycobacterium abscessus isolates: the role of drinking water. Am J Respir Crit Care Med. 2025. https:\/\/doi.org\/10.1164\/rccm.202409-1824OC.","journal-title":"Am J Respir Crit Care Med"},{"key":"4563_CR28","unstructured":"European Centre for Disease Prevention and Control. EU protocol for case detection, laboratory diagnosis and environmental testing of Mycobacterium chimaera infections potentially associated with heater-cooler units: case definition and environmental testing methodology. Stockholm: ECDC; 2015.\u00a0https:\/\/www.ecdc.europa.eu\/en\/publications-data\/eu-protocol-case-detection-laboratory-diagnosis-and-environmental-testing."},{"key":"4563_CR29","unstructured":"Richter E, Beer J, Diel R, et al. Qualit\u00e4tsstandards in der mikrobiologisch-infektiologischen diagnostik: MIQ--5 tuberkulose mybakteriose. Elsevier, Urban und Fischer, M\u00fcnchen; 2010. ISBN-13: 978-3437415319"},{"key":"4563_CR30","unstructured":"Woods GL, Wengenack NL, Grace Lin D, Barbara Brown-Elliott MA, Daniela Maria Cirillo M, Conville PS, et al. M62: performance standards for susceptibility testing of mycobacteria, nocardia spp., and other aerobic actinomycetes. 2018. Available: www.clsi.org."},{"key":"4563_CR31","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1186\/1756-0500-6-561","volume":"6","author":"IN de Almeida","year":"2013","unstructured":"de Almeida IN, Carvalho WDS, Rossetti ML, Costa ERD, de Miranda SS. Evaluation of six different DNA extraction methods for detection of Mycobacterium tuberculosis by means of PCR-IS6110: preliminary study. BMC Res Notes. 2013;6:561. https:\/\/doi.org\/10.1186\/1756-0500-6-561.","journal-title":"BMC Res Notes"},{"key":"4563_CR32","doi-asserted-by":"publisher","first-page":"e0128036","DOI":"10.1371\/journal.pone.0128036","volume":"10","author":"M Baym","year":"2015","unstructured":"Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM, Kishony R. Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS One. 2015;10:e0128036. https:\/\/doi.org\/10.1371\/journal.pone.0128036.","journal-title":"PLoS One"},{"key":"4563_CR33","unstructured":"NTMtools\/scripts\/NTMseq at main \u00b7 ngs-fzb\/NTMtools. Available: https:\/\/github.com\/ngs-fzb\/NTMtools\/tree\/main\/scripts\/NTMseq. Cited 28 May 2024."},{"key":"4563_CR34","unstructured":"GitHub - s-andrews\/FastQC: a quality control analysis tool for high throughput sequencing data. Available: https:\/\/github.com\/s-andrews\/FastQC. Cited 11 Aug 2023."},{"key":"4563_CR35","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","volume":"32","author":"P Ewels","year":"2016","unstructured":"Ewels P, Magnusson M, Lundin S, K\u00e4ller M. Multiqc: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32:3047\u20138. https:\/\/doi.org\/10.1093\/bioinformatics\/btw354.","journal-title":"Bioinformatics"},{"key":"4563_CR36","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","volume":"20","author":"DE Wood","year":"2019","unstructured":"Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019;20:257. https:\/\/doi.org\/10.1186\/s13059-019-1891-0.","journal-title":"Genome Biol"},{"key":"4563_CR37","unstructured":"GitHub - jodyphelan\/NTM-profiler: profiling NTM WGS data. Available: https:\/\/github.com\/jodyphelan\/NTM-Profiler. Cited 11 Aug 2023."},{"key":"4563_CR38","unstructured":"GitHub - tseemann\/shovill: assemble bacterial isolate genomes from Illumina paired-end reads. Available: https:\/\/github.com\/tseemann\/shovill. Cited 11 Aug 2023."},{"key":"4563_CR39","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","volume":"19","author":"A Bankevich","year":"2012","unstructured":"Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455\u201377. https:\/\/doi.org\/10.1089\/cmb.2012.0021.","journal-title":"J Comput Biol"},{"key":"4563_CR40","doi-asserted-by":"publisher","first-page":"12728","DOI":"10.1038\/s41598-021-91456-0","volume":"11","author":"M Feldgarden","year":"2021","unstructured":"Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH, et al. AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep. 2021;11:12728. https:\/\/doi.org\/10.1038\/s41598-021-91456-0.","journal-title":"Sci Rep"},{"key":"4563_CR41","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s13073-014-0090-6","volume":"6","author":"M Inouye","year":"2014","unstructured":"Inouye M, Dashnow H, Raven LA, Schultz MB, Pope BJ, Tomita T, et al. