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1. Pneumocystis jirovecii Pneumonia in Patients with or without AIDS, France

Author: Antoine Roux, Emmanuel Canet, Sandrine Valade, Florence Gangneux-Robert, Samia Hamane, Ariane Lafabrie, Daniéle Maubon, Anne Debourgogne, Soléne Le Gal, Fréderic Dalle, Marion Leterrier, Dominique Toubas, Christelle Pomares, Anne Pauline Bellanger, Julie Bonhomme, Antoine Berry, Isabelle Durand-Joly, Denis Magne, Denis Pons, Christophe Hennequin, Eric Maury, Patricia Roux, and Élie Azoulay
Subjects: Immune suppression, HIV/AIDS, cancer, transplantation, mechanical ventilation, viruses, Medicine, Infectious and parasitic diseases, RC109-216
Abstract: Pneumocystis jirovecii pneumonia (PCP) in patients without AIDS is increasingly common. We conducted a prospective cohort study of consecutive patients with proven PCP; of 544 patients, 223 (41%) had AIDS (AIDS patients) and 321 (59%) had other immunosuppressive disorders (non-AIDS patients). Fewer AIDS than non-AIDS patients required intensive care or ventilation, and the rate of hospital deaths—17.4% overall—was significantly lower for AIDS versus non-AIDS patients (4% vs. 27%; p
Published: 2014
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2. Diversity of the bacterial and fungal microflora from the midgut and cuticle of phlebotomine sand flies collected in North-Western Iran.

Author: Mohammad Akhoundi, Rounak Bakhtiari, Thomas Guillard, Ahmad Baghaei, Reza Tolouei, Denis Sereno, Dominique Toubas, Jérôme Depaquit, and Mehdi Razzaghi Abyaneh
Subjects: Medicine, Science
Abstract: BackgroundPhlebotomine sand flies are the vectors of the leishmaniases, parasitic diseases caused by Leishmania spp. Little is known about the prevalence and diversity of sand fly microflora colonizing the midgut or the cuticle. Particularly, there is little information on the fungal diversity. This information is important for development of vector control strategies.Methodology/principal findingsFIVE SAND FLY SPECIES: Phlebotomus papatasi, P. sergenti, P. kandelakii, P. perfiliewi and P. halepensis were caught in Bileh Savar and Kaleybar in North-Western Iran that are located in endemic foci of visceral leishmaniasis. A total of 35 specimens were processed. Bacterial and fungal strains were identified by routine microbiological methods. We characterized 39 fungal isolates from the cuticle and/or the midgut. They belong to six different genera including Penicillium (17 isolates), Aspergillus (14), Acremonium (5), Fusarium (1), Geotrichum (1) and Candida (1). We identified 33 Gram-negative bacteria: Serratia marcescens (9 isolates), Enterobacter cloacae (6), Pseudomonas fluorescens (6), Klebsiella ozaenae (4), Acinetobacter sp. (3), Escherichia coli (3), Asaia sp. (1) and Pantoea sp. (1) as well as Gram-positive bacteria Bacillus subtilis (5) and Micrococcus luteus (5) in 10 isolates.Conclusion/significanceOur study provides new data on the microbiotic diversity of field-collected sand flies and for the first time, evidence of the presence of Asaia sp. in sand flies. We have also found a link between physiological stages (unfed, fresh fed, semi gravid and gravid) of sand flies and number of bacteria that they carry. Interestingly Pantoea sp. and Klebsiella ozaenae have been isolated in Old World sand fly species. The presence of latter species on sand fly cuticle and in the female midgut suggests a role for this arthropod in dissemination of these pathogenic bacteria in endemic areas. Further experiments are required to clearly delineate the vectorial role (passive or active) of sand flies.
Published: 2012
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3. Characteristics and outcome according to underlying disease in non-AIDS patients with acute respiratory failure due to Pneumocystis pneumonia

Author: Christophe Hennequin, Virginie Lemiale, Julie Bonhomme, Antoine Roux, Xavier Iriart, M. Leterrier, Anne-Pauline Bellanger, Solène Le Gal, Dominique Toubas, Samia Hamane, Danièle Maubon, Isabelle Durand-Joly, Sandrine Valade, Lucie Biard, Eric Maury, Florence Robert-Gangneux, Anne Debourgogne, Denis Pons, Christelle Pomares, Denis Magne, Frédéric Dalle, Gaston Burghi, Elie Azoulay, Antoine Berry, Université Paris Diderot - Paris 7 (UPD7), Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de biostatistique et information médicale de l’hôpital Saint Louis (Equipe ECSTRA) (SBIM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut national du cancer [Boulogne] (INCA)-Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université de Paris (UP), Hôpital Foch [Suresnes], Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Centre Hospitalier Universitaire [Grenoble] (CHU), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Procédés Alimentaires et Microbiologiques [Dijon] (PAM), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre hospitalier universitaire de Nantes (CHU Nantes), Centre Hospitalier Universitaire de Reims (CHU Reims), Hôpital Pasteur [Nice] (CHU), Centre méditerranéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), Centre de Physiopathologie Toulouse Purpan (CPTP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CHU Toulouse [Toulouse], Hôpital Claude Huriez [Lille], CHU Lille, CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), CHU Gabriel Montpied [Clermont-Ferrand], CHU Clermont-Ferrand, Centre de Recherche Saint-Antoine (CR Saint-Antoine), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), French ministry of health, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Cité (UPCité), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Université Nice Sophia Antipolis (1965 - 2019) (UNS), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Centre de Recherche Saint-Antoine (CRSA), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)
Subjects: 0301 basic medicine, Microbiology (medical), Male, medicine.medical_specialty, medicine.medical_treatment, Chronic lymphocytic leukemia, [SDV]Life Sciences [q-bio], 030106 microbiology, Pneumocystis pneumonia, Organ transplantation, 03 medical and health sciences, 0302 clinical medicine, Immune system, Medical microbiology, Acquired immunodeficiency syndrome (AIDS), Internal medicine, medicine, Humans, 030212 general & internal medicine, Prospective Studies, Aged, Outcome, business.industry, Pneumocystis, Pneumonia, Pneumocystis, Immunosuppression, General Medicine, Middle Aged, medicine.disease, Hematologic Diseases, 3. Good health, Leukemia, Lymphoid, Infectious Diseases, Acute Disease, ICU, Observational study, Female, business, Respiratory Insufficiency
Abstract: International audience; In the non-AIDS group, several underlying conditions and immune defects could lead to different PCP presentations. This study compared PCP presentation and outcome according to the underlying disease. A secondary analysis of a previously published prospective observational study including 544 PCP patients was done. Only non-AIDS patients were included. Underlying disease was defined as chronic lymphocytic leukemia (CLL), organ transplantation, solid cancer, allogeneic hematopoietic stem cell transplant (AHSCT), other hematological diseases, and immunosuppressive treatment. Clinical characteristics and outcomes were compared between groups. Multiple correspondent analyses compared clinical characteristics at diagnosis. Day 30 mortality was analyzed. Three hundred and twenty-one patients were included in the study. The underlying diseases were hematological malignancy (n = 75), AHSCT (n = 14), CLL (n = 19), solid organ transplant (n = 94), solid tumor (n = 39), and immunosuppressive treatment (n = 57). Compared with other underlying diseases, PCP related to CLL was closer to PCP related to AIDS presentation (long duration of symptoms before diagnosis, high level of dyspnea, and low oxygen saturation at diagnosis). Day 30 mortality was associated with underlying disease, oxygen flow, and shock at ICU admission. PCP presentations may vary according to the underlying reason for immunosuppression. Response to treatment and adjuvant steroid therapy should be analyzed regarding this result.
Published: 2021
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4. Scedosporiosis/lomentosporiosis observational study (SOS): Clinical significance of Scedosporium species identification

Author: Boris Melloni, Benoit Roze, Lilia Hasseine, Jacques-Olivier Bay, Laurence Delhaes, Dominique Toubas, Gaelle Guillerm, Xavier Iriart, Thomas Similowski, Valérie Letscher-Bru, Liana Carausu, Adela Angoulvant, Eric Caumes, Marie-Elisabeth Bougnoux, Yves Leprince, Taieb Chouaki, Cécile Molucon-Chabrot, Eric Dannaoui, Hervé Dutronc, Youssef El-Samad, Florent Morio, Morgane Mourguet, Alexandre Alanio, Berengere Gruson, Pierre Cahen, Stéphane Ranque, Anne Boullié, Julie Bonhomme, Violaine Noel, Françoise Dromer, Elisabeth Chachaty, Felipe Suarez, Beate Heym, François Bissuel, Cécile Jensen, Jean-Pierre Gangneux, Emmanuelle Mouchon, Philippe Zann, Patricia Mariani, Bernard Bouteille, Véronique Leflon-Guibout, Dea Garcia-Hermoso, Anne Scemla, Stéphane Blanche, Agnes Lefort, Dorothée Raoux-Barbot, Didier Bronnimann, Olivier Lortholary, Matthieu Revest, Fanny Lanternier, Philippe Poirier, Luc Quaesaet, Marie Machouart, Françoise Botterel-Chartier, Viviane Queyrel-Moranne, Thomas Perpoint, Anne De Tinteniac, Pascale Penn, Ana Presedo, Marie Balsat, Anne Huynh, Lelia Escaut, Noémie Gadaud, Antoine Huguenin, Martine Gari-Toussaint, Sophie Brun, Jean-Marie Forel, Blandine Rammaert, Nicole Desbois, Alain Delmer, Valérie Moal, Arnaud Fekkar, Damien Hoinard, Elizabeth Rivaud, Delphine Lancement, Laurence Pougnet, Valérie Zeller, Jacques Grill, Florence Pasquier, Fabrice Larosa, Jean-François Papon, Nina Arakelyan-Laboure, Thomas Daix, Catherine Cordonnier, Nicolas Limal, Patrick Lutz, Laurence Maulin, Céline Nourrisson, Stéphane Bretagne, Françoise Uettwiller, Florence Ader, Céline Dieval, Nicolas Traversier, Sophie Bayle, Sorya Belaz, Frédéric Villega, Flore Sicre De Fontbrune, Didier Poisson, Olivier Moquet, Guillaume Martin-Blondel, Kamel Laribi, Delphine Horeau-Langlard, Gilles Nevez, Stéphanie Branger, Audrey Hessel, Philippe Herman, Jérémie Orain, Emilie Catherinot, Frédéric Mechai, Cristina Audoly, Frédéric Gabriel, Jean-François Velly, Caroline Fritz, Muriel Alvarez, Romain Guillemain, Pascal Turlure, Grégoire Leclerc, Frederic Pene, Lionel Mannone, Frédéric Grenouillet, Yoann Prevot, Louis-Jean Couderc, Isabelle Degasne, Giovanna Ingenuo, Joséphine Dorin, Florence Persat, Pierre-Marie Roger, Nathalie Brieu, David Boutoille, Pierre Frange, Nicolas Paleiron, Christophe Joubert, Laurent Hustache-Mathieu, Raoul Herbrecht, Frédéric Janvier, Lenaïg Le Clech, Cécile Gautier, Joelle Guitard, Nicolas Durrleman, Romain Guery, Stéphane De Botton, Sophie Cassaing, Marine Paul, Rachel Brault, Claire Briere-Bellier, Catherine Kauffmann-Lacroix, Nicolas Engrand, Audrey Berric, Hôpital Henri Mondor, Diane Bouvry, André Paugam, CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Victor Segalen - Bordeaux 2, Université Paris Cité (UPCité), Mycologie moléculaire - Molecular Mycology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence Mycoses Invasives et Antifongiques - National Reference Center Invasive Mycoses & Antifungals (CNRMA), Institut Pasteur [Paris] (IP), Centre d'infectiologie Necker-Pasteur [CHU Necker], Institut Pasteur [Paris] (IP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre Hospitalier du Pays d'Aix, CHU Amiens-Picardie, The National Reference Center for Invasive Mycoses and Antifungals is supported in part by Santé Publique France and Institut Pasteur., Université de Paris (UP), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut Pasteur [Paris], and Institut Pasteur [Paris]-CHU Necker - Enfants Malades [AP-HP]
Subjects: Adult, Male, medicine.medical_specialty, Antifungal Agents, Adolescent, LOMENTOSPORA PROLIFICANS, Lomentospora prolificans, Microbial Sensitivity Tests, Neutropenia, Scedosporium sp, Scedosporium, Young Adult, 03 medical and health sciences, Scedosporium species, Internal medicine, Humans, Medicine, Clinical significance, Child, Mycological Typing Techniques, scedosporiosis, Phylogeny, Fungemia, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Aged, Retrospective Studies, 030304 developmental biology, Aged, 80 and over, 0303 health sciences, 030306 microbiology, business.industry, Infant, Newborn, Infant, Scedosporium apiospermum, General Medicine, Middle Aged, medicine.disease, cardiovascular localization, 3. Good health, Infectious Diseases, Child, Preschool, outcome, Female, Observational study, France, business, Invasive Fungal Infections
Abstract: International audience; Scedosporiosis/lomentosporiosis is a devastating emerging fungal infection. Our objective was to describe the clinical pattern and to analyze whether taxonomic grouping of the species involved was supported by differences in terms of clinical presentations or outcomes. We retrospectively studied cases of invasive scedosporiosis in France from 2005 through 2017 based on isolates characterized by polyphasic approach. We recorded 90 cases, mainly related to Scedosporium apiospermum (n = 48), S. boydii/S. ellipsoideum (n = 20), and Lomentospora prolificans (n = 14). One-third of infections were disseminated, with unexpectedly high rates of cerebral (41%) and cardiovascular (31%) involvement. In light of recent Scedosporium taxonomic revisions, we aimed to study the clinical significance of Scedosporium species identification and report for the first time contrasting clinical presentations between infections caused S. apiospermum, which were associated with malignancies and cutaneous involvement in disseminated infections, and infections caused by S. boydii, which were associated with solid organ transplantation, cerebral infections, fungemia, and early death. The clinical presentation of L. prolificans also differed from that of other species, involving more neutropenic patients, breakthrough infections, fungemia, and disseminated infections. Neutropenia, dissemination, and lack of antifungal prescription were all associated with 3-month mortality. Our data support the distinction between S. apiospermum and S. boydii and between L. prolificans and Scedosporium sp. Our results also underline the importance of the workup to assess dissemination, including cardiovascular system and brain. Lay Summary Scedosporiosis/lomentosporiosis is a devastating emerging fungal infection. Our objective was to describe the clinical pattern and to analyze whether taxonomic grouping of the species involved was supported by differences in terms of clinical presentations or outcomes.
Published: 2020
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5. Epidemiological investigation for grouped cases of Trichosporon asahii using whole genome and IGS1 sequencing

