{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T08:06:39Z","timestamp":1775721999056,"version":"3.50.1"},"reference-count":137,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2020,10,11]],"date-time":"2020-10-11T00:00:00Z","timestamp":1602374400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JoF"],"abstract":"<jats:p>Breakthrough invasive fungal infections (bIFI) cause significant morbidity and mortality. Their diagnosis can be challenging due to reduced sensitivity to conventional culture techniques, serologic tests, and PCR-based assays in patients undergoing antifungal therapy, and their diagnosis can be delayed contributing to poor patient outcomes. In this review, we provide consensus recommendations on behalf of the European Confederation for Medical Mycology (ECMM) for the diagnosis of bIFI caused by invasive yeasts, molds, and endemic mycoses, to guide diagnostic efforts in patients receiving antifungals and support the design of future clinical trials in the field of clinical mycology. The cornerstone of lab-based diagnosis of breakthrough infections for yeast and endemic mycoses remain conventional culture, to accurately identify the causative pathogen and allow for antifungal susceptibility testing. The impact of non-culture-based methods are not well-studied for the definite diagnosis of breakthrough invasive yeast infections. Non-culture-based methods have an important role for the diagnosis of breakthrough invasive mold infections, in particular invasive aspergillosis, and a combination of testing involving conventional culture, antigen-based assays, and PCR-based assays should be considered. Multiple diagnostic modalities, including histopathology, culture, antibody, and\/or antigen tests and occasionally PCR-based assays may be required to diagnose breakthrough endemic mycoses. A need exists for diagnostic tests that are effective, simple, cheap, and rapid to enable the diagnosis of bIFI in patients taking antifungals.<\/jats:p>","DOI":"10.3390\/jof6040216","type":"journal-article","created":{"date-parts":[[2020,10,12]],"date-time":"2020-10-12T10:18:00Z","timestamp":1602497880000},"page":"216","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Diagnosis of Breakthrough Fungal Infections in the Clinical Mycology Laboratory: An ECMM Consensus Statement"],"prefix":"10.3390","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6632-9587","authenticated-orcid":false,"given":"Jeffrey D.","family":"Jenks","sequence":"first","affiliation":[{"name":"Division of General Internal Medicine, Department of Medicine, University of California San Diego, San Diego, CA 92103, USA"},{"name":"Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, San Diego, CA 92103, USA"},{"name":"Clinical and Translational Fungal-Working Group, University of California San Diego, La Jolla, CA 92093, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4974-5607","authenticated-orcid":false,"given":"Jean-Pierre","family":"Gangneux","sequence":"additional","affiliation":[{"name":"Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Sant\u00e9, Environnement et Travail)\u2014UMR_S 1085, F-35000 Rennes, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7522-0281","authenticated-orcid":false,"given":"Ilan S.","family":"Schwartz","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8651-4405","authenticated-orcid":false,"given":"Ana","family":"Alastruey-Izquierdo","sequence":"additional","affiliation":[{"name":"Mycology Reference Laboratory, National Centre for Microbiology. Instituto de Salud Carlos III. Majadahonda, 28222 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8668-1350","authenticated-orcid":false,"given":"Katrien","family":"Lagrou","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium"},{"name":"National Reference Centre for Mycosis, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"George R.","family":"Thompson III","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Department of Internal Medicine and Department of Medical Microbiology and Immunology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2946-7785","authenticated-orcid":false,"given":"Cornelia","family":"Lass-Fl\u00f6rl","sequence":"additional","affiliation":[{"name":"Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1653-2824","authenticated-orcid":false,"given":"Martin","family":"Hoenigl","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, San Diego, CA 92103, USA"},{"name":"Clinical and Translational Fungal-Working Group, University of California San Diego, La Jolla, CA 92093, USA"},{"name":"Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"European Confederation of Medical Mycology (ECMM) Council","family":"Investigators","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,10,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1111\/myc.13148","article-title":"Breakthrough Invasive Fungal Infections: Who is at risk?","volume":"63","author":"Jenks","year":"2020","journal-title":"Mycoses"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1016\/j.jmii.2013.03.002","article-title":"Breakthrough disseminated cryptococcosis during micafungin therapy","volume":"48","author":"Lee","year":"2015","journal-title":"J. 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