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 2014;6:90. https:\/\/doi.org\/10.1186\/s13073-014-0090-6.","journal-title":"Genome Med"},{"key":"4563_CR42","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-60","author":"JP Meier-Kolthoff","year":"2013","unstructured":"Meier-Kolthoff JP, Auch AF, Klenk HP, G\u00f6ker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics. 2013. https:\/\/doi.org\/10.1186\/1471-2105-14-60.","journal-title":"BMC Bioinformatics"},{"key":"4563_CR43","doi-asserted-by":"publisher","first-page":"2798","DOI":"10.1093\/molbev\/msv150","volume":"32","author":"V Lefort","year":"2015","unstructured":"Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program: table 1. Mol Biol Evol. 2015;32:2798\u2013800. https:\/\/doi.org\/10.1093\/molbev\/msv150.","journal-title":"Mol Biol Evol"},{"key":"4563_CR44","doi-asserted-by":"publisher","first-page":"D801","DOI":"10.1093\/nar\/gkab902","volume":"50","author":"JP Meier-Kolthoff","year":"2022","unstructured":"Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, G\u00f6ker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res. 2022;50:D801-7. https:\/\/doi.org\/10.1093\/nar\/gkab902.","journal-title":"Nucleic Acids Res"},{"key":"4563_CR45","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","volume":"49","author":"I Letunic","year":"2021","unstructured":"Letunic I, Bork P. Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49:W293-6. https:\/\/doi.org\/10.1093\/nar\/gkab301.","journal-title":"Nucleic Acids Res"},{"key":"4563_CR46","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1111\/2041-210X.12628","volume":"8","author":"G Yu","year":"2017","unstructured":"Yu G, Smith D, Zhu H, Guan Y, Lam TTY. Ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017;8:28\u201336. https:\/\/doi.org\/10.1111\/2041-210X.12628.","journal-title":"Methods Ecol Evol"},{"key":"4563_CR47","unstructured":"R Core Team. R: a language and environment for statistical computing. Vienna; 2018. Available: https:\/\/www.r-project.org\/."},{"key":"4563_CR48","doi-asserted-by":"crossref","unstructured":"Wickham H. ggplot2: elegant graphics for data analysis. Springer-Verlag New York; 2016. Available: https:\/\/ggplot2.tidyverse.org.","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"4563_CR49","doi-asserted-by":"crossref","unstructured":"Kahle D, Wickham H. ggmap: spatial visualization with ggplot2. R J. 2013;5:144\u2013161. Available: https:\/\/journal.r-project.org\/archive\/2013-1\/kahle-wickham.pdf.","DOI":"10.32614\/RJ-2013-014"},{"key":"4563_CR50","doi-asserted-by":"publisher","first-page":"419","DOI":"10.3201\/eid1703.101510","volume":"17","author":"JO Falkinham III","year":"2011","unstructured":"Falkinham JO III. Nontuberculous mycobacteria from household plumbing of patients with nontuberculous mycobacteria disease. Emerg Infect Dis. 2011;17:419\u201324. https:\/\/doi.org\/10.3201\/eid1703.101510.","journal-title":"Emerg Infect Dis"},{"key":"4563_CR51","doi-asserted-by":"publisher","first-page":"e110554","DOI":"10.1371\/journal.pone.0110554","volume":"9","author":"T Ichijo","year":"2014","unstructured":"Ichijo T, Izumi Y, Nakamoto S, Yamaguchi N, Nasu M. Distribution and respiratory activity of mycobacteria in household water system of healthy volunteers in Japan. PLoS ONE. 2014;9:e110554. https:\/\/doi.org\/10.1371\/journal.pone.0110554.","journal-title":"PLoS ONE"},{"key":"4563_CR52","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1513\/AnnalsATS.201812-915OC","volume":"17","author":"CL Tzou","year":"2020","unstructured":"Tzou CL, Dirac MA, Becker AL, Beck NK, Weigel KM, Meschke JS, et al. Association between mycobacterium avium complex pulmonary disease and mycobacteria in home water and soil a case-control study. Ann Am Thorac Soc. 2020;17:57\u201362. https:\/\/doi.org\/10.1513\/AnnalsATS.201812-915OC.","journal-title":"Ann Am Thorac Soc"},{"key":"4563_CR53","doi-asserted-by":"publisher","first-page":"6017","DOI":"10.1128\/AEM.00843-10","volume":"76","author":"J van Ingen","year":"2010","unstructured":"van Ingen J, Blaak H, de Beer J, de Roda Husman AM, van Soolingen D. Rapidly growing nontuberculous mycobacteria cultured from home tap and shower water. Appl Environ Microbiol. 2010;76:6017\u20139. https:\/\/doi.org\/10.1128\/AEM.00843-10.","journal-title":"Appl Environ Microbiol"},{"key":"4563_CR54","doi-asserted-by":"publisher","first-page":"276","DOI":"10.7883\/yoken.67.276","volume":"67","author":"M Kobayashi","year":"2014","unstructured":"Kobayashi M, Oana K, Kawakami Y. Bath water contamination with Legionella and nontuberculous mycobacteria in 24-hour home baths, hot springs, and public bathhouses of Nagano prefecture, Japan. Jpn J Infect Dis. 2014;67:276\u201381. https:\/\/doi.org\/10.7883\/yoken.67.276.","journal-title":"Jpn J Infect Dis"},{"key":"4563_CR55","first-page":"79","volume":"30","author":"X Shi","year":"2024","unstructured":"Shi X, Wang J, Huang X, Sha W, Qin L. Isolation of non-tuberculous mycobacteria (NTM) from household water of patients with NTM pulmonary disease. Altern Ther Health Med. 2024;30:79\u201383.","journal-title":"Altern Ther Health Med"},{"key":"4563_CR56","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-017-2939-y","author":"N Monde","year":"2018","unstructured":"Monde N, Munyeme M, Muwonge A, Muma JB, Malama S. Characterization of non-tuberculous mycobacterium from humans and water in an agropastoral area in Zambia. BMC Infect Dis. 2018. https:\/\/doi.org\/10.1186\/s12879-017-2939-y.","journal-title":"BMC Infect Dis"},{"key":"4563_CR57","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-022-02674-z","author":"S Moghaddam","year":"2022","unstructured":"Moghaddam S, Nojoomi F, Dabbagh Moghaddam A, Mohammadimehr M, Sakhaee F, Masoumi M, et al. Isolation of\u00a0nontuberculous mycobacteria species from different water sources: a study of six hospitals in Tehran, Iran. BMC Microbiol. 