Author: N. Brieu, B. Sendid, E. Sitterle, Frédéric Gabriel, I. Poilane, D. Moissenet, Christine Aznar, V. Blanc, N. Traversier, M. Sasso, N. Godineau, O. Eloy, Corinne Maufrais, Danièle Maubon, H. Rabérin, C. Lawrence, P. Mariani, P. Cahen, C. Bonnal, B. Bouteille, M. Cornet, F. Moriot, B. Heym, Elisabeth Chachaty, Dominique Toubas, M. Nicolas, Sophie Cassaing, A. Paugam, S. Picot, E. Moalic, Adela Angoulvant, Loïc Favennec, Françoise Dromer, M. Gari‐toussaint, Marc Pihet, Taieb Chouaki, Magalie Pierre Demar, Frédéric Grenouillet, N. Fauchet, L. Collet, Frédéric Dalle, Marie-Elisabeth Bougnoux, Céline Nourrisson, Marie Desnos-Ollivier, O. Faure, Françoise Botterel, C. Nabet, N. Bourgeois, E. Bailly, Dorothée Quinio, Alexandre Alanio, O. Mouquet, S. Brun, S. Bland, Julie Bonhomme, Jean-Pierre Gangneux, Stéphane Ranque, Philippe Poirier, N. Desbois, Florence Persat, Anne-Pauline Bellanger, H. Piarroux, E. Forget, L. Lachaux, V. Bru, Laurence Millon, A. Minoza, C. Kauffman, L. Hasseine, Martine Wallon, A.L. Roux, D. Poisson, S. Bonacorsi, Mycologie moléculaire - Molecular Mycology, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre d'Informatique pour la Biologie, Institut Pasteur [Paris], Laboratoire de Parasitologie-Mycologie (CHU d'Angers), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP), Université d'Angers (UA), SFR UA 4208 Interactions Cellulaires et Applications Thérapeutiques (ICAT), Laboratoire Hospitalo-Universitaire de Parasitologie-Mycologie, Coordination Régionale de la lutte contre le Virus de L'Immunodéficience Humaine (COREVIH)-Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française]-Université des Antilles (UA), Observatoires Régionaux du Pneumocoque, Partenaires INRAE, Université de Picardie Jules Verne (UPJV), Service de parasitologie et mycologie [CHRU de Besançon], Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire de Parasitologie-Mycologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Thérapeutique Recombinante Expérimentale (TIMC-IMAG-TheREx ), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications Grenoble - UMR 5525 (TIMC-IMAG), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Laboratoire de parasitologie [Pointe-à-Pitre], CHU Pointe-à-Pitre/Abymes [Guadeloupe], Ecosystemes Amazoniens et Pathologie Tropicale (EPat), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Guyane (UG), CHU Tenon [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CHU Sud Saint Pierre [Ile de la Réunion], Centre Hospitalier de Versailles André Mignot (CHV), Hôpital Huriez, CHU Limoges, Hospices Civils de Lyon (HCL), Institut de parasitologie et mycologie médicale, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Service de Maladies Infectieuses et Tropicales [Fort-de-France, Martinique], CHU Fort de France-CHU de la Martinique [Fort de France]-Hôpital Pierre Zobda-Quitman [CHU de la Martinique], CHU de la Martinique [Fort de France], Hydrosciences Montpellier (HSM), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire de Nice (CHU Nice), Matrice extracellulaire et dynamique cellulaire - UMR 7369 (MEDyC), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Service de Parasitologie-Mycologie [Rennes], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes], Epidémiosurveillance de protozooses à transmission alimentaire et vectorielle (ESCAPE), Université de Reims Champagne-Ardenne (URCA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Hôpital Delafontaine, Centre Hospitalier de Saint-Denis [Ile-de-France], Centre Hospitalier Universitaire de Saint-Etienne (CHU de Saint-Etienne), Service de Parasitologie et Mycologie, CHU Toulouse [Toulouse]-Institut Fédératif de Biologie (IFB) - Hôpital Purpan, Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse], Hôpital universitaire Bichat, Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Hopital Saint-Louis [AP-HP] (AP-HP), CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut Curie [Paris], Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Laboratoire Chrono-environnement (UMR 6249) (LCE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Reims Champagne-Ardenne (URCA)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes], Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), Service de Parasitologie et Mycologie [CHU Toulouse], Institut Fédératif de Biologie (IFB), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Pôle Biologie [CHU Toulouse], and Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)
Subjects: 0301 basic medicine, Adult, Male, Antifungal Agents, Adolescent, Genotype, Genotyping Techniques, [SDV]Life Sciences [q-bio], 030106 microbiology, Single-nucleotide polymorphism, Dermatology, Trichosporon asahii, Biology, Genome, DNA, Ribosomal, 030207 dermatology & venereal diseases, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Trichosporonosis, medicine, Humans, Child, DNA, Fungal, Mycological Typing Techniques, Genotyping, Phylogeny, ComputingMilieux_MISCELLANEOUS, Aged, Genetics, Voriconazole, Whole genome sequencing, Whole Genome Sequencing, Basidiomycota, Haplotype, Infant, General Medicine, Sequence Analysis, DNA, Middle Aged, medicine.disease, 3. Good health, Infectious Diseases, Child, Preschool, Female, France, Genome, Fungal, medicine.drug
Abstract: BACKGROUND Trichosporonosis is a rare invasive infection in humans mainly due to Trichosporon asahii, and especially recovered from patients having haematological malignancy. Since 2012, IGS1 region sequencing is used as a genotyping method to distinguish isolates, with high frequency of one haplotype worldwide and a geographic specificity for some haplotypes. OBJECTIVES We compared the IGS1 genotyping method and whole genome sequencing (WGS) to study the relationship between clinical isolates involved in two grouped cases in France. METHODS IGS1 sequencing and antifungal susceptibility testing were performed for 54 clinical isolates. Clinical data for 28 isolates included in surveillance programs were analysed. Whole genome was sequenced for 32 clinical isolates and the type strain. RESULTS All isolates were intrinsically resistant to flucytosine, while voriconazole had the most potent in vitro activity. The majority of the isolates was recovered from patients with haematological malignancies (42.86%), with a high proportion of children (
Published: 2020
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6. Pulmonary adverse events related to idelalisib therapy: A single centre experience

Author: Alain Delmer, Dominique Toubas, Yohan Nguyen, Aurélien Giltat, Caroline Migault, O. Toubas, Delphine Lebrun, François Lebargy, Gautier Julien, Firouzé Bani-Sadr, Service de Médecine interne, Maladies Infectieuses et Immunologie Clinique [Reims], Centre Hospitalier Universitaire de Reims (CHU Reims), Médecine interne, maladies infectieuses, immunologie clinique, Hôpital Robert Debré-Centre Hospitalier Universitaire de Reims (CHU Reims), Laboratoire de Virologie Médicale et Moléculaire - EA 4684 (CardioVir), Université de Reims Champagne-Ardenne (URCA)-Centre Hospitalier Universitaire de Reims (CHU Reims)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV), Matrice extracellulaire et dynamique cellulaire - UMR 7369 (MEDyC), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Service d'hématologie [Reims], Hôpital Robert Debré, and Hôpital Robert Debré-Centre Hospitalier Universitaire de Reims (CHU Reims)-Hôpital Robert Debré-Centre Hospitalier Universitaire de Reims (CHU Reims)
Subjects: Male, Oncology, medicine.medical_specialty, Drug-Related Side Effects and Adverse Reactions, Antineoplastic Agents, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, medicine, Humans, Pharmacology (medical), Adverse effect, Lung, ComputingMilieux_MISCELLANEOUS, Aged, Quinazolinones, Pharmacology, business.industry, TOR Serine-Threonine Kinases, Pneumonia, Middle Aged, 3. Good health, Single centre, Infectious Diseases, Purines, 030220 oncology & carcinogenesis, Idelalisib, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, 030215 immunology
Abstract: Idelalisib is a potent and selective inhibitor of the PI3Kδ approved since September 2014 for the treatment of several types of B cell malignancies. Pulmonary adverse events related to idelalisib are an emerging serious adverse event. We report here a single centre cohort of 16 patients who initiated idelalisib as routine treatment. Five of them experienced severe pulmonary adverse events related to idelalisib therapy. Comparison of the 5 patients with severe pulmonary events versus the 11 patients without identified no predisposing factors. Severe pulmonary adverse events were related to infectious pneumonia and/or to a drug-induced pneumonitis. The mechanisms of idelalisib-associated pneumonitis are unknown but consistent with the drug-induced pneumonitis described with mTOR inhibitors. Indeed, by inhibiting PI3Kδ, idelalisib also inhibits the mTOR pathway. Clinicians should be aware that any idelalisib-treated patient who presents with pulmonary symptoms should be evaluated for pneumonitis. Corticosteroids should be considered in addition to anti-infective therapy in case of severe pneumonitis or persistent pulmonary symptoms despite adequate antibiotic therapy.
Published: 2018
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7. Pneumocystis Infection Outbreaks in Organ Transplantation Units in France: A Nation-Wide Survey

Author: M. Leterrier, Anne Totet, Céline Damiani, Danièle Maubon, Solène Le Gal, Isabelle Accoceberry, Julie Bonhomme, Pierre Marty, E. Bailly, Ermanno Candolfi, Anne Debourgogne, Laurence Millon, Frédéric Dalle, Anne-Pauline Bellanger, Patrice Le Pape, Denis Pons, Christelle Pomares, Yann Le Meur, Marie Machouard, Marie-Laure Dardé, Laurence Delhaes, Ahmed Abou Bacar, Dominique Toubas, Frédéric Gabriel, Estelle Cateau, Gilles Nevez, Loïc Favennec, Marie-Hélène Rodier, Xavier Iriart, Eric Dannaoui, Laurence Lachaud, Guillaume Desoubeaux, Pierre Flori, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Laboratoire de Parasitologie et Mycologie (Parasito - Myco - BREST), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Matrice extracellulaire et dynamique cellulaire - UMR 7369 (MEDyC), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Service de parasitologie et de mycologie médicales, Université de Picardie Jules Verne (UPJV)-CHU Amiens-Picardie, Laboratoire de parasitologie mycologie (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Institut de Parasitologie et de Pathologie Tropicale de Strasbourg, Faculté de Médecine de Strasbourg, Université de Strasbourg, CHRU Brest - Service de Nephrologie (CHU - BREST - Nephrologie), Microbiologie cellulaire et moléculaire et pathogénicité (MCMP), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), Service de parasitologie et mycologie [CHU de Besançon], Centre Hospitalier Régional Universitaire [Besançon] (CHRU Besançon), Laboratoire Chrono-environnement - UFC (UMR 6249) (LCE), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université de Caen Normandie (UNICAEN), Normandie Université (NU), Microbiologie de l'Eau (MDE), Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Institut de Parasitologie et de Pathologie Tropicale, UMR-I 01 - AMIENS, Université de Picardie Jules Verne (UPJV), Unité de Parasitologie-Mycologie [CHU HEGP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Université de Limoges (UNILIM), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Université de Bordeaux (UB), Centre d’Etude des Pathologies Respiratoires (CEPR), UMR 1100 (CEPR), Université de Tours-Institut National de la Santé et de la Recherche Médicale (INSERM), Epidémiosurveillance de protozooses à transmission alimentaire et vectorielle (ESCAPE), Université de Reims Champagne-Ardenne (URCA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Anofel Cryptosporidium National Network, Institut d'Histoire de la Pensée Classique (IHPC), École normale supérieure - Lyon (ENS Lyon)-Université Lumière - Lyon 2 (UL2)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), CHU Bordeaux [Bordeaux], Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Laboratoire de Microbiologie (CHD de la Roche-Sur-Yon), CHD Vendee (La Roche Sur Yon), Cibles et médicaments de l'infection, de l'immunité et du cancer (IICiMed), Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN), Laboratoire de recherche en Hydrodynamique, Énergétique et Environnement Atmosphérique (LHEEA), École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Centre méditerranéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Gabriel Montpied (CHU), CHU Clermont-Ferrand, Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Hôpital de la Cavale Blanche - CHRU Brest (CHU - BREST ), SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), Departments of Medical Parasitology and Mycology, Service de néphrologie, Sagem - SAFRAN Gr., Université de Strasbourg (UNISTRA), Centre National de Référence (CNR) Toxoplasmose/Toxoplasma Biological Resource Center (BRC) (CNR Toxoplasmose-Toxoplasma BRC), CHU Limoges, Service de Parasitologie-Mycologie [CHRU Nancy], Stress, Immunité, Pathogènes (SIMPA), Université de Lorraine (UL), Appareil Digestif Environnement Nutrition (ADEN ), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Groupe Immunité des Muqueuses et Agents Pathogènes (GIMAP), Université Jean Monnet [Saint-Étienne] (UJM), Service de parasitologie et de mycologie, Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre hospitalier universitaire de Nantes (CHU Nantes), Laboratoire Chrono-environnement - CNRS - UFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Infections Parasitaires : Transmission, Physiopathologie et Thérapeutiques (IP-TPT), Service de Santé des Armées-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP), Université d'Angers (UA), Laboratoire de Parasitologie et Mycologiede [CHRU Brest], Laboratoire de parasitologie et de mycologie médicales [CHU Amiens], CHU Amiens-Picardie, Service de parasitologie et mycologie [CHRU de Besançon], Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Périnatalité et Risques Toxiques - UMR INERIS_I 1 (PERITOX), Université de Picardie Jules Verne (UPJV)-CHU Amiens-Picardie-Institut National de l'Environnement Industriel et des Risques, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), CHU Gabriel Montpied [Clermont-Ferrand], Mycologie moléculaire, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut d’Histoire des Représentations et des Idées dans les Modernités (IHRIM), Université Lumière - Lyon 2 (UL2)-École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Université Clermont Auvergne (UCA)-Université Jean Monnet [Saint-Étienne] (UJM), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Service de Santé des Armées, Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Université de Reims Champagne-Ardenne (URCA), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Microbiology (medical), medicine.medical_specialty, Genotype, Pneumocystis carinii, Organ transplantation, Disease Outbreaks, 03 medical and health sciences, 0302 clinical medicine, genotypes, Surveys and Questionnaires, Internal medicine, Humans, Medicine, Pneumocystis jirovecii, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, 030212 general & internal medicine, Genotyping, ComputingMilieux_MISCELLANEOUS, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Retrospective Studies, Transplant recipients, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 0303 health sciences, biology, 030306 microbiology, business.industry, Pneumocystis, Pneumonia, Pneumocystis, Outbreak, Organ Transplantation, biology.organism_classification, 3. Good health, Transplantation, Infectious Diseases, Renal transplant, France, business, Pneumocystis Infections
Abstract: The burden of nosocomial Pneumocystis infections in transplantation units in France was evaluated through a retrospective survey. Over 12 years, 16 outbreaks occurred, including 13 among renal transplant recipients (RTRs). We performed Pneumocystis jirovecii genotyping in 5 outbreaks, which suggested that specific strains may have been selected by RTRs.
Published: 2019
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8. Donor Derived Candida stellimalicola in a Clinical Specimen: Preservation Fluid Contamination During Pancreas Procurement

Author: Véronique Reiter, Dominique Toubas, Emmanuel Morelon, Damien Dupont, Antoine Huguenin, Martine Wallon, Isabelle Villena, Lionel Badet, Elodie Tisserand, Service de parasitologie et mycologie médicale [Hôpital de la Croix Rousse, Lyon], Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Centre de recherche en neurosciences de Lyon (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire de Reims (CHU Reims), Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL), Epidémiosurveillance de protozooses à transmission alimentaire et vectorielle (ESCAPE), Université de Reims Champagne-Ardenne (URCA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Matrice extracellulaire et dynamique cellulaire - UMR 7369 (MEDyC), SFR CAP Santé (Champagne-Ardenne Picardie Santé), and Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Adult, 0301 basic medicine, medicine.medical_specialty, Antifungal Agents, Veterinary (miscellaneous), medicine.medical_treatment, 030106 microbiology, Microbial Sensitivity Tests, Drug resistance, Pancreas transplantation, Biology, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, Medical microbiology, Pharmacotherapy, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Disease Transmission, Infectious, medicine, Ascitic Fluid, Humans, Pathogen, ComputingMilieux_MISCELLANEOUS, Candida, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, Candidiasis, Tissue Donors, Transplant Recipients, 3. Good health, Transplantation, Treatment Outcome, medicine.anatomical_structure, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Immunology, Female, Pancreas Transplantation, Pancreas, Agronomy and Crop Science, Fluconazole, medicine.drug
Abstract: We report here a case of possible donor-derived Candida stellimalicola infection after pancreas transplantation. Candida stellimalicola, an environmental non-filamentous yeast, was isolated from both the peritoneal fluid of the graft donor and the preservation fluid of the transplanted pancreas. Interestingly, this strain exhibited high minimum inhibitory concentrations to azoles. These results justified the use of echinocandins as therapy instead of fluconazole. This switch permitted a favorable outcome. To our knowledge, this is the first report of C. stellimalicola from clinical samples and therefore the first reported case of a possible human infection. This case report highlights the need for standardized microbiological procedures in solid organ transplant settings. Moreover, it underlines the importance of using molecular identification technique when routine techniques do not allow successful identification of the pathogen. It is of utmost importance to determine sensitivity profile, even in the absence of species-level identification, because resistance to fluconazole is not uncommon, especially in emergent species.
Published: 2018
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9. Severe post-artesunate delayed onset anaemia responding to corticotherapy: a case report

