{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T00:01:16Z","timestamp":1783987276495,"version":"3.55.0"},"reference-count":17,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2021,12,29]],"date-time":"2021-12-29T00:00:00Z","timestamp":1640736000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>We present the case of a 72-year-old female patient with acute contained rupture of a biological composite graft, 21 months after replacement of the aortic valve and the ascending aorta due to an aortic dissection. Auramine-rhodamine staining of intraoperative biopsies showed acid-fast bacilli, but classical culture and molecular methods failed to identify any organism. Metagenomic analysis indicated infection with Mycobacterium\u00a0chelonae, which was confirmed by target-specific qPCR. The complexity of the sample required a customized bioinformatics pipeline, including cleaning steps to remove sequences of human, bovine ad pig origin. Our study underlines the importance of multiple testing to increase the likelihood of pathogen identification in highly complex samples.<\/jats:p>","DOI":"10.3390\/ijms23010381","type":"journal-article","created":{"date-parts":[[2021,12,29]],"date-time":"2021-12-29T23:31:35Z","timestamp":1640820695000},"page":"381","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Mycobacterium chelonae Infection Identified by Metagenomic Next-Generation Sequencing as the Probable Cause of Acute Contained Rupture of a Biological Composite Graft\u2014A Case Report"],"prefix":"10.3390","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4872-0376","authenticated-orcid":false,"given":"Andrea C.","family":"B\u00fcchler","sequence":"first","affiliation":[{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6839-2536","authenticated-orcid":false,"given":"Vladimir","family":"Lazarevic","sequence":"additional","affiliation":[{"name":"Genomic Research Laboratory, Geneva University Hospitals, University of Geneva, 1206 Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadia","family":"Ga\u00efa","sequence":"additional","affiliation":[{"name":"Genomic Research Laboratory, Geneva University Hospitals, University of Geneva, 1206 Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Myriam","family":"Girard","sequence":"additional","affiliation":[{"name":"Genomic Research Laboratory, Geneva University Hospitals, University of Geneva, 1206 Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Friedrich","family":"Eckstein","sequence":"additional","affiliation":[{"name":"Department of Cardiac Surgery, University Hospital Basel, 4031 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3564-8603","authenticated-orcid":false,"given":"Adrian","family":"Egli","sequence":"additional","affiliation":[{"name":"Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland"},{"name":"Applied Microbiology Research, University of Basel, 4031 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah Tschudin","family":"Sutter","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacques","family":"Schrenzel","sequence":"additional","affiliation":[{"name":"Genomic Research Laboratory, Geneva University Hospitals, University of Geneva, 1206 Geneva, Switzerland"},{"name":"Bacteriology Laboratory, Geneva University Hospitals, 1205 Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,12,29]]},"reference":[{"key":"ref_1","first-page":"93","article-title":"Mycobacterial endocarditis: A comprehensive review","volume":"30","author":"Yuan","year":"2015","journal-title":"Rev. Bras. Cir. Cardiovasc."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"67","DOI":"10.3389\/fmicb.2018.00067","article-title":"Phylogenomics and comparative genomic studies robustly support division of the genus Mycobacterium into an emended genus Mycobacterium and four novel genera","volume":"9","author":"Gupta","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1016\/j.jinf.2010.03.008","article-title":"Mycobacterium chelonae valve endocarditis resulting from contaminated biological prostheses","volume":"60","author":"Strabelli","year":"2010","journal-title":"J. Infect."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Hooda, A., Pati, P.K., John, B., George, P.V., and Michael, J.S. (2014). Disseminated Mycobacterium chelonae infection causing pacemaker lead endocarditis in an immunocompetent host. BMJ Case Rep., 2014.","DOI":"10.1136\/bcr-2014-206042"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1007\/s10156-012-0492-6","article-title":"Native-valve endocarditis caused by Mycobacterium chelonae, misidentified as polymicrobial gram-positive bacillus infection","volume":"19","author":"Takekoshi","year":"2013","journal-title":"J. Infect. Chemother."},{"key":"ref_6","first-page":"254","article-title":"Spontaneous endocarditis caused by rapidly growing non-tuberculous Mycobacterium chelonae in an immunocompetent patient with rheumatic heart disease","volume":"4","author":"Jagadeesan","year":"2013","journal-title":"J. Cardiovasc. Dis. Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1007\/s40265-021-01572-4","article-title":"The potential role of clinical metagenomics in infectious diseases: Therapeutic perspectives","volume":"81","author":"Salmona","year":"2021","journal-title":"Drugs"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"203","DOI":"10.3389\/fmed.2019.00203","article-title":"Next-generation sequencing for the diagnosis of challenging culture-negative endocarditis","volume":"6","author":"Kolb","year":"2019","journal-title":"Front. Med."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Ounit, R., Wanamaker, S., Close, T.J., and Lonardi, S. (2015). CLARK: Fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genom., 16.","DOI":"10.1186\/s12864-015-1419-2"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation","volume":"44","author":"Wright","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1613","DOI":"10.1099\/ijsem.0.001755","article-title":"Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies","volume":"67","author":"Yoon","year":"2017","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"V\u011btrovsk\u00fd, T., and Baldrian, P. (2013). The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0057923"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"954","DOI":"10.1101\/gr.245373.118","article-title":"Human contamination in bacterial genomes has created thousands of spurious proteins","volume":"29","author":"Breitwieser","year":"2019","journal-title":"Genome Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2745","DOI":"10.1093\/eurheartj\/ehv342","article-title":"Healthcare-associated prosthetic heart valve, aortic vascular graft, and disseminated Mycobacterium chimaera infections subsequent to open heart surgery","volume":"36","author":"Kohler","year":"2015","journal-title":"Eur. Heart J."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/1\/381\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T07:55:46Z","timestamp":1760169346000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/1\/381"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,12,29]]},"references-count":17,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,1]]}},"alternative-id":["ijms23010381"],"URL":"https:\/\/doi.org\/10.3390\/ijms23010381","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,12,29]]}}}