2022. https:\/\/doi.org\/10.1186\/s12866-022-02674-z.","journal-title":"BMC Microbiol"},{"key":"4563_CR58","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1016\/j.ijid.2020.02.059","volume":"93","author":"N Wetzstein","year":"2020","unstructured":"Wetzstein N, Kohl TA, Andres S, Schultze TG, Geil A, Kim E, et al. Comparative analysis of phenotypic and genotypic antibiotic susceptibility patterns in Mycobacterium avium complex. Int J Infect Dis. 2020;93:320\u20138. https:\/\/doi.org\/10.1016\/j.ijid.2020.02.059.","journal-title":"Int J Infect Dis"},{"key":"4563_CR59","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1186\/s13073-024-01359-8","volume":"16","author":"N Wetzstein","year":"2024","unstructured":"Wetzstein N, Diricks M, Anton TB, Andres S, Kuhns M, Kohl TA, et al. Clinical and genomic features of Mycobacterium avium complex: a multi-national European study. Genome Med. 2024;16:86. https:\/\/doi.org\/10.1186\/s13073-024-01359-8.","journal-title":"Genome Med"},{"key":"4563_CR60","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S12879-019-4683-Y","volume":"19","author":"Y VandeWeygaerde","year":"2019","unstructured":"VandeWeygaerde Y, Cardinaels N, Bomans P, Chin T, Boelens J, Andr\u00e9 E, et al. Clinical relevance of pulmonary non-tuberculous mycobacterial isolates in three reference centres in Belgium: a multicentre retrospective analysis. BMC Infect Dis. 2019;19:1\u201310. https:\/\/doi.org\/10.1186\/S12879-019-4683-Y.","journal-title":"BMC Infect Dis"},{"key":"4563_CR61","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/S1473-3099(12)70277-3","volume":"13","author":"TM Walker","year":"2013","unstructured":"Walker TM, Ip CLC, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis. 2013;13:137\u201346. https:\/\/doi.org\/10.1016\/S1473-3099(12)70277-3.","journal-title":"Lancet Infect Dis"},{"key":"4563_CR62","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.05166","author":"PEM Fine","year":"2015","unstructured":"Fine PEM, Crampin AC, Houben RMGJ, Mzembe T, Mallard K, Coll F, et al. Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. Elife. 2015. https:\/\/doi.org\/10.7554\/eLife.05166.","journal-title":"Elife"}],"container-title":["BMC Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-025-04563-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12866-025-04563-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-025-04563-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,13]],"date-time":"2025-12-13T10:00:21Z","timestamp":1765620021000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12866-025-04563-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,7]]},"references-count":62,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["4563"],"URL":"https:\/\/doi.org\/10.1186\/s12866-025-04563-7","relation":{},"ISSN":["1471-2180"],"issn-type":[{"value":"1471-2180","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,7]]},"assertion":[{"value":"7 July 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 November 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 December 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Permissions were obtained to collect water samples both in private residences and in the hospital setting. All participants provided informed consent to contribute water samples from their households to the study. Genomic investigation of environmental and clinical NTM isolates was approved by the ethics committees of the University Hospital Frankfurt (ethical vote 2022\u2013162) and University of L\u00fcbeck (ethical vote 2024\u2013608). Informed patient consent was not required as clinical NTM strains were isolated during routine clinical diagnostics or were already publicly available. Informed consent was therefore waived by the Institutional Review board of the University of L\u00fcbeck, ethical vote 2024\u2013608.\u00a0Data processing complied with the European General Data Protection Regulation (EU) 2016\/679 and \u00a727 of the Bundesdatenschutzgesetz (BDSG). The study has been conducted in accordance with the principles of the Helsinki Declaration.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Clinical trial number"}},{"value":"Not applicable.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"Margo Diricks, Denia Frank, Inna Friesen, Stefan Niemann and Nils Wetzstein have nothing to disclose. Thomas A. Wichelhaus reports research grants from BMBF, JPIAMR, Deutsche Krebshilfe, MSD as well as speaker fees and consulting honoraria from Landes\u00e4rztekammer Hessen, Insmed, Osartis, all outside the submitted work.","order":5,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"792"}}