{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T19:38:33Z","timestamp":1790797113760,"version":"4.1.0"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,12,23]],"date-time":"2023-12-23T00:00:00Z","timestamp":1703289600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,9]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Aspergillosis of the newborn remains a rare but severe disease. We report four cases of primary cutaneous Aspergillus flavus infections in premature newborns linked to incubators contamination by putative clonal strains. Our objective was to evaluate the ability of matrix-assisted laser desorption\/ionisation time of flight (MALDI\u2013TOF) coupled to convolutional neural network (CNN) for clone recognition in a context where only a very small number of strains are available for machine learning. Clinical and environmental A. flavus isolates (n\u00a0=\u00a064) were studied, 15 were epidemiologically related to the four cases. All strains were typed using microsatellite length polymorphism. We found a common genotype for 9\/15 related strains. The isolates of this common genotype were selected to obtain a training dataset (6 clonal isolates\/25 non-clonal) and a test dataset (3 clonal isolates\/31 non-clonal), and spectra were analysed with a simple CNN model. On the test dataset using CNN model, all 31 non-clonal isolates were correctly classified, 2\/3 clonal isolates were unambiguously correctly classified, whereas the third strain was undetermined (i.e., the CNN model was unable to discriminate between GT8 and non-GT8). Clonal strains of A. flavus have persisted in the neonatal intensive care unit for several years. Indeed, two strains of A. flavus isolated from incubators in September 2007 are identical to the strain responsible for the second case that occurred 3 years later.<\/jats:p><jats:p>MALDI\u2013TOF is a promising tool for detecting clonal isolates of A. flavus using CNN even with a limited training set for limited cost and handling time.<\/jats:p>","DOI":"10.1093\/mmy\/myad136","type":"journal-article","created":{"date-parts":[[2023,12,24]],"date-time":"2023-12-24T03:18:50Z","timestamp":1703387930000},"source":"Crossref","is-referenced-by-count":8,"title":["Nosocomial transmission of<i>Aspergillus flavus<\/i>in a neonatal intensive care unit: Long-term persistence in environment and interest of MALDI\u2013ToF mass-spectrometry coupled with convolutional neural network for rapid clone recognition"],"prefix":"10.1093","volume":"62","author":[{"given":"Noshine","family":"Mohammad","sequence":"first","affiliation":[{"name":"Sorbonne Universit\u00e9, INSERM, Institut Pierre-Louis d'Epid\u00e9miologie et de Sant\u00e9 Publique, AP-HP , Paris , France"},{"name":"Groupe Hospitalier Piti\u00e9-Salp\u00eatri\u00e8re, Service de Parasitologie-Mycologie , Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1341-9965","authenticated-orcid":false,"given":"Antoine","family":"Huguenin","sequence":"additional","affiliation":[{"name":"Laboratoire de Parasitologie-Mycologie, P\u00f4le de Biologie et de Pathologie, CHU de Reims , Reims , France"},{"name":"Universit\u00e9 de Reims Champagne Ardenne , ESCAPE EA7510, Reims , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annick","family":"Lefebvre","sequence":"additional","affiliation":[{"name":"Equipe Op\u00e9rationnelle d'Hygi\u00e8ne , CHU de Reims , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Menvielle","sequence":"additional","affiliation":[{"name":"CHU de Reims, H\u00f4pital Am\u00e9ricain, Service de r\u00e9animation n\u00e9onatale , 45 rue Cognaq Jay, Reims , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominique","family":"Toubas","sequence":"additional","affiliation":[{"name":"Laboratoire de Parasitologie-Mycologie, P\u00f4le de Biologie et de Pathologie, CHU de Reims, Reims , France"},{"name":"Universit\u00e9 de Reims Champagne Ardenne , ESCAPE EA7510, Reims , France"},{"name":"Equipe Op\u00e9rationnelle d'Hygi\u00e8ne , CHU de Reims , France"},{"name":"CHU de Reims, H\u00f4pital Am\u00e9ricain, Service de r\u00e9animation n\u00e9onatale , 45 rue Cognaq Jay, Reims , France"},{"name":"BioSpecT (Translational BioSpectroscopy) EA 7506, SFR Sant\u00e9, Universit\u00e9 de Reims Champagne-Ardenne , Reims , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"St\u00e9phane","family":"Ranque","sequence":"additional","affiliation":[{"name":"IHU-M\u00e9diterran\u00e9e Infection , Marseille , France"},{"name":"Aix-Marseille Universit\u00e9, AP-HM, IRD, SSA, VITROME , Marseille , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabelle","family":"Villena","sequence":"additional","affiliation":[{"name":"Laboratoire de Parasitologie-Mycologie, P\u00f4le de Biologie et de Pathologie, CHU de Reims, Reims , France"},{"name":"Universit\u00e9 de Reims Champagne Ardenne , ESCAPE EA7510, Reims , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xavier","family":"Tannier","sequence":"additional","affiliation":[{"name":"Sorbonne Universit\u00e9, INSERM, Universit\u00e9 Sorbonne Paris Nord, Laboratoire d'Informatique M\u00e9dicale et d'Ing\u00e9nierie des connaissances en e-Sant\u00e9, LIMICS , Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9589-4603","authenticated-orcid":false,"given":"Anne-C\u00e9cile","family":"Normand","sequence":"additional","affiliation":[{"name":"Groupe Hospitalier 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