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Rapport D'activités Type TABLE DES MATIERES 1 RESUME ANALYTIQUE ....................................................................................................................................... 1 2 SUMMARY .............................................................................................................................................................. 2 3 MISSIONS ET ORGANISATION DU CNR ......................................................................................................... 3 4 ACTIVITES D’EXPERTISE .................................................................................................................................. 3 4.1 ÉVOLUTIONS DES TECHNIQUES ............................................................................................................................ 3 4.2 TRAVAUX D’EVALUATION DES TECHNIQUES, REACTIFS ET TROUSSES ................................................................. 4 4.3 TECHNIQUES TRANSFEREES VERS D'AUTRES LABORATOIRES ............................................................................... 4 4.4 COLLECTIONS DE MATERIEL BIOLOGIQUE ........................................................................................................... 4 4.5 ACTIVITES D’EXPERTISE ...................................................................................................................................... 5 4.5.1 Expertise 2019 sur les levures .................................................................................................................... 6 4.5.2 Expertise 2019 sur les champignons filamenteux ..................................................................................... 10 4.5.3 Expertise 2019 sur la sensibilité aux antifongiques ................................................................................. 14 4.5.4 Expertise 2019 sur les mycoses endémiques ............................................................................................. 16 4.5.5 Expertise 2019 en anatomopathologie ..................................................................................................... 16 4.5.6 Expertise 2019 pour les diagnostics moléculaires .................................................................................... 17 4.5.7 Activités de séquençage ............................................................................................................................ 18 5 ACTIVITES DE SURVEILLANCE ..................................................................................................................... 19 5.1 DESCRIPTION DU RESEAU DE PARTENAIRES ....................................................................................................... 19 5.2 SURVEILLANCE DE L’EVOLUTION ET DES CARACTERISTIQUES DES INFECTIONS ................................................. 21 5.2.1 Cryptococcoses ......................................................................................................................................... 22 5.2.2 Fongémies................................................................................................................................................. 23 5.2.3 Pneumocystoses ........................................................................................................................................ 24 5.2.4 Mucormycoses .......................................................................................................................................... 25 5.2.5 Aspergilloses ............................................................................................................................................. 26 5.2.6 Fusarioses ................................................................................................................................................ 28 5.3 SURVEILLANCE DE LA RESISTANCE DES AGENTS PATHOGENES AUX ANTI-INFECTIEUX ...................................... 28 5.3.1 Définitions utilisées pour exprimer la résistance ..................................................................................... 29 5.3.2 Résultats de la surveillance des résistances aux antifongiques pour les levures ...................................... 30 5.3.3 Résultats de la surveillance des résistances aux antifongiques pour les filamenteux ............................... 32 5.3.4 Analyse des tendances .............................................................................................................................. 36 5.4 INTERFACES AVEC LES RESEAUX DE SURVEILLANCE NATIONAUX OU INTERNATIONAUX ................................... 38 5.5 ENQUETES OU ETUDES PONCTUELLES CONCOURANT A LA SURVEILLANCE ........................................................ 38 5.5.1 Cas groupés d'infection à Saprochaete clavata ........................................................................................ 38 5.5.2 Colonisation à Candida auris ................................................................................................................... 39 5.5.3 Cas groupés de pneumocystose chez des patients transplantés de rein .................................................... 40 6 ALERTES ............................................................................................................................................................... 40 7 ACTIVITES DE RETRO-INFORMATION, DE FORMATION ET DE CONSEIL ...................................... 41 7.1 CONSEIL ET EXPERTISE AUX PROFESSIONNELS DE SANTE .................................................................................. 41 7.2 CONSEIL ET EXPERTISE AUX AUTORITES SANITAIRES ........................................................................................ 41 7.2.1 Au plan national ....................................................................................................................................... 41 7.2.2 Au plan international ................................................................................................................................ 42 7.3 ACTIVITE DE FORMATION .................................................................................................................................. 43 8 TRAVAUX DE RECHERCHE ET PUBLICATIONS ....................................................................................... 43 8.1 ACTIVITES DE RECHERCHE EN LIEN DIRECT AVEC LES MISSIONS ET ACTIVITES DU CNR ................................... 43 8.1.1 Diagnostic de la pneumocystose ............................................................................................................... 43 8.1.2 Travaux sur l'aspergillose invasive .......................................................................................................... 43 8.1.3 Travaux sur la cryptococcose ................................................................................................................... 44 8.2 PUBLICATIONS ET COMMUNICATIONS EN LIEN DIRECT AVEC LES MISSIONS/ACTIVITES DU CNR ....................... 44 8.2.1 Publications 2019 ..................................................................................................................................... 44 8.2.2 Publications 2020 ..................................................................................................................................... 47 8.2.3 Communications nationales...................................................................................................................... 49 8.2.4 Communications internationales .............................................................................................................. 49 8.2.5 Séminaires sur invitations ........................................................................................................................ 49 9 COOPERATION AVEC LES LABORATOIRES DE SANTE ANIMALE, D’HYGIENE ALIMENTAIRE, ENVIRONNEMENTAUX ........................................................................................................................................ 50 10 PROGRAMME D’ACTIVITE POUR LES ANNEES SUIVANTES .............................................................. 50 10.1 EXPERTISE MICROBIOLOGIQUE ........................................................................................................................ 50 10.1.1 Analyse de la cohérence des seuils de détection de la résistance aux échinocandines .......................... 50 10.1.2 Description des profils de sensibilité aux antifongiques des espèces rares ............................................ 50 10.1.3 Poursuite du développement des techniques d'identification et de typage ............................................. 50 10.1.4 Poursuite du développement de méthodes diagnostiques par qPCR pour le diagnostic des infections à champignons dimorphiques. .............................................................................................................................. 50 10.1.5 Harmonisation du diagnostic de la pneumocystose et des attitudes thérapeutiques .............................. 51 10.1.6 Analyse des génotypes circulants de Pneumocystis jirovecii chez les transplantés rénaux français...... 52 10.2 SURVEILLANCE MICROBIOLOGIQUE ET EPIDEMIOLOGIQUE .............................................................................. 52 10.2.1 Analyse des IFI diagnostiquées en France (2012-2018) ........................................................................ 52 10.2.2 Analyse des infections fongiques compliquant les infections COVID-19 sévères en réanimation ......... 52 10.2.3 Poursuite des études collaboratives
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