Author: Aurélie Brunet, Firouzé Bani-Sadr, Thierry Floch, Gautier Julien, Juliette Romaru, Joël Cousson, Dominique Toubas, Delphine Lebrun, Yohan Nguyen, Aurélien Giltat, Médecine interne, maladies infectieuses, immunologie clinique, Hôpital Robert Debré-Centre Hospitalier Universitaire de Reims (CHU Reims), Sanofi-Aventis R&D, SANOFI Recherche, Service de médecine interne [CHU Reims], Centre Hospitalier Universitaire de Reims (CHU Reims), Matrice extracellulaire et dynamique cellulaire - UMR 7369 (MEDyC), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), and Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Adult, Male, Hemolytic anemia, Anemia, Hemolytic, medicine.medical_specialty, Combination therapy, Anemia, [SDV]Life Sciences [q-bio], 030231 tropical medicine, Artesunate, Parasitemia, Hemolysis, Gastroenterology, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Immune system, Adrenal Cortex Hormones, Internal medicine, medicine, Humans, 030212 general & internal medicine, Malaria, Falciparum, ComputingMilieux_MISCELLANEOUS, Travel, business.industry, Delayed onset, General Medicine, medicine.disease, Haemolysis, Artemisinins, 3. Good health, Coombs Test, Corticosteroid therapy, chemistry, Administration, Intravenous, business
Abstract: Delayed onset haemolysis occurring post-artesunate and post-artemisinin combination therapy is secondary to delayed clearance of infected erythrocytes spared by pitting during treatment. We report a case of severe post-treatment delayed haemolytic anaemia with a positive direct antiglobulin test and a positive response to corticosteroid therapy, suggesting an associated immune mechanism.
Published: 2017
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10. Differentiation and identification of filamentous fungi by high-throughput FTIR spectroscopic analysis of mycelia

Author: Michel Manfait, Dominique Toubas, Georges Barbier, W. Ablain, A. Lecellier, Vincent Gaydou, Ganesh D. Sockalingum, L. Castrec, and Jérôme Mounier
Subjects: Fastidious organism, Chromatography, Mycelium, Phylum, Fungi, Discriminant Analysis, Reproducibility of Results, Context (language use), General Medicine, Biology, Microbiology, DNA sequencing, Spectroscopy, Fourier Transform Infrared, Botany, Identification (biology), Fourier transform infrared spectroscopy, Mycological Typing Techniques, Spectroscopy, Food Science
Abstract: Routine identification of fungi based on phenotypic and genotypic methods can be fastidious and time-consuming. In this context, there is a constant need for new approaches allowing the rapid identification of molds. Fourier-transform infrared (FTIR) spectroscopy appears as such an indicated method. The objective of this work was to evaluate the potential of FTIR spectroscopy for an early differentiation and identification of filamentous fungi. One hundred and thirty-one strains identified using DNA sequencing, were analyzed using FTIR spectroscopy of the mycelia obtained after a reduced culture time of 48 h compared to current conventional methods. Partial least square discriminant analysis was used as a chemometric method to analyze the spectral data and for identification of the fungal strains from the phylum to the species level. Calibration models were constructed using 106 strains pertaining to 14 different genera and 32 species and were used to identify 25 fungal strains in a blind manner. Identification levels of 98.97% and 98.77% achieved were correctly assigned to the genus and species levels respectively. FTIR spectroscopy with its high discriminating power and rapidity therefore shows strong promise for routine fungal identification. Upgrading of our database is ongoing to test the technique's robustness.
Published: 2014
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11. A misleading false-negative result of Pneumocystis real-time PCR assay due to a rare punctual mutation: A French multicenter study

Author: Laurence Pougnet, Sorya Belaz, Yann Pépino, Solène Le Gal, Lilia Hasseine, Christophe Hennequin, Stéphane Valot, Michèle Virmaux, Florence Robert-Gangneux, Jean-Philippe Bouchara, Mélanie Pitous, Eloise Lissillour, Thibaud Guillaud-Saumur, Gilles Nevez, Céline Damiani, Anne Totet, Dominique Toubas, Florent Morio, Paul Gueguen, Laboratoire de Parasitologie et Mycologiede [CHRU Brest], Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP), Université d'Angers (UA), Service de Parasitologie-Mycologie [Rennes], Université de Rennes (UR)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes], Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Brest (UBO), Périnatalité et Risques Toxiques - UMR INERIS_I 1 (PERITOX), Institut National de l'Environnement Industriel et des Risques (INERIS)-Université de Picardie Jules Verne (UPJV)-CHU Amiens-Picardie, Laboratoire de parasitologie et de mycologie médicales [CHU Amiens], CHU Amiens-Picardie, Génétique, génomique fonctionnelle et biotechnologies (UMR 1078) (GGB), EFS-Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Brestois Santé Agro Matière (IBSAM), Laboratoire de Génétique Moléculaire et d'Histocompatibilité [Brest], Hôpital Morvan [Brest]-Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Matrice extracellulaire et dynamique cellulaire - UMR 7369 (MEDyC), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire de Reims (CHU Reims), CHU Dijon, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Centre d'Immunologie et des Maladies Infectieuses (CIMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre hospitalier universitaire de Nantes (CHU Nantes), Centre Hospitalier Universitaire de Nice (CHU Nice), Agents infectieux, résistance et chimiothérapie - UR UPJV 4294 (AGIR ), Université de Picardie Jules Verne (UPJV)-CHU Amiens-Picardie, ERANet-LAC CAPRI-PC HID-0254, European Union, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes], Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Santé et de la Recherche Médicale (INSERM)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université d'Angers (UA), Université de Picardie Jules Verne (UPJV)-CHU Amiens-Picardie-Institut National de l'Environnement Industriel et des Risques, Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO)-Université de Brest (UBO)-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Service de Parasitologie - Mycologie [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Centre d'Immunologie et de Maladies Infectieuses (CIMI), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), Departments of Medical Parasitology and Mycology, Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest)-Hôpital Morvan [Brest], SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Male, Pneumocystis pneumonia, Pneumocystis carinii, law.invention, Gene Frequency, law, Mutation frequency, Child, DNA, Fungal, False Negative Reactions, Polymerase chain reaction, Pneumocystis jirovecii, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Aged, 80 and over, Real time-PCR, biology, Pneumonia, Pneumocystis, General Medicine, Middle Aged, 3. Good health, PCP, Infectious Diseases, Real-time polymerase chain reaction, Molecular Diagnostic Techniques, Child, Preschool, Mutation (genetic algorithm), Female, France, Adult, Adolescent, 030106 microbiology, Real-Time Polymerase Chain Reaction, DNA, Mitochondrial, DNA, Ribosomal, 03 medical and health sciences, Young Adult, medicine, Humans, Point Mutation, Gene, TaqMan® MGB probe, Aged, Sequence Analysis, DNA, Ribosomal RNA, medicine.disease, biology.organism_classification, Virology, RNA, Ribosomal, mutation
Abstract: International audience; This article describes a previously unreported mutation at position 210 (C210T) of the mitochondrial large subunit ribosomal RNA (mtLSUrRNA) gene of Pneumocystis jirovecii, which led to a false-negative result of a real-time polymerase chain reaction (PCR) assay. Since the aforementioned real-time PCR assay is widely used in France, a French multicenter study was conducted to estimate the mutation frequency and its potential impact on the routine diagnosis of Pneumocystis pneumonia (PCP). Through analysis of data obtained from eight centers, the mutation frequency was estimated at 0.28%. This low frequency should not call into question the routine use of this PCR assay. Nonetheless, the occurrence of the false-negative PCR result provides arguments for maintaining microscopic techniques combined to PCR assays to achieve PCP diagnosis.
Published: 2016
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12. Surveillance mycologique de l’eau pour la prévention des mycoses invasives dans les établissements de santé

Author: Annick Datry, Anne Bousseau, M Gari-Toussaint, Marie Machouart, Laurence Delhaes, Frédéric Dalle, Claire Lacroix, Christophe Hennequin, O. Morin, Dominique Toubas, Marie-Pierre Brenier-Pinchart, and Catherine Kauffmann-Lacroix
Subjects: Gynecology, medicine.medical_specialty, business.industry, Medicine, General Medicine, business
Abstract: Resume Objectifs Evaluer le risque fongique lie a l’eau dans differents centres hospitaliers et preciser les conditions methodologiques pour une standardisation des prelevements ont ete les objectifs de l’etude principale conduite entre fevrier 2004 et mars 2005 dans 10 centres hospitaliers en France metropolitaine. Methodes Pour evaluer ce parametre, une etude preliminaire a permis d’optimiser l’analyse mycologique de l’eau. Nous avons employe les memes conditions operatoires que pour les analyses bacteriologiques : filtration de l’eau et ensemencement de la membrane d’acetate de cellulose sur gelose. Des services hebergeant des malades a risque, dont les services d’hematologie, de transplantation d’organes, des brules, ont ete choisis. L’eau et les surfaces pouvant s’y rapporter ont ete etudiees au niveau de 98 points de prelevements. Trois prelevements de 1 L d’eau (1er jet, froide, chaude) et 2 a 3 prelevements de surfaces (interieur du robinet, du pommeau de douche, siphon) ont ete effectues pour chaque point de prelevement. Une fiche epidemiologique a permis d’obtenir des informations sur le lieu du prelevement, le(s) traitement(s) de l’eau (chlore ou autre) ainsi que sa temperature. Resultats Il existait une difference significative (p = 0,039) en fonction des differents types d’eaux. Les eaux chaudes (≥ 50 °C) etaient significativement moins colonisees que les autres : 4 % d’entres elles ont revele la presence de champignons contre 52 % des eaux froides. Les eaux etaient, en general, faiblement colonisees sauf pour 2 centres ou il existait une contamination generale du reseau (flore monomorphe a Exophiala sp et a Fusarium sp). Soixante-dix-neuf pour cent des prelevements d’eau froide presentaient moins de 5 UFC/L, tout en etant plus colonises que l’eau chaude. Les Dematies ont ete retrouves frequemment, Aspergillus sp a ete rarement isole. Les prelevements de surfaces liees a l’eau (en moyenne 15 UFC/prelevement) etaient moins frequemment positifs (13 %) que les prelevements d’eau. Les siphons etaient plus souvent positifs que les autres surfaces (23 %), or les champignons isoles n’avaient pas la meme repartition que dans l’eau. Les rapports avec la flore bacterienne et P. aeruginosa ont ete envisages ainsi que l’effet des differents traitements de l’eau. Conclusion La reglementation impose uniquement des controles bacteriologiques de l’eau. En l’absence de seuil de contamination fongique de l’eau a partir duquel il existe un risque d’infection fongique invasive nosocomiale pour les patients, il est difficile d’imposer des controles systematiques. En cas de travaux et en cas d’enquete epidemiologique au cours d’une infection nosocomiale, lorsque les prelevements d’air n’ont pas ete concluants, des controles mycologiques de l’eau sont necessaires.
Published: 2008
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13. Matrix-assisted laser desorption ionization-time of flight identification ofSchizophyllum commune: perspectives on the review by Chowdharyet al

Author: Jérôme Depaquit, Dominique Toubas, Alexandre Mzabi, Emilie Dupuis, Jean-Claude Merol, Aurélie Lorot, Isabelle Villena, Véronique Lehrter, Antoine Huguenin, Dominique Zachar, Oriane Dudez, Centre Hospitalier Universitaire de Reims (CHU Reims), Protozooses Transmises par l'Alimentation (Cryptosporidiose, Giardose et Toxoplasmose) : Mode de Contamination et Pathogénie (PROTAL) - EA 3800 (PROTAL), Université de Reims Champagne-Ardenne (URCA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV), Transmission Vectorielle et Épidémiosurveillance de Maladies Parasitaires - EA 4688 (VECPAR), SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA), Matrice extracellulaire et dynamique cellulaire - UMR 7369 (MEDyC), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), and Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, biology, Basidiomycota, Schizophyllum commune, Matrix assisted laser desorption ionization time of flight, General Medicine, biology.organism_classification, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Mycoses, Computational chemistry, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Botany, Humans, Identification (biology), ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2015
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14. Scedosporium apiospermum Otitis Complicated by a Temporomandibular Arthritis: A Case Report and Mini-Review

Author: Dominique Toubas, Isabelle Villena, V. Noel, A. Rogez, Antoine Huguenin, C. Chemla, Centre Hospitalier Universitaire de Reims (CHU Reims), Protozooses Transmises par l'Alimentation (Cryptosporidiose, Giardose et Toxoplasmose) : Mode de Contamination et Pathogénie (PROTAL) - EA 3800 (PROTAL), Université de Reims Champagne-Ardenne (URCA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), and Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)
Subjects: Male, medicine.medical_specialty, Antifungal Agents, Veterinary (miscellaneous), Ear infection, Otomycosis, Arthritis, Applied Microbiology and Biotechnology, Microbiology, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Humans, Scedosporium, ComputingMilieux_MISCELLANEOUS, Voriconazole, Aged, 80 and over, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, Temporomandibular Joint, business.industry, Scedosporium apiospermum, Temporomandibular Joint Disorders, medicine.disease, Otitis Externa, 3. Good health, Surgery, Temporomandibular joint, Otitis, medicine.anatomical_structure, Treatment Outcome, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Mycoses, medicine.symptom, Complication, business, Tomography, X-Ray Computed, Agronomy and Crop Science, Head, medicine.drug
Abstract: Scedosporium apiospermum is an ubiquitous fungus responsible for various infections in immunocompromised and immunocompetent patients. Ear infections are infrequent. We report an exceptional case of S. apiospermum external otitis complicated by temporomandibular joint arthritis. After 6 months of antibiotherapy, diagnosis was established by mycological analysis of external auditory canal and infratemporal fossae needle sampling. A satisfactory outcome was obtained after 2 months of voriconazole alone. We have reviewed 15 cases of S. apiospermum otitis. Seven of these patients were immunocompromised. Most common clinical presentation included a chronic external otitis lasting months or years before complication stage. Most common clinical features included recurrent unilateral otalgia (11/15) and purulent otorrhea (13/15). Diagnosis was often made at later stage (12/15) with local extension to bones and/or soft tissues (9/15) or cerebral lethal dissemination (3/15).The extremely low incidence of S. apiospermum otomycosis and its non-specific presentation results in a frequent diagnosis delay. A mycological investigation should be performed in case of persistent external otitis and/or osteolysis despite prolonged antibiotic treatment to prevent further extension of the disease.
Published: 2015
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15. FTIR spectroscopy as a potential tool to analyse structural modifications during morphogenesis of Candida albicans

Author: Isabelle Adt, Michel Manfait, Ganesh D. Sockalingum, Jean-Michel Pinon, Dominique Toubas, Matrice extracellulaire et dynamique cellulaire - UMR 7369 (MEDyC), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Parasitologie-Mycologie (LPM), IFR 53, Université de Reims Champagne-Ardenne (URCA)-Université de Reims Champagne-Ardenne (URCA)-CHU Maison Blanche-UPRES EA 2070, Médicaments : Dynamique Intracellulaire et Architecture Nucléaire (MéDIAN), and Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Hypha, Hyphae, Morphogenesis, Polysaccharide, Biochemistry, Microbiology, Mannans, Cell wall, 03 medical and health sciences, Candida albicans, Spectroscopy, Fourier Transform Infrared, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Genetics, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Glucans, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, 030306 microbiology, fungi, Gastrula, General Medicine, Fungi imperfecti, Spores, Fungal, biology.organism_classification, Yeast, Corpus albicans, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, chemistry
Abstract: Candida albicans is a polymorphic organism that grows under certain conditions as blastospores, hyphae or pseudohyphae. The potentials of FTIR spectroscopy for assessing structural differences in C. albicans blastospores and hyphae were investigated. The main observed differences were localised in the polysaccharide (950-1,185 cm(-1)), protein (1,480-1,720 cm(-1)), and the fatty acids (2,840-3,000 cm(-1)) regions. Quantitative evaluation of differences between hyphae and blastospores by curve-fitting of these regions indicate that these modifications could be due to both changes in structure and content of components of the cell wall such as beta-glucans, mannoproteins, and lipids. Furthermore, glycogen consumption could be involved during hyphae elongation. Thus, FTIR spectroscopy can be an interesting tool to investigate differences in structure and in content between blastospores and hyphae. We also demonstrate through this study that differentiation of C. albicans clinical strains using hyphae is feasible, as this has been previously shown with blastospores. This preliminary work on identification of C. albicans using hyphae is a prelude to a larger clinical study for early typing within 7 h from a pure culture.
Published: 2006
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16. Use of Fourier-Transform Infrared Spectroscopy for Typing of Candida albicans Strains Isolated in Intensive Care Units

Author: C. Sandt, Michel Manfait, M. Jaussaud, Dominique Aubert, H. Lepan, Jean-Michel Pinon, Ganesh D. Sockalingum, A. Leon, C. Lepouse, and Dominique Toubas
Subjects: Adult, Male, Microbiology (medical), Pathology, medicine.medical_specialty, Infrared spectroscopy, Mycology, Intensive care, Candida albicans, Spectroscopy, Fourier Transform Infrared, medicine, Humans, Typing, Fourier transform infrared spectroscopy, Spectroscopy, Aged, Chromatography, biology, Middle Aged, Reference Standards, biology.organism_classification, Corpus albicans, RAPD, Intensive Care Units, Multivariate Analysis, Female
Abstract: Comparative studies of Candida albicans strains are essential for proving cross-infections in epidemiological investigations. Typing of C . albicans strains is mainly based on genotypic methods. Fourier-transform infrared (FTIR) spectroscopy is described in this study as a novel phenotypic approach to the typing of C . albicans . The first step in the approach was the standardization of sample preparation (culture conditions and sampling parameters) and acquisition and classification parameters (spectral acquisition, spectral window selection, classification algorithm, and heterogeneity threshold). The second step consisted of validating the established parameters with a set of 79 strains of C . albicans isolated over 4 months from nine patients hospitalized in two intensive care units. Strains were isolated from multiple anatomical sites with repeated sampling. FTIR spectroscopy results were compared to randomly amplified polymorphic DNA (RAPD) results; this analysis showed that the amplification patterns of strains isolated from a given patient were identical and that different patients had different profiles. FTIR spectroscopy data were analyzed by hierarchical clustering performed with the second-derivative spectra. This classification revealed nine groups, one per patient. Only one spectrum out of 79 was misclassified by the FTIR spectroscopy method. RAPD and FTIR spectroscopy results were in good agreement, showing that, when nosocomial candidiasis transmission is suspected and urgent information is needed, this technique may be useful as a quick identification tool to give solid clues before confirmation by a genotypic method.
Published: 2003
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17. Use of co-immunoelectrodiffusion to detect presumed disease-associated precipitating antibodies, and time-course value of specific isotypes in bird-breeder's disease

Author: Cathy Chemla, Isabelle Villena, J. M. Pinon, Dominique Aubert, Dominique Toubas, and Frédérique Foudrinier
Subjects: Male, Immunoglobulin A, Immunodiffusion, Immunology, Immunologic Tests, Sensitivity and Specificity, Antibodies, Crop milk, Immune system, Bird Fancier's Lung, Antigen, Positive predicative value, Animals, Humans, Immunology and Allergy, Medicine, Columbidae, Aged, biology, business.industry, Hemagglutination Tests, Gold standard (test), Allergens, Middle Aged, Prognosis, Precipitin Tests, Isotype, Immunoglobulin Isotypes, Precipitins, Case-Control Studies, biology.protein, Female, Antibody, business
Abstract: Background and objective : The practical value of immunological diagnosis of bird-breeder's disease (BBD) is controversial, because of difficulties in distinguishing active disease patients from simple contact subjects. The aim of this study was to determine the diagnostic and prognostic value of (a) presumed disease-associated antibodies precipitating pigeon antigens (immunoglobulin A (IgAp) and P2 component), (b) characterization of specific isotypes (IgG, IgM, and IgA), and (c) antibody kinetics after antigen eradication. Methods : 405 subjects (775 sera) in contact with birds were studied [by means of co-immunoelectrodiffusion (Co-IED) and enzyme-linked immunofiltration (ELIFA)] with soluble extracts of pigeon droppings and squab crop milk. These patients were divided into two groups based on the final clinical evaluation of the patients' physicians, which was taken as the gold standard (positive in 90 and negative in 315 cases). Results : On the basis of this gold standard, the detection of presumed disease-associated precipitating antibodies by Co-IED had a specificity of 95.5%, a sensitivity of 98.7%, an accuracy of 98%, and positive and negative predictive values of 95.5% and 98.7%, respectively. Most of the patients with a final positive diagnosis of BBD had specific IgG, IgM, and IgA antibodies by ELIFA. After antigen eradication, anti IgAp and/or P2 antibodies disappeared more rapidly than other precipitating systems. Conclusion : Identification by Co-IED of precipitating immune complexes IgAp and/or P2 significantly reinforces the intrinsic credibility of immunological diagnosis of BBD. Compared to these presumed disease-associated precipitating antibodies, detection and time course of specific IgM, IgA antibodies, provided no additional diagnostic value or prognostic arguments to judge disease activity after antigen eradication.
Published: 2003
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18. FTIR characterization of Candida species: a study on some reference strains and pathogenic C. albicans isolates from HIV+ patients

Author: P. Pina, Isabelle Beguinot, Dominique Aubert, J. E. Gómez, F. Witthuhn, Dominique Toubas, Ganesh D. Sockalingum, C. Sandt, P Allouch, Michel Manfait, and Jean-Michel Pinon
Subjects: Human immunodeficiency virus (HIV), C. albicans, Biology, medicine.disease_cause, biology.organism_classification, Corpus albicans, Yeast, Microbiology, Genotype, Pulsed-field gel electrophoresis, medicine, Candida albicans, Spectroscopy, Fluconazole, medicine.drug
Abstract: ATR–FTIR has been used together with principal components analysis to study some reference strains belonging to five different Candida species and 20 Candida albicans isolates from three HIV + patients under different fluconazole regimens. The five reference strains were easily differentiated by using first derivative spectra of the carbohydrate region comprising the spectral range 900–1200 cm −1 . For the C. albicans clinical isolates, classification obtained by Fourier-transform infrared (FTIR) spectroscopy was compared with data from the genotypic method, PFGE. Results show a good correlation between the two methods for one patient who presented a partially conserved immune system with no previous fluconazole treatment, where all C. albicans strains isolated were susceptible to this antifungal agent. Divergences in the two methods appear for the two immuno-compromised patients receiving long-term fluconazole treatment. It is very probable that such iterative antifungal treatment can cause strong alterations in the yeast cell wall membrane and that the mismatch of the two techniques highlights the complex situation of strain-level identification and differentiation of clinical isolates originating from patients under prolonged treatment.
Published: 2002
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19. Pneumocystis jirovecii Pneumonia in Patients with or without AIDS, France

Author: Emmanuel Canet, Denis Magne, Anne-Pauline Bellanger, Elie Azoulay, Sandrine Valade, Frédéric Dalle, Ariane Lafabrie, M. Leterrier, Samia Hamane, Solène Le Gal, Julie Bonhomme, Dominique Toubas, Christelle Pomares, Patricia Roux, Christophe Hennequin, Antoine Roux, Antoine Berry, Florence Gangneux-Robert, Anne Debourgogne, Isabelle Durand-Joly, Eric Maury, Denis Pons, Danièle Maubon, Droits International, Comparé et Européen/ Institut Louis Favoreu - Groupe d 'études et de recherches sur la justice constitutionnelle [DICE - UMR 7318] (DICE / ILF-GERJC), Droits International, Comparé et Européen (DICE), Aix Marseille Université (AMU)-Université de Pau et des Pays de l'Adour (UPPA)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Université de Pau et des Pays de l'Adour (UPPA)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut d'Études Politiques [IEP] - Aix-en-Provence, Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de réanimation médicale, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Centre Hospitalier Universitaire [Rennes], Institut de Biologie et Pathologie, CHU Grenoble, Stress, Immunité, Pathogènes (SIMPA), Université de Lorraine (UL), Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Laboratoire de parasitologie mycologie (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Centre hospitalier universitaire de Nantes (CHU Nantes), Matrice extracellulaire et dynamique cellulaire - UMR 7369 (MEDyC), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire de Reims (CHU Reims), Infections Parasitaires : Transmission, Physiopathologie et Thérapeutiques (IP-TPT), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Service de Santé des Armées, Groupe d'Acoustique de l'Université de Sherbrooke (GAUS), Département de génie mécanique [Sherbrooke] (UdeS), Université de Sherbrooke (UdeS)-Université de Sherbrooke (UdeS), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Centre de recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Service de Parasitologie - Mycologie [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Centre d'Immunologie et de Maladies Infectieuses (CIMI), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service des Soins Intensifs [CHU Saint-Antoine], Laboratoire de sciences cognitives et psycholinguistique (LSCP), Département d'Etudes Cognitives - ENS Paris (DEC), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Centre National de la Recherche Scientifique (CNRS), Hopital Saint Louis Paris, CHU Saint Louis [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris Diderot - Paris 7 (UPD7)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), Service de Santé des Armées-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Département de génie mécanique [Sherbrooke], Université de Sherbrooke [Sherbrooke]-Université de Sherbrooke [Sherbrooke], Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Saint-Antoine [APHP], École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS)-École des hautes études en sciences sociales (EHESS), Centre orthopédique médicochirurgical, Hôpital Foch [Suresnes], CHU, Dauphine Recherches en Management ( DRM ), Université Paris-Dauphine-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Magmas et Volcans ( LMV ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université Jean Monnet [Saint-Étienne] ( UJM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre Hospitalier Universitaire de Rennes, CHU Pontchaillou [Rennes], Laboratoire de parasitologie-mycologie, Service de Parasitologie-Mycologie [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy ( CHRU Nancy ), Relations Hôte-Environnement ( RHEM ), Université Henri Poincaré - Nancy 1 ( UHP ), Centre Hospitalier Régional Universitaire de Brest ( CHRU Brest ), CHU Dijon, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon ), Centre Hospitalier Regional Universitaire de Nantes, Centre Hospitalier Universitaire de Reims ( CHU Reims ), service de parasitologie mycologie CHU Jean Minjoz BESANCON, Hôpital Jean Minjoz, Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), CHU Caen, Centre Hospitalier Universitaire de Toulouse - CHU Toulouse (FRANCE), Centre Hospitalier Régional Universitaire [Lille] ( CHRU Lille ), CHU Saint-Antoine [APHP], Institut de Chimie et Biochimie Moléculaires et Supramoléculaires ( ICBMS ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique ( CNRS ), CHU Gabriel Montpied ( CHU ), CHU Clermont-Ferrand, Service de Réanimation Médicale [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Saint-Antoine [APHP], Dauphine Recherches en Management (DRM), Université Paris Dauphine-PSL-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Relations Hôte-Environnement (RHEM), Université Henri Poincaré - Nancy 1 (UHP), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Laboratoire Chrono-environnement - UFC (UMR 6249) (LCE), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), CHU Toulouse [Toulouse], Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique (CNRS), CHU Gabriel Montpied (CHU), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Reims Champagne-Ardenne (URCA)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), UL, SIMPA, and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)
Subjects: Male, Epidemiology, medicine.medical_treatment, lcsh:Medicine, Pneumocystis carinii, 0302 clinical medicine, Risk Factors, Odds Ratio, 030212 general & internal medicine, Prospective Studies, Prospective cohort study, immunosuppressive disorder, Pneumocystis jirovecii, 0303 health sciences, biology, Pneumonia, Pneumocystis, Middle Aged, 3. Good health, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, HIV/AIDS, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, France, prophylaxis, Microbiology (medical), Adult, medicine.medical_specialty, [SDV.IMM] Life Sciences [q-bio]/Immunology, mechanical ventilation, lcsh:Infectious and parasitic diseases, [ SDV.EE.SANT ] Life Sciences [q-bio]/Ecology, environment/Health, 03 medical and health sciences, respiratory infections, Acquired immunodeficiency syndrome (AIDS), Intensive care, Internal medicine, Immune suppression, medicine, Humans, cancer, pneumonia, lcsh:RC109-216, viruses, Mortality, Intensive care medicine, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Mechanical ventilation, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, Acquired Immunodeficiency Syndrome, AIDS-Related Opportunistic Infections, 030306 microbiology, business.industry, Research, lcsh:R, Odds ratio, biology.organism_classification, medicine.disease, Transplantation, Pneumonia, fungi, business, transplantation
Abstract: Immunosuppressed patients without AIDS had longer time to treatment and a higher rate of death than did patients with AIDS., Pneumocystis jirovecii pneumonia (PCP) in patients without AIDS is increasingly common. We conducted a prospective cohort study of consecutive patients with proven PCP; of 544 patients, 223 (41%) had AIDS (AIDS patients) and 321 (59%) had other immunosuppressive disorders (non-AIDS patients). Fewer AIDS than non-AIDS patients required intensive care or ventilation, and the rate of hospital deaths—17.4% overall—was significantly lower for AIDS versus non-AIDS patients (4% vs. 27%; p
Published: 2014
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20. Implementation of an FTIR spectral library of 486 filamentous fungi strains for rapid identification of molds

Author: W. Ablain, Ganesh D. Sockalingum, Antoine Hermet, A. Lecellier, Georges Barbier, Jérôme Mounier, Dominique Toubas, Vincent Gaydou, L. Castrec, and Michel Manfait
Subjects: Chromatography, Animal health, Databases, Factual, Microorganism, Food spoilage, Analytical chemistry, Fungi, Discriminant Analysis, Biology, Microbiology, Rapid identification, chemistry.chemical_compound, chemistry, Partial least squares regression, Spectroscopy, Fourier Transform Infrared, Food Microbiology, Fourier transform infrared spectroscopy, Least-Squares Analysis, Spectroscopy, Mycotoxin, Food Science
Abstract: Filamentous fungi may cause food and feed spoilage and produce harmful metabolites to human and animal health such as mycotoxins. Identification of fungi using conventional phenotypic methods is time-consuming and molecular methods are still quite expensive and require specific laboratory skills. In the last two decades, it has been shown that Fourier transform infrared (FTIR) spectroscopy was an efficient tool for microorganism identification. The aims of this study were to use a simple protocol for the identification of filamentous fungi using FTIR spectroscopy coupled with a partial least squares discriminant analysis (PLS-DA), to implement a procedure to validate the obtained results, and to assess the transferability of the method and database. FTIR spectra of 486 strains (43 genera and 140 species) were recorded. An IR spectral database built with 288 strains was used to identify 105 different strains. It was found that 99.17% and 92.3% of spectra derived from these strains were correctly assigned at the genus and species levels, respectively. The establishment of a score and a threshold permitted to validate 80.79% of the results obtained. A standardization function (SF) was also implemented and tested on FTIR data from another instrument on a different site and permitted to increase the percentage of well predicted spectra for this set from 72.15% to 89.13%. This study confirms the good performance of high throughput FTIR spectroscopy for fungal identification using a spectral library of molds of industrial relevance.
Published: 2013

21. Diversity of the Bacterial and Fungal Microflora from the Midgut and Cuticle of Phlebotomine Sand Flies Collected in North-Western Iran

Author: Mehdi Razzaghi Abyaneh, Denis Sereno, Thomas Guillard, Jérôme Depaquit, Dominique Toubas, Ahmad Baghaei, R Bakhtiari, Mohammad Akhoundi, R. Tolouei, Transmission Vectorielle et Épidémiosurveillance de Maladies Parasitaires - EA 4688 (VECPAR), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Reims Champagne-Ardenne (URCA), Institut Pasteur d'Iran, Réseau International des Instituts Pasteur (RIIP), Tehran University of Medical Sciences (TUMS), SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA), Centre Hospitalier Universitaire de Reims (CHU Reims), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Matrice extracellulaire et dynamique cellulaire - UMR 7369 (MEDyC), Université de Reims Champagne-Ardenne (URCA)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes - Faculté des sciences pharmaceutiques et biologiques (UR Pharmacie), Université de Rennes (UR), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 - Faculté des sciences pharmaceutiques et biologiques (UR1 Pharmacie), Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)
Subjects: Bacterial Diseases, Epidemiology, Plant Science, Disease Vectors, Iran, medicine.disease_cause, Klebsiella ozaenae, 0302 clinical medicine, Phlebotomus, Phylogeny, 0303 health sciences, Multidisciplinary, biology, Fungal Diseases, Enterobacter, Biodiversity, Bacterial Pathogens, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Medicine, Female, Veterinary Pathology, Research Article, Cuticle, Science, 030231 tropical medicine, Geotrichum, Mycology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Gram-Positive Bacteria, Microbiology, Infectious Disease Epidemiology, 03 medical and health sciences, Gram-Negative Bacteria, parasitic diseases, medicine, Animals, Biology, 030304 developmental biology, fungi, Fungi, Botany, Pathogenic bacteria, Midgut, Vectors and Hosts, biology.organism_classification, Leishmania, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Veterinary Science
Abstract: International audience; Background: Phlebotomine sand flies are the vectors of the leishmaniases, parasitic diseases caused by Leishmania spp. Little is known about the prevalence and diversity of sand fly microflora colonizing the midgut or the cuticle. Particularly, there is little information on the fungal diversity. This information is important for development of vector control strategies.Methodology/Principal Findings: Five sand fly species: Phlebotomus papatasi, P. sergenti, P. kandelakii, P. perfiliewi and P. halepensis were caught in Bileh Savar and Kaleybar in NorthWestern Iran that are located in endemic foci of visceral leishmaniasis. A total of 35 specimens were processed. Bacterial and fungal strains were identified by routine microbiological methods. We characterized 39 fungal isolates from the cuticle and/or the midgut. They belong to six different genera including Penicillium (17 isolates), Aspergillus (14), Acremonium (5), Fusarium (1), Geotrichum (1) and Candida (1). We identified 33 Gram-negative bacteria: Serratia marcescens (9 isolates), Enterobacter cloacae (6), Pseudomonas fluorescens (6), Klebsiella ozaenae (4), Acinetobacter sp. (3), Escherichia coli (3), Asaia sp. (1) and Pantoea sp. (1) as well as Gram-positive bacteria Bacillus subtilis (5) and Micrococcus luteus (5) in 10 isolates.Conclusion/Significance: Our study provides new data on the microbiotic diversity of field-collected sand flies and for the first time, evidence of the presence of Asaia sp. in sand flies. We have also found a link between physiological stages (unfed, fresh fed, semi gravid and gravid) of sand flies and number of bacteria that they carry. Interestingly Pantoea sp. and Klebsiella ozaenae have been isolated in Old World sand fly species. The presence of latter species on sand fly cuticle and in the female midgut suggests a role for this arthropod in dissemination of these pathogenic bacteria in endemic areas. Further experiments are required to clearly delineate the vectorial role (passive or active) of sand flies.
Published: 2012
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22. [Is Candida famata a pathogen?]

Author: Jérôme Depaquit and Dominique Toubas
Subjects: Male, Immunocompromised Host, media_common.quotation_subject, Candidemia, Humans, General Medicine, Art, Humanities, Genus Candida, media_common, Candida
Abstract: abc.2012.0736 Auteur(s) : Dominique Toubas1,2 dtoubas@chu-reims.fr, Jerome Depaquit1,3 1 Laboratoire de parasitologie mycologie, CHU de Reims, Universite Reims Champagne Ardenne, Hopital Maison Blanche, Reims, France 2 Unite MEDyC, FRE 3481 URCA CNRS, Faculte de medecine, Universite de Reims Champagne-Ardenne, Reims, France 3 EA 4688 - USC ANSES « Transmission vectorielle et epidemiosurveillance de maladies parasitaires (VECPAR)», Faculte de pharmacie, Universite de Reims Champagne-Ardenne, [...]
Published: 2012

23. Detection of specific immunoglobulin E in patients with toxoplasmosis

Author: J. M. Pinon, F. Foudrinier, A. Bonnin, G Mougeot, C. Marx, H. Lepan, Dominique Toubas, M. Villaume, and A Bonhomme
Subjects: Adult, Microbiology (medical), medicine.drug_class, Antibodies, Protozoan, Biology, Monoclonal antibody, Immunoglobulin E, Sensitivity and Specificity, Umbilical cord, Toxoplasmosis, Congenital, Uterine Cervical Diseases, Pregnancy, Placenta, medicine, Animals, Humans, Infectious Mononucleosis, Acquired Immunodeficiency Syndrome, Fetus, Infant, Newborn, Reproducibility of Results, medicine.disease, Virology, Toxoplasmosis, Immunoglobulin A, Agglutination (biology), medicine.anatomical_structure, Immunoglobulin M, Immunology, biology.protein, Female, Antibody, Toxoplasma, Research Article
Abstract: An immunocapture assay was developed to detect Toxoplasma gondii-specific immunoglobulin E (IgE) in sera from adults with acute acquired infection or reactivation and from babies with congenital toxoplasmosis. The components of this assay were monoclonal antibody to human IgE, samples from patients, and T. gondii tachyzoites treated with Formalin. When T. gondii-specific IgE antibodies were present, visually detectable agglutination occurred. Sera, umbilical cord blood, fetal blood, cerebrospinal fluid, and amniotic fluid were tested by this method. Specific IgE antibodies were detected in sera from 25 (86%) of 29 adults who developed specific IgG antibody during pregnancy or had specific IgA and IgM antibodies. Specific IgE was present early during infection, at the time that IgM antibodies were present, and slightly preceding the presence of specific IgA antibodies. In 23 patients tested serially, IgE antibodies never persisted for longer than 4 months. No nonspecific anti-T. gondii IgE was detected in sera from uninfected individuals. Maternal IgE antibodies did not cross the placenta. In sera of patients with congenital toxoplasmosis, specific IgE antibodies were found at birth, during the first year of life, and during immunologic recrudescence following discontinuation of pyrimethamine-sulfonamide therapy. The IgE immunocapture assay is simple to perform. It is especially useful for determining when T. gondii was acquired by recently infected pregnant women.
Published: 1990
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24. Epidemiological investigation and typing of Candida glabrata clinical isolates by FTIR spectroscopy

Author: Fabienne Bourgeade, Alain Leon, Michel Manfait, Dominique Toubas, Mohammed Essendoubi, Claire Lepouse, Jean-Michel Pinon, and Ganesh D. Sockalingum
Subjects: Microbiology (medical), Molecular Epidemiology, biology, Candida glabrata, Genotype, Strain typing, Candidiasis, biology.organism_classification, Microbiology, DNA Fingerprinting, RAPD, Random Amplified Polymorphic DNA Technique, Spectroscopy, Fourier Transform Infrared, Humans, Typing, Internal validation, Fourier transform infrared spectroscopy, Candida albicans, DNA, Fungal, Mycological Typing Techniques, Molecular Biology
Abstract: Candida glabrata has emerged as one of the leading agents of fungal infections and strain typing is essential for epidemiological investigation that is generally achieved by molecular techniques. In this work, we studied twenty-nine C. glabrata strains isolated from different patients, using a phenotypic approach based on Fourier Transform Infrared (FTIR) spectroscopy, which has been in a previous study successfully applied as a rapid typing method for Candida albicans. A two-step procedure was used for the analysis. The first step included sixteen strains for the internal validation phase, which aimed at finding the spectral windows that would provide the best differentiation between strains. In this phase, hierarchical cluster analysis (HCA) carried out using three spectral windows (900–1200, 1540–1800, 2800–3000 cm− 1) allowed to obtain the best classification, where each patient strains could be clustered together. A genotypic technique based on randomly amplified polymorphic DNA-analysis (RAPD) confirmed these results. In a second step, the external validation phase, thirteen other clinical strains of C. glabrata isolated from multiple sites in four ICU patients, were tested by FTIR spectroscopy. The analysis was based on the spectral regions previously found in the first step. HCA classification of the strains gave four groups, one group per patient. These results suggest that no inter-human transmission took place. This study shows the potential of FTIR approach for typing of C. glabrata with several advantages compared to other techniques. FTIR typing is fast, effective, and reagent free. Moreover, it is applicable to all micro-organisms and requires a small quantity of biomass.
Published: 2007

25. [Prevention of fungal infections related to the water supply in French hospitals: proposal for standardization of methods]

Author: Catherine, Kauffmann-Lacroix, Anne, Bousseau, Frédéric, Dalle, Marie-Pierre, Brenier-Pinchart, Laurence, Delhaes, Marie, Machouart, Martine, Gari-Toussaint, Annick, Datry, Claire, Lacroix, Christophe, Hennequin, Dominique, Toubas, and Odile, Morin
Subjects: Cross Infection, Water Supply, Pseudomonas aeruginosa, Colony Count, Microbial, Temperature, Humans, France, Mitosporic Fungi, Water Microbiology, Hospitals
Abstract: The aims of this study were to assess the risk of fungal infections related to the water supply in several hospitals and to clarify the appropriate methodology in order to standardize the technical conditions of the controls and develop guidelines. It was conducted in 10 university hospital centers across the country from February 2004 through March 2005.A preliminary study allowed us to optimize the mycological analysis. The study was conducted under the same conditions as for bacteriological controls: water filtration through a cellulose acetate membrane cultured on agar. Departments with the highest patient risk were selected, including hematology, organ transplantation, and burn units. We selected 98 sites and sampled both water and water-related surfaces at each: three one-liter water samples (the first flow, cold and hot water) and two or three surface samples (inside the tap, pommel of the shower and siphon). At each site, a form was filled to specify its location in the unit, any water treatment (chlorine or other), filtering, and temperature. Water from taps equipped with sterilized filtration was sampled without the filter.There was a significant difference (p=0.039) in the number of positive cultures between the three types of water sampled: hot water (50 degrees C) was colonized less often than first flow or cold water. Only 4% of the hot-water samples had positive cultures, compared to the 52% of the cold-water samples. Except in two hospitals with generalized contamination of the water pipes (one with Exophiala spp and the other with Fusarium spp), colonization was usually slight. Cold water was more colonized than hot water, but 79% of the samples yielded fewer than 5CFU/L. Dematiaceous hyphomycetes were isolated; Aspergillus spp were rare. The number of CFU in surface samples (that is, biofilms) was higher (mean=15 CFU per sample) but surfaces were positive less often than water (13% compared with 43% of all water samples). Sampling from siphons was productive more often than from taps (23%), but the molds isolated differed from those in the related water. Relations to bacterial flora and P. aeruginosa were also studied, together with the effects of chemical treatment.Current regulations require only bacteriological survey. The absence of knowledge about the threshold of contamination at which there is a risk of nosocomial invasive fungal infections makes it difficult to impose routine monitoring. Mycological surveys of water are required during hospital renovation, plumbing work, pipe maintenance and when air samples are negative during nosocomial infection investigations.
Published: 2007

26. FTIR spectroscopy in medical mycology: applications to the differentiation and typing of Candida

Author: Jean-Michel Pinon, Ganesh D. Sockalingum, Dominique Toubas, Mohammed Essendoubi, Isabelle Adt, Michel Manfait, Matrice extracellulaire et dynamique cellulaire - UMR 7369 (MEDyC), SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), Interactions cellulaires et moléculaires (ICM), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Bioingénierie et Dynamique Microbienne aux Interfaces Alimentaires (BIODYMIA), Isara-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Laboratoire de Parasitologie-Mycologie (LPM), IFR 53, Université de Reims Champagne-Ardenne (URCA)-Université de Reims Champagne-Ardenne (URCA)-CHU Maison Blanche-UPRES EA 2070, Université de Reims Champagne-Ardenne (URCA), Médicaments : Dynamique Intracellulaire et Architecture Nucléaire (MéDIAN), Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), and Université Claude Bernard Lyon 1 (UCBL)
Subjects: medicine.medical_specialty, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Medical mycology, Medical laboratory, Mycology, Aspergillosis, Biochemistry, Analytical Chemistry, 03 medical and health sciences, Species Specificity, Intensive care, Spectroscopy, Fourier Transform Infrared, [SDV.IDA]Life Sciences [q-bio]/Food engineering, medicine, Humans, Typing, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Mycological Typing Techniques, Intensive care medicine, ComputingMilieux_MISCELLANEOUS, Candida, 030304 developmental biology, 0303 health sciences, 030306 microbiology, business.industry, Candidiasis, Outbreak, medicine.disease, Corpus albicans, 3. Good health, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Identification (biology), business
Abstract: The incidence of fungal infections, in particular candidiasis and aspergillosis, has considerably increased during the last three decades. This is mainly due to advances in medical treatments and technologies. In high risk patients (e.g. in haematology or intensive care), the prognosis of invasive candidiasis is relatively poor. Therefore, a rapid and correct identification of the infectious agent is important for an efficient and prompt therapy. Most clinical laboratories rely on conventional identification methods that are based on morphological, physiological and nutritional characteristics. However, these have their limitations because they are time-consuming and not always very accurate. Moreover, molecular methods may be required to determine the genetic relationship between the infectious strains, for instance in Candida outbreaks. In addition, the latter methods require time, expensive consumables and highly trained staff to be performed adequately. In this study, we have applied the FTIR spectroscopic approach to different situations encountered in routine mycological diagnosis. We show the potentials of this phenotypic approach, used in parallel with routine identification methods, for the differentiation of 3 frequently encountered Candida species (C. albicans, C. glabrata and C. krusei) by using both suspensions and microcolonies. This approach, developed for an early discrimination, may help in the initial choice of antifungal treatment. Furthermore, we demonstrate the feasibility of the method for intraspecies comparison (typing) of 3 Candida species (C. albicans, C. glabrata and C. parapsilosis), particularly when an outbreak is suspected.
Published: 2007
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27. À propos d’un cas de sinusite à Schizophyllum commune : intérêt de la spectrométrie MALDI-TOF pour l’identification

Author: Alexandre Mzabi, Jean-Claude Merol, Dominique Zachar, Aurélie Lorot, Oriane Dudez, Emilie Dupuis, Jérôme Depaquit, Antoine Huguenin, Dominique Toubas, and Magali Fernandes
Subjects: Infectious Diseases
Abstract: Introduction Schizophyllum commune est un champignon filamenteux basidiomycete dont le pouvoir pathogene a ete recemment etabli. Les infections chez l’homme sont peu frequentes. Nous rapportons un cas de sinusite maxillaire a S. commune chez l’immunocompetent au cours de laquelle l’identification a pu etre realisee par spectrometrie de masse de type MALDI-TOF. Cas clinique Madame C., âgee de 76 ans, sans antecedents particuliers, se plaint depuis plusieurs mois d’une obstruction nasale gauche. Apres un bilan scannographique evoquant un polype de Killian du sinus maxillaire et de la fosse nasale gauche, l’ablation est realisee par voie endoscopique endonasale. L’examen anatomoclinique de la piece operatoire permet de conclure a une sinusite fongique allergique. L’examen mycologique met en evidence a l’examen direct, des filaments myceliens hyalins et permet d’isoler sur milieu de Sabouraud plusieurs colonies blanches laineuses poussant rapidement a 28 °C. En l’absence de fructifications l’identification ne peut etre realisee. L’analyse par spectrometrie MALDI-TOF (Microflex LT, Bruker Daltonics) d’une culture de 48 h en milieu Sabouraud liquide permet d’identifier S. commune (logscore > 2). Apres plus d’une semaine d’incubation, l’observation de la culture sur lame permet de visualiser des spicules et des clamp-connexions caracteristiques d’un basidiomycete. Le sequencage de la region D1/D2 permettra de confirmer l’identification. L’evolution clinique est rapidement favorable apres l’intervention, sans traitement antifongique. Discussion S. commune est un champignon cosmopolite, frequemment isole de matieres organiques en decomposition, en particulier du bois pourri. Il est principalement responsable d’infections bronchopulmonaires allergiques et de sinusites. Ces dernieres annees, la spectrometrie MALDI-TOF a revolutionne la demarche d’identification des bacteries et des levures. Son application a l’identification des champignons filamenteux est en plein essor et sera conditionnee par la qualite de la base de donnees spectrales. Cette technique presente de multiples avantages (rapidite, simplicite, cout) sur l’identification moleculaire. La prevalence des infections fongiques a basidiomycetes filamenteux est probablement sous-estimee en raison des difficultes d’identification morphologique. Une methode d’identification simple et rapide de ces champignons contribuera a mieux preciser leur role pathogene chez l’homme.
Published: 2015
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28. Rapid identification of Candida species by FT-IR microspectroscopy

Author: Michel Manfait, Dominique Toubas, Mohammed Essendoubi, Jean-Michel Pinon, Ganesh D. Sockalingum, and Mohamed Bouzaggou
Subjects: Microscopy, biology, Candida glabrata, Biophysics, Candidiasis, biology.organism_classification, Candida parapsilosis, Biochemistry, Yeast, Microbiology, Candida tropicalis, Rapid identification, Candida krusei, Spectroscopy, Fourier Transform Infrared, Humans, Candida albicans, Molecular Biology, Candida kefyr, Candida
Abstract: Due to the continuous increase of human candidiasis and the great diversity of yeasts of the Candida genera, it is indispensable to identify this yeast as early as possible. Early identification enables an early diagnostic and patient-adapted anti-fungal therapy, thus reducing morbidity and mortality related to these infections. In view of this, we have in this study investigated microcolonies using a method based on Fourier transform-infrared microspectroscopy (FTIRM) for a rapid and early identification of the most frequent Candida species encountered in human pathology. FTIR spectroscopy is a whole-cell "fingerprinting" method by which microorganisms can be identified. By exploiting the huge discriminating capacity of this technique, we identified 6 species (Candida albicans, Candida glabrata, Candida parapsilosis, Candida tropicalis, Candida krusei, and Candida kefyr) from a collection of 57 clinical strains of Candida, isolated from hospitalised patients. Data obtained on 10- to 18-h-old microcolonies were compared to cultures of 24 h. Our results clearly show the efficiency and the robustness of FTIR (micro)spectroscopy in identifying species with a classification rate of 100% for both microcolonies and 24-h cultures. FTIR microspectroscopy is thus a promising clinical approach, because compared to conventional and molecular techniques, it is time and money saving, has great identification and discriminating potentials, and is amenable to an automated high-throughput routine system.
Published: 2005

29. Analyse du mycélium par spectroscopie infrarouge à transformé de Fourier pour l’identification des champignons filamenteux

Author: Jérôme Mounier, S. Huet, Dominique Toubas, Michel Manfait, A. Lecellier, Georges Barbier, L. Castrec, Ganesh D. Sockalingum, W. Ablain, and Vincent Gaydou
Subjects: Infectious Diseases
Published: 2013
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30. Comparing FTIR and RAPD techniques in the typing of C. albicans in a clinical set-up

Author: Christophe L. Sandt, Maryse Jaussaud, Jean-Michel Pinon, Ganesh D. Sockalingum, Dominique Aubert, Dominique Toubas, Alain Leon, Claire Lepouse, Herve Lepan, and Michel Manfait
Subjects: biology, RAPD Techniques, Genotype, C. albicans, Typing, Fourier transform infrared spectroscopy, Candida albicans, biology.organism_classification, Corpus albicans, Microbiology, RAPD
Abstract: Candida albicans is an opportunistic pathogen, generally though to be of endogenous origin, with however reported outbreaks. Epidemilogy of C. albicans has been studied so far by genotypic methods mainly, including the classical RAPD analysis. Albeit powerful, genotypic techniques are expensive, time consuming and complex to implement. FTIR spectroscopy is simple, rapid, inexpensive and an increasingly used technique for the identification of microorganisms. As a phenotypic method, it provides rapid whole cells 'fingerprinting' using few consumables and can detect very subtle differences between strains of the same species. In this study, C. albicans strains isolated from 50 patients from six hospital units were collected and studied by FTIR spectroscopy and RAPD-PCR. Discrimination of strains was computed using classification algorithms on selected features of the spectral data. Results from 10 patients, for whom iterative sampling was possible, are presented and discussed. Emphasis was laid on the reproducibility of dat for strain-level identification. FTIR analysis shows that (a) the C. albicans spectra were different from one patient to another, (b) seven patients exhibit each a homogeneous group while three patients display each two groups of strains. RAPD-PCR and FTIR analyses correlate quite well showing that FTIR spectroscopy could be a potential epidemiological tool in the control of nosocomial fungal infections.
Published: 2002
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31. Cas groupés d’infections à Pneumocystis jirovecii en milieu hospitalier. Résultats de l’enquête nationale menée auprès d’Anofel

Author: Frédéric Dalle, Alain Bonnin, S. Le Gal, Michèle Virmaux, Céline Damiani, P Roux, G. Nevez, Anne Totet, A Abou-Bacar, Dominique Toubas, Ermanno Candolfi, and et les membres d’Anofel
Subjects: Infectious Diseases
Published: 2014
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32. Characterisation of Candida reference strains by ATR- FTIR

Author: Dominique Toubas, J. E. Gómez, Michel Manfait, F. Witthuhn, Ganesh D. Sockalingum, Jean-Michel Pinon, and Dominique Aubert
Subjects: Biochemistry, biology, Chemistry, medicine, Biochemical reactions, Fourier transform infrared spectroscopy, medicine.symptom, Candida albicans, biology.organism_classification, Corpus albicans, Yeast, Confusion
Abstract: Differentiation of Candida species resides on biochemical reactions and morphological features. However, phenotypic variations within some species such as Candida albicans has led to confusion in taxonomical and clinical classification of Candida species. Recent developments in analytical instrumentation and statistical methods, have enabled Fourier Transform Infrared Spectroscopy (FTIR) to emerge as a rapid, accurate and inexpensive method to characterize microorganisms [1–3]. The aim of present study is to characterize 5 reference strains of Candida species (C. albicans, C. parapsilosis, C. knisei, C. glabrata and C. tropicalis) using attenuated total-reflectance (ATR)- FTIR spectroscopy, i.e., without any preparation of the yeast colonies. These results could in turn be used to construct a data base for comparison of clinical strains.
Published: 1999
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33. Outbreak of pneumocystis pneumonia occurring in late post-transplantation period

Author: Alain Wynckel, Dominique Toubas, Natacha Noël, Olivier Toupance, and Philippe Rieu
Subjects: Male, Transplantation, Pediatrics, medicine.medical_specialty, business.industry, Period (gene), Outbreak, Pneumocystis carinii, Pneumocystis pneumonia, medicine.disease, Kidney Transplantation, Post transplant, Pneumocystis Infections, Nephrology, Humans, Medicine, Female, business
Published: 2011
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34. Les auteurs

Author: Françoise, Botterel, Muriel, Cornet, Marie-Laure, Dardé, Sandrine, Houzé, Laurence, Lachaud, Florent, Morio, Stéphane, Ranque, Marc, Thellier, Anne, Totet, Adéla, Angoulvant, Alexandre, Alanio, Bernard, Bouteille, Marie-Pierre, Brenier-Pinchart, Stéphane, Bretagne, Ermanno, Candolfi, Dominique, Chabasse, Jacques, Chandenier, Frédéric, Dalle, Anne, Debourgogne, Brigitte, Degeilh, Ludovic, de Gentile, Guillaume, Desoubeaux, Loïc, Favennec, Jean-Pierre, Gangneux, Claude, Guiguen, Arezki, Izri, Catherine, Kauffmann-Lacroix, Solène, Le Gal, Valérie, Letcher-Bru, Marie, Machouart, Pierre, Marty, Danièle, Maubon, Gilles, Nevez, Luc, Paris, Hervé, Pelloux, François, Peyron, Renaud, Piarroux, Stéphane, Picot, Marc, Pihet, Dominique, Richard-Lenoble, Florence, Robert-Gangneux, Marie-Hélène, Rodier, Dominique, Toubas, Isabelle, Villena, Chabasse, Dominique, Danis, Martin, Datry, Annick, and Richard-Lenoble, Dominique
Published: 2019
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35. Les auteurs

Author: Françoise, Botterel, Dominique, Chabasse, Muriel, Cornet, Marie-Laure, Dardé, Claude, Guiguen, Laurence, Lachaud, Florent, Morio, Stéphane, Ranque, Marc, Thellier, Adéla, Angoulvant, Alexandre, Alanio, Alain, Bonnin, Patrice, Bourée, Bernard, Bouteille, Marie-Pierre, Brenier-Pinchart, Stéphane, Bretagne, Ermanno, Candolfi, Jacques, Chandenier, Nelly, Contet-Audonneau, Frédéric, Dalle, Martin, Danis, Annick<ce:sup loc='post">†</ce:sup>, Datry, Anne, Debourgogne, Brigitte, Degeilh, Ludovic, de Gentile, Francis<ce:sup loc='post">†</ce:sup>, Derouin, Guillaume, Desoubeaux, Michel, Develoux, Chantal, Duhamel, Hai, Duong Thanh, Jean, Dupouy-Camet, Alexandra, Faussart, Loïc, Favennec, Bernard<ce:sup loc='post">†</ce:sup>, Fortier, Jean-Pierre, Gangneux, Martine, Gari-Toussaint, Alice, Gaudart, Françoise, Gay-Andrieu, Arezki, Izri, Catherine, Kauffmann-Lacroix, Yves, Le Fichoux, Solène, Le Gal, Anne-Sophie, Le Guern, Valérie, Letcher-Bru, Marie, Machouart, Jean-François, Magnaval, Pierre, Marty, Danièle, Maubon, Gilles, Pr Nevez, Michel, Miégeville, Muriel, Nicolas, Luc, Paris, Jean-François, Pays, Hervé, Pelloux, François, Peyron, Renaud, Piarroux, Stéphane, Picot, Marc, Pihet, Christian, Raccurt, Dominique, Richard-Lenoble, Florence, Robert-Gangneux, Marie-Hélène, Rodier, Claudine, Sarfati, Dominique, Toubas, Isabelle, Villena, Philippe, Vincendeau, Guiguen, Claude, and Botterel, Françoise
Published: 2016
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36. Active Surveillance Program to Increase Awareness on Invasive Fungal Diseases: the French RESSIF Network (2012 to 2018)

Author: Bretagne, Stéphane, Sitbon, Karine, Desnos-Ollivier, Marie, Garcia-Hermoso, Dea, Letscher-Bru, Valérie, Cassaing, Sophie, Millon, Laurence, Morio, Florent, Gangneux, Jean-Pierre, Hasseine, Lilia, Favennec, Loïc, Cateau, Estelle, Bailly, Eric, Moniot, Maxime, Bonhomme, Julie, Desbois-Nogard, Nicole, Chouaki, Taieb, Paugam, André, Bouteille, Bernard, Pihet, Marc, Dalle, Frédéric, Eloy, Odile, Sasso, Milène, Demar, Magalie, Mariani-Kurkdjian, Patricia, Robert, Vincent, Lortholary, Olivier, Dromer, Françoise, French Mycoses Study Group, The, Damiani, Céline, Dupont, Hervé, Maizel, Julien, Totet, Anne, Bouchara, Jean-Philippe, Bellanger, Anne Pauline, Berceanu, Ana, Navellou, Jean Christophe, Scherer, Emeline, Abboud, Philippe, Aznar, Christine, Blanchet, Denis, Djossou, Félix, Cayot, Sophie, Garrouste, Cyril, Lesens, Olivier, Moluçon, Cécile, Nourrisson, Céline, Poirier, Philippe, Bailly, Éloïse, Basmaciyan, Louise, Belaid, Bouhemad, Blot, Mathieu, Caillot, Denis, Charles, Pierre-Emmanuel, Quenot, Jean Pierre, Amazan, Emmanuelle, Baubion, Emilie, Cabie, André, Chabartier, Cyrille, Deligny, Christophe, Emal, Violaine, Flechelle, Olivier, Hatchuel, Yves, Le Govic, Yohann, Merle, Harold, Miossec, Charline, Turmel, Jean-Marie, Valentino, Ruddy, Durieux, Marie-Fleur, Turlure, Pascal, Mercier, Victor, Gari-Toussaint, Martine, Risso, Karine, Simon, Loïc, Bretonnière, Cedric, Boutoille, David, Gastinne, Thomas, Lakhal, Karim, Launay, Elise, Lepoivre, Thierry, Peterlin, Pierre, Rialland, Fanny, Le Pape, Patrice, Canoui, Etienne, Dahane, Naima, Kerneis, Solène, Angebault, Cécile, Bougnoux, Marie-Elisabethh, Guennouni, Nadia, Lanternier, Fanny, Neven, Bennedicte, Oualha, Mehdi, Scemla, Anne, Sitterlé, Emilie, Suarez, Felipe, Toubiana, Julie, Bonacorci, Stéphane, Alanio, Alexandre, Bergeron, Anne, Denis, Blandine, Gits-Muselli, Maud, Hamane, Samia, Touratier, Sophie, Chaumeil, Christine, Merabet, Lilia, Claudéon, Joelle, Curlier, Elodie, Galantine, Valérie, Gallois, Jean Claude, Markowicz, Samuel, Nicolas, Muriel, Musson, Pascal, Schepers, Kinda, Minoza, Alida, Kauffmann-Lacroix, Catherine, Guégan, Hélène, Costa, Damien, Dehais, Marion, Gargala, Gilles, Bajolet, Odile, Banisadr, Firouze, Cousson, Joel, Himberlin, Chantal, Huguenin, Antoine, Toubas, Dominique, Flori, Pierre, Mahinc, Caroline, Raberin, Hélène, Denis, Julie, Herbrecht, Raoul, Mertes, Paul-Michel, Meziani, Fehrat, Sabou, Marcela, Schneider, Francis, Bertozzi, Anne-Isabelle, Chauvin, Pamela, Charpentier, Elena, Cointault, Olivier, Cottrel, Claire, Delavigne, Karen, Faguer, Stanislas, Fillaux, Judith, Guemas, Emilie, Iriart, Xavier, Lelièvre, Lucie, Ruiz, Jean, Bastides, Frédéric, Chesnay, Adélaïde, Desoubeaux, Guillaume, Therby, Audrey, Chachaty, Elisabeth, Gachot, Bertrand, Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Software and Databasing, Mycologie moléculaire - Molecular Mycology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre National de Référence Mycoses Invasives et Antifongiques - National Reference Center Invasive Mycoses & Antifungals (CNRMA), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Dynamique des interactions hôte pathogène (DIHP), Université de Strasbourg (UNISTRA), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Nantes Université (Nantes Univ), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Centre Hospitalier Universitaire de Nice (CHU Nice), CHU Rouen, Normandie Université (NU), Centre hospitalier universitaire de Poitiers (CHU Poitiers), Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), CHU Clermont-Ferrand, CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), CHU de la Martinique [Fort de France], CHU Amiens-Picardie, Hôpital Cochin [AP-HP], CHU Limoges, SFR UA 4208 Interactions Cellulaires et Applications Thérapeutiques (ICAT), Université d'Angers (UA), Laboratoire de Parasitologie-Mycologie (CHU d'Angers), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Infections Respiratoires Fongiques (IRF), Université d'Angers (UA)-Université de Brest (UBO), Procédés Alimentaires et Microbiologiques [Dijon] (PAM), Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre Hospitalier de Versailles André Mignot (CHV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Hôpital Robert Debré Paris, Hôpital Robert Debré, Westerdijk Fungal Biodiversity Institute [Utrecht] (WI), Royal Netherlands Academy of Arts and Sciences (KNAW), Service des Maladies infectieuses et tropicales [CHU Necker], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Agents infectieux, résistance et chimiothérapie - UR UPJV 4294 (AGIR ), Université de Picardie Jules Verne (UPJV)-CHU Amiens-Picardie, Simplification des soins chez les patients complexes - UR UPJV 7518 (SSPC), Université de Picardie Jules Verne (UPJV), Mécanismes physiopathologiques et conséquences des calcifications vasculaires - UR UPJV 7517 (MP3CV), Laboratoire de Parasitologie-Mycologie [CHU Angers], Hôpital Bretonneau, Centre d’Etude des Pathologies Respiratoires (CEPR), UMR 1100 (CEPR), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), This work was supported by recurrent financial support from Santé Publique France and Institut Pasteur. The funders had no role in study design, data collection, analysis, interpretation of data, or the decision to submit the work for publication., We thank Didier Che (Direction des Maladies Infectieuses, Santé Publique France) for his continuous support and interest in invasive fungal infections and Etienne Sevin (EpiConcept, Paris, France) for his contribution in the development of the RESSIF website using the VOOZANOO platform. We are thankful for the technical help of Catherine Blanc, Anne Boullié, Cécile Gautier, Virginie Geolier, and Damien Hoinard (Institut Pasteur) for the characterization of the isolates received at the NRCMA., The French Mycoses Study Group includes collaborators who contributed to these data by their involvement in the management of patients, expertise in diagnostic tools, and/or characterization of fungal isolates. They are listed in alphabetical order of a city in France and for each center, in alphabetical order of the last names: in Amiens, Céline Damiani, Hervé Dupont, Julien Maizel, and Anne Totet, in Angers, Jean-Philippe Bouchara, in Besançon, Anne Pauline Bellanger, Ana Berceanu, Jean Christophe Navellou, and Emeline Scherer, in Cayenne, Philippe Abboud, Christine Aznar, Denis Blanchet, and Félix Djossou, in Clermont-Ferrand, Sophie Cayot, Cyril Garrouste, Olivier Lesens, Cécile Moluçon, Céline Nourrisson, and Philippe Poirier, in Dijon, Éloïse Bailly, Louise Basmaciyan, Bouhemad Belaid, Mathieu Blot, Denis Caillot, Pierre-Emmanuel Charles, and Jean Pierre Quenot, in Fort de France, Emmanuelle Amazan, Emilie Baubion, André Cabie, Cyrille Chabartier, Christophe Deligny, Violaine Emal, Olivier Flechelle, Yves Hatchuel, Yohann Le Govic, Harold Merle, Charline Miossec, Jean-Marie Turmel, and Ruddy Valentino, in Limoges, Marie-Fleur Durieux and Pascal Turlure, in Nîmes, Victor Mercier, in Nice, Martine Gari-Toussaint, Karine Risso, and Loïc Simon, in Nantes, Cedric Bretonnière, David Boutoille, Thomas Gastinne, Karim Lakhal, Elise Launay, Thierry Lepoivre, Pierre Peterlin, Fanny Rialland, and Patrice Le Pape, in Paris, in Hôpital Cochin, Etienne Canoui, Naima Dahane, and Solène Kerneis, in Hôpital Necker-Enfants Malades, Cécile Angebault, Marie-Elisabethh Bougnoux, Nadia Guennouni, Fanny Lanternier, Bennedicte Neven, Mehdi Oualha, Anne Scemla, Emilie Sitterlé, Felipe Suarez, and Julie Toubiana, in Hôpital Robert-Debré, Stéphane Bonacorci, in Hôpital Saint-Louis, Alexandre Alanio, Anne Bergeron, Blandine Denis, Maud Gits-Muselli, Samia Hamane, and Sophie Touratier, in hôpital des XV-XX, Christine Chaumeil and Lilia Merabet, in Pointe-à-Pitre, Joelle Claudéon, Elodie Curlier, Valérie Galantine, Jean Claude Gallois, Samuel Markowicz, Muriel Nicolas, Pascal Musson, and Kinda Schepers, in Poitiers, Alida Minoza and Catherine Kauffmann-Lacroix, in Rennes, Hélène Guégan, in Rouen, Damien Costa, Marion Dehais, and Gilles Gargala, in Reims, Odile Bajolet, Firouze Banisadr, Joel Cousson, Chantal Himberlin, Antoine Huguenin, and Dominique Toubas, in Saint Etienne, Pierre Flori, Caroline Mahinc, and Hélène Raberin, in Strabourg, Julie Denis, Raoul Herbrecht, Paul-Michel Mertes, Fehrat Meziani, Marcela Sabou, and Francis Schneider, in Toulouse, Anne-Isabelle Bertozzi, Pamela Chauvin, Elena Charpentier, Olivier Cointault, Claire Cottrel, Karen Delavigne, Stanislas Faguer, Judith Fillaux, Emilie Guemas, Xavier Iriart, Lucie Lelièvre, and Jean Ruiz, in Tours, Frédéric Bastides, Adélaïde Chesnay, and Guillaume Desoubeaux, in Versailles, Audrey Therby, and in Villejuif, Elisabeth Chachaty and Bertrand Gachot., and CLEMENT, Nathalie
Subjects: Antifungal Agents, pneumocytosis, invasive fungal infections, Pneumonia, Pneumocystis, [SDV]Life Sciences [q-bio], candidemia, Microbiology, [SDV.MP.MYC] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, mucormycosis, [SDV] Life Sciences [q-bio], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Virology, Humans, aspergillosis, epidemiology, Watchful Waiting, Fungemia, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Aged
Abstract: International audience; The French National Reference Center for Invasive Mycoses and Antifungals leads an active and sustained nationwide surveillance program on probable and proven invasive fungal diseases (IFDs) to determine their epidemiology in France. Between 2012 and 2018, a total of 10,886 IFDs were recorded. The incidence increased slightly over time (2.16 to 2.36/10,000 hospitalization days, P = 0.0562) in relation with an increase of fungemia incidence (1.03 to 1.19/10,000, P = 0.0023), while that of other IFDs remained stable. The proportion of ≥65-year-old patients increased from 38.4% to 45.3% (P < 0.0001). Yeast fungemia (n = 5,444) was due mainly to Candida albicans (55.6%) with stable proportions of species over time. Echinocandins became the main drug prescribed (46.7% to 61.8%), but global mortality rate remained unchanged (36.3% at 1 month). Pneumocystis jirovecii pneumonia (n = 2,106) was diagnosed mostly in HIV-negative patients (80.7%) with a significantly higher mortality than in HIV-positive patients (21.9% versus 5.4% at 1 month, P < 0.0001). Invasive aspergillosis (n = 1,661) and mucormycosis (n = 314) were diagnosed mostly in hematology (>60% of the cases) with a global mortality rate of 42.5% and 59.3%, respectively, at 3 months and significant changes in diagnosis procedure over time. More concurrent infections were also diagnosed over time (from 5.4% to 9.4% for mold IFDs, P = 0.0115). In conclusion, we observed an aging of patients with IFD with a significant increase in incidence only for yeast fungemia, a trend toward more concurrent infections, which raises diagnostic and therapeutic issues. Overall, global survival associated with IFDs has not improved despite updated guidelines and new diagnostic tools.IMPORTANCE The epidemiology of invasive fungal diseases (IFDs) is hard to delineate given the difficulties in ascertaining the diagnosis that is often based on the confrontation of clinical and microbiological criteria. The present report underlines the interest of active surveillance involving mycologists and clinicians to describe the global incidence and that of the main IFDs. Globally, although the incidence of Pneumocystis pneumonia, invasive aspergillosis, and mucormycosis remained stable over the study period (2012 to 2018), that of yeast fungemia increased slightly. We also show here that IFDs seem to affect older people more frequently. The most worrisome observation is the lack of improvement in the global survival rate associated with IFDs despite the increasing use of more sensitive diagnostic tools, the availability of new antifungal drugs very active in clinical trials, and a still low/marginal rate of acquired in vitro resistance in France. Therefore, other tracks of improvement should be investigated actively.
Published: 2022
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37. Evaluation of a new Histoplasma spp. reverse transcriptase quantitative PCR assay

Author: Alanio, Alexandre, Gits-Muselli, Maud, Lanternier, Fanny, Sturny-Leclère, Aude, Benazra, Marion, Hamane, Samia, Rodrigues, Anderson Messias, Garcia-Hermoso, Dea, Lortholary, Olivier, Dromer, Françoise, Bretagne, Stéphane, French Mycoses Study Group, The, Mycologie moléculaire - Molecular Mycology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris Cité (UPCité), Centre National de Référence Mycoses Invasives et Antifongiques - National Reference Center Invasive Mycoses & Antifungals (CNRMA), Institut Pasteur [Paris] (IP), Centre d'infectiologie Necker-Pasteur [CHU Necker], Institut Pasteur [Paris] (IP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Federal University of Sao Paulo (Unifesp), The authors report no funding for this study., The French mycoses study group is composed of: Marine Gosset Woimant, Geneviève blanchard (Centre Hospitaler de Pontoise, Pontoise), Souad Silhadi (Centre Hospitalier de Chambéry, Chambéry), Nicolas Vignier, Aurelia Pitsch, Kaoutar Jidar (Centre Hospitalier de Melun, Melun), Nicolas Traversier (Centre Hospitalier Felix Guyon, La Réunion), Didier Poisson, Claire Lecointre (Centre Hospitalier Régional d'Orléans, Orléans), Françoise Foulet, Françoise Botterel, Nawel Ait Ammar, Amsellem (CHU Henri Mondor, Créteil), Frederic Gabriel (CHU de Bordeau-GH Pellegrin, Bordeaux), Philipe Poirier (CHU de Clermont Ferrand, Clermont-Ferrand), Marjorie Cornu, Severine Loridant (CHU de Lille, Lille), Florent Morio, David Boutoille, Fakhri Jeddi (CHU de Nantes, Nantes), Lilia Hasseine (CHU de Nice, Nice), Rachida Ouissa (CHU de Pointe à Pitre, Guadeloupe), Dominique Toubas (CHU de Reims, Reims), Eric Bailly, Guillaume Désoubeaux (CHU deTours), Emily Ronez (Hôpital Ambroise Paré, Boulogne), Guillaume Foulon, Sebastien Lefrançois (Hôpital Américain, Neuilly), Christine Bonnal (Hôpital Bichat, Paris), André Paugam, Maxime Dougados (Hôpital Cochin, Paris), Marine Desroches (Hôpital d'Instruction des Armées Percy, Clamart), Hélène Barazzutti, Nicolas Paleiron (Hôpital d'Instruction des Armées, Toulon), Meja rabodonirina (Hôpital de la Croix Rousse, Lyon), Emilie Catherinot, Emilie Cardot-Martin, Chrisian Hiesse, Hélène Salvator (Hôpital Foch, Suresnes), Claire Aguilar, Anne Gigandon, Thomas de Montpreville (Hôpital Marie Lannelongue, Le Plessis-Robinson), Marie-Elisabeth Bougnoux, Emilie Sitterlé (Hôpital Necker Enfants Malades, Paris), Arnaud Fekkar, Sébastien Imbert, Alexandre Bleibtreu (Hôpital Pité Salpétrière), Yaye Senghor (Hôpital Saint Joseph, Paris), Blandine Denis, Jean-Michel Molina, Geoffroy Liegeon, Anne-Lise Munnier, Marion Malphettes (Hôpital Saint Louis, Paris), Julie Denis (Hôpitaux Civils de Strasbourg, Strasbourg), Alain Berlioz-Arthaud (Institut Pasteur de Bangui, Bangui, République centrafricaine), Franciska Lange (Centre Hospitalier Sallanches-Chamonix, Sallanches), Myriam Chiaruzzi, Loic Epelboin (Centre Hospitalier Andrée Rosemon, Cayenne, Guyane Française), The authors are grateful to the technical staff of the mycology-parasitology laboratory at Hospital Saint Louis, Paris, France for handling specimens and performing this assay routinely, in particular, Elodie Da Silva, Thierry Pautet, Dieyenaba Siby-Diakite, Sarah seng and Julie Bui, who performed optimization experiments., Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université de Paris (UP), Institut Pasteur [Paris], and Institut Pasteur [Paris]-CHU Necker - Enfants Malades [AP-HP]
Subjects: Whole blood, qPCR, quantification cycle, whole nucleic acids, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, reverse transcriptase, bacterial infections and mycoses, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Histoplasmosis, fungal load, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology
Abstract: International audience; Laboratory diagnosis of histoplasmosis is based on various methods including microscopy, culture, antigen and DNA detection of Histoplasma capsulatum var. capsulatum (Hcc) or H. capsulatum var. duboisii (Hcd). To improve sensitivity of existing quantitative PCR assays, we developed a new reverse transcriptase qPCR (RTqPCR) assay allowing amplification of whole nucleic acids of Histoplasma spp.. and validated on suspected cases.The limit of detection was 20 copies and the specificity against 114 fungal isolates/species was restricted to Histoplasma spp.. Whole nucleic acids of 1,319 prospectively collected consecutive samples from 907 patients suspected of histoplasmosis were tested routinely between May 2015 and May 2019 in parallel with standard diagnostic procedures performed in parallel. 44 had proven histoplasmosis due to Hcc (n=40) or Hcd (n=4) infections. RTqPCR was positive in 43/44 patients (97.7% sensitivity), in at least one specimen. Nine out of 863 cases (99% specificity) were RTqPCR positive and therefore classified as possible cases. RTqPCR was positive in 13/30 (43.3%) blood tested in proven cases. A positive RTqPCR in blood was significantly associated with Hcc progressive disseminated histoplasmosis with a positive RTqPCR in 92.3% of the immunocompromised patients with disseminated disease. This new Histoplasma RTqPCR assay enabling amplification of hcc and hcd is highly sensitive and allows the diagnosis of histoplasmosis advantageously from blood and BAL.
Published: 2021
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38. Antifungal susceptibility testing practices in mycology laboratories in France, 2018

Author: E. Mazars, Jean-Pierre Gangneux, Isabelle Accoceberry, Valérie Letscher-Bru, B. Bouteille, O. Augereau, V. Risco-Castillo, Sophie Brun, Jean-Philippe Bouchara, Arnaud Fekkar, Jacques Guillot, E. Bailly, André Paugam, Y. Le Govic, R.-A. Lavergne, Taieb Chouaki, C. Angebault, Emilie Frealle, Damien Costa, Adela Angoulvant, J. Dorin, Florence Persat, P. Bourdeau, Eric Dannaoui, Céline Nourrisson, Julie Bonhomme, S. Larréché, K. Brunet, Françoise Foulet, L. Hasseine, Anne-Pauline Bellanger, Y. Senghor, Stéphane Ranque, A.-M. Camin-Ravenne, Marie Machouart, Juliette Guitard, N. Desbois, F. Bert, Françoise Botterel, Marie-Elisabeth Bougnoux, Laurence Lachaud, S. Le Gal, Sophie Cassaing, Milène Sasso, Marc Sautour, Boualem Sendid, A. Fiacre, Antoine Huguenin, C. Bonnal, M. Cornet, Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Service de parasitologie [Mondor], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Hôpital universitaire Bichat, CHU Bordeaux [Bordeaux], Dynamic Microbiology - EA 7380 (DYNAMIC), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est (UPE)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Service de Parasitologie-Mycologie, AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre Hospitalier Régional d'Orléans (CHRO), Hôpital Universitaire de Tours, Hôpital Beaujon, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP), Université d'Angers (UA), Laboratoire de Parasitologie-Mycologie (CHU d'Angers), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Biologie et Pathogénicité fongiques - Fungal Biology and Pathogenicity (BPF), Institut Pasteur [Paris] (IP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), CHU Limoges, Hôpital Avicenne [AP-HP], Centre hospitalier universitaire de Poitiers (CHU Poitiers), Pharmacologie des anti-infectieux (PHAR), Université de Poitiers-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier de Bigorre [Tarbes], Service de Parasitologie et Mycologie [CHU Toulouse], Institut Fédératif de Biologie (IFB), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Pôle Biologie [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Université de Picardie Jules Verne (UPJV), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications Grenoble - UMR 5525 (TIMC-IMAG), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), CHU Rouen, Normandie Université (NU), Service de Maladies Infectieuses et Tropicales [Fort-de-France, Martinique], CHU Fort de France-CHU de la Martinique [Fort de France]-Hôpital Pierre Zobda-Quitman [CHU de la Martinique], CHU de la Martinique [Fort de France], Service de Parasitologie-Mycologie [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de Parasitologie-Mycologie [CHRU LIlle], Institut de Microbiologie [CHRU Lille], Pôle de Biologie Pathologie Génétique [CHU Lille], Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Pôle de Biologie Pathologie Génétique [CHU Lille], Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Ecologie du parasitisme - EA 3609 (ECOPA), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Université de Lille, Droit et Santé, Service de Parasitologie-Mycologie [Rennes], Université de Rennes (UR)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes], CHU Saint-Antoine [AP-HP], Centre Hospitalier Universitaire de Nice (CHU Nice), Epidémiosurveillance de protozooses à transmission alimentaire et vectorielle (ESCAPE), Université de Reims Champagne-Ardenne (URCA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre Hospitalier Universitaire de Reims (CHU Reims), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Hôpital d'Instruction des Armées Begin, Service de Santé des Armées, Centre hospitalier universitaire de Nantes (CHU Nantes), Laboratoire de Parasitologie et Mycologiede [CHRU Brest], Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Les Hôpitaux Universitaires de Strasbourg (HUS), CHU Valenciennes, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Hôpital Cochin [AP-HP], Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Laboratoire de Biomécanique et Biomatériaux Ostéo-Articulaires (B2OA), Université Paris Diderot - Paris 7 (UPD7), Laboratoire de parasitologie mycologie (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Institute for Translational Research in Inflammation - U 1286 (INFINITE (Ex-Liric)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Hôpital Henri Mondor, Unité de Parasitologie-Mycologie [CHU HEGP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), We are very grateful to Dominique Toubas for all the help she provided for the preparation and smooth running of our meeting. We also thank all our colleagues who participate to the meeting and discuss the results of the present survey., Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Research Group Dynamyc , EA 7380, EnvA (DynamYc), École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est (UPE), Institut Pasteur [Paris]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Centre Hospitalier de Bigorre (Tarbes), Service de Parasitologie et Mycologie, CHU Toulouse [Toulouse]-Institut Fédératif de Biologie (IFB) - Hôpital Purpan, Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse], Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP*, TIMC-IMAG, Grenoble, France, EA3609, Laboratoire ECOPA, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes], Service de Parasitologie - Mycologie [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525 (TIMC ), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut Fédératif de Biologie (IFB) - Hôpital Purpan, CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Rouen Normandie (UNIROUEN), and Normandie Université (NU)-Normandie Université (NU)-Université de Reims Champagne-Ardenne (URCA)
Subjects: Antifungal, Quality Control, medicine.medical_specialty, Susceptibility testing, Laboratory Proficiency Testing, Antifungal Agents, medicine.drug_class, Laboratory practice, Microbial Sensitivity Tests, Mycology, History, 21st Century, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Disk Diffusion Antimicrobial Tests, Drug Resistance, Fungal, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Surveys and Questionnaires, medicine, Humans, Medical physics, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Antifungal susceptibility testing, Etest, 0303 health sciences, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 030306 microbiology, Professional Practice, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Infectious Diseases, Geography, Mic values, MIC value interpretation, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, France, Laboratories
Abstract: International audience; A survey of mycology laboratories for antifungal susceptibility testing (AFST) was undertaken in France in 2018, to better understand the difference in practices between the participating centers and to identify the difficulties they may encounter as well as eventual gaps with published standards and guidelines. The survey captured information from 45 mycology laboratories in France on how they perform AFST (number of strains tested, preferred method, technical and quality aspects, interpretation of the MIC values, reading and interpretation difficulties). Results indicated that 86% of respondents used Etest as AFST method, with a combination of one to seven antifungal agents tested. Most of the participating laboratories used similar technical parameters to perform their AFST method and a large majority used, as recommended, internal and external quality assessments. Almost all the participating mycology laboratories (98%) reported difficulties to interpret the MIC values, especially when no clinical breakpoints are available. The survey highlighted that the current AFST practices in France need homogenization, particularly for MIC reading and interpretation.
Published: 2020
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39. Mortality from malaria in France, 2005 to 2014

Author: Kendjo, Eric, Thellier, Marc, Noël, Harold, Jauréguiberry, Stéphane, Septfons, Alexandra, Mouri, Oussama, Gay, Frédérick, Tantaoui, Ilhame, Caumes, Eric, Houzé, Sandrine, Piarroux, Renaud, Musset, Lise, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de Référence du Paludisme [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Santé publique France Guyane, Santé publique France - French National Public Health Agency [Saint-Maurice, France], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Mère et enfant en milieu tropical : pathogènes, système de santé et transition épidémiologique (MERIT - UMR_D 216), Institut de Recherche pour le Développement (IRD)-Université de Paris (UP), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Laboratoire de Parasitologie [Cayenne, Guyane française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre National de Référence du Paludisme [Cayenne, Guyane française] (CNR), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Mère et enfant en milieu tropical : pathogènes, système de santé et transition épidémiologique (MERIT - UMR_D 261), Institut de Recherche pour le Développement (IRD)-Université Paris Cité (UPCité), Réseau International des Instituts Pasteur (RIIP), Centre National de Référence du Paludisme [Cayenne, Guyane française] (CNR - laboratoire associé), Centre Collaborateur OMS pour la surveillance de la résistance aux antipaludiques [Cayenne, Guyane française] (CCOMS), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), The French imported malaria Study group: C. Strady (CHU Reims), Caroline Lohmann (CH du Moenchsberg, Mulhouse), Celine Arriuberge (CH Trousseau, Paris), Emmanuel Grimprel (CH Trousseau, Paris), Jean-Marie Delarbre (CH du Moenchsberg, Mulhouse), Michel Thibault (CH René Dubos, Pontoise), Mohamadou Niang (CHR Orléans), A. Barrans (CH Sète), A. Martin (CH Périgueux), A. Spiegel (DESP Nord), A. Valentin (CHU Toulouse), A.S. Le Guern (Institut Pasteur, Paris), Adela Angoulvant (CHU Kremlin-Bicêtre, Paris), Adeline Dubois (CH Alès), Adrien Genin (CH Pays d'Aix), Agathe Lebuisson (CHU Cochin), Agnes Riche (CH Angoulême), Agnès Durand (Institut Pasteur, Paris), Agnès Fromont (CH Auxerre), Ahmed Aboubacar (CHU de Strasbourg), Ahmed Fateh Ousser (CH Louis Mourier), Aida Taieb (INTS, Paris), Alain Domergue (CH Alès - Cévennes), Alain Gravet (CH du Moenchsberg, Mulhouse), Alain Lecoustumier (CH de Cahors), Albert Faye (CHU Robert Debré, Paris), Alexander Pfaff (CHU de Strasbourg), Alexandra Faussart (CHU Bichat-Claude Bernard, Paris), Alexandre Chlilek (CHU Nîmes), Alice Borel (CHU Amiens), Alice Pérignon (CHU Pitié-Salpêtrière, Paris), Ana Mendes-Mreira (CH La Rochelle), André Gardrat (CH d’Evreux), Ange Kissila (CH Provins), Angèle LI (CH Creil (Laënnec)), Anne Cady (CH Bretagne Atlantique), Anne Debourgogne (CHU de Nancy), Anne Delaval (CHI Robert Ballanger, Aulnay-sous-Bois), Anne Goepp (CHI Villeneuve St Georges), Anne Marfaing-Koka (Hôpital Antoine-Béclère), Anne Pauline Bellanger (CHU Besançon, Jean Minjoz), Anne Vincenot-Blouin (CH Meaux), Anne-Marie Teychene-Coutet (CH Bondy-Jean Verdier), Anne-Sophie Deleplancque (CH Lille), Annick Verhaeghe (CH de Dunkerque), Annie Motard-Picheloup (CHI Fréjus St Raphaël), Antoine Berry (CHU Toulouse), Antoine Huguenin (CHU Reims), Arnaud Bouvet (CH Bretagne Atlantique), Audrey Merens (HIA Begin), Aurelie Roide (CHU Lariboisière, Paris), Aurore Sanson (CH Jacques Cœur, Bourges), Aurélie Fricot (CHU Necker), Aurélie Guigon (CHR Orléans), Benfatallah Dhouha (CHU Necker, Paris), Benjamin Wyplosz (CHU Kremlin-Bicêtre, Paris), Benoît Henri (INTS, Paris), Bernadette Buret (CH Niort), Bernadette Cuisenier (CHU Dijon), Bernadette Worms (CHU Dijon), Bernard Faugère (CH Timone, Marseille), Biligui Sylvestre (CHU Pitié-Salpêtrière, Paris), Boualem Sendid (CH Lille), Bruno Megarbane (CHU Lariboisière, Paris), Bruno Pradines (Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France, Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France, IHU Méditerranée Infection, 13005 Marseille, France, Centre National de Référence du Paludisme, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France), Béatrice Quinet (CH Trousseau, Paris), C. Braidy (CH du Sud Seine et Marne), C. Farrugia (CH de Dourdan), C. Finot (CH de Dreux), Camille Roussel (INTS, Paris), Camille Runel-Belliard (CHU de Bordeaux), Caren Brump (CHU Lariboisière, Paris), Carine Dokoula (CH Jacques Cœur, Bourges), Carmina Camal (CH Louis Mourier), Carole Mackosso (CHU Bichat-Claude Bernard, Paris), Carole Poupon (CH de Gonesse), Caroline Garandeau (CH Angoulême), Catherine Benoit (CH du Sud Seine et Marne), Catherine Branger (CH Louis Mourier), Catherine Brehant (CH La Rochelle), Catherine Desideri-Vaillant (HIA Clermont Tonnerre, Brest), Catherine Kauffmann Lacroix (CH Poitiers), Catherine Lafaurie (CH d’Epernay), Cecile Hombrouck-Alet (CH Blois), Cecile Ramade (Lyon-Croix-Rousse), Celine Damiani (CHU Amiens), Celine Gourmel (CHU Lariboisière, Paris), Chantal Duhamel (CHU Côte de Nacre), Chantal Garabedian (CH Pays d'Aix), Chralotte Chambrion (INTS, Paris), Christelle Morelle (CHU Montpellier), Christelle Pomares Estran (CH Universitaire de Nice), Christelle Prince (CH de Cayenne Andrée Rosemon), Christian Durand (CH Provins), Christian Fulleda (CHU Lariboisière, Paris), Christian Raccurt (CHU Amiens), Christine Chaigneau (GHPSO, Creil), Christine Chemla (CHRU de Reims), Christine Van batten (CH Laënnec, Creil), Christophe Martinaud (HIA Percy, Clamart), Christophe Rapp (HIA Begin), Claire Augé (CHU Bichat-Claude Bernard, Paris), Claire Malbrunot (CH Corbeil Essonne), Claudine Febvre (CH de Montbéliard), Claudine Sarfati (Hôpital Saint-Louis, Paris), Coralie l'Ollivier (CH de la Timone, Marseille), Corinne Huet (Hôpital Louis-Pasteur, Cherbourg-Octeville), Cournac Jean-Marie (HIA Percy, Clamart), Cynthia Pianetti (CH Gabriel Martin, La Réunion), Cécile Angebault (CHU Necker, Paris), Cécile Ficko (HIA Begin), Cécile Garnaud (CHU de Grenoble), Cécile Leprince (CHI Robert Ballanger, Aulnay-sous-Bois), Céliat Merat (CHU Nantes), Céline Dard (CHU de Grenoble), Céline Nourrisson (CHRU Clermont-Ferrand), Céline Tournus (Hôpital Delafontaine, Saint-Denis), Daniel Azjenberg (CHU Dupuytren, Limoges), Daniel Camus (CH Lille), Daniel Lusina (CHI Robert Ballanger, Aulnay-sous-Bois), Daniel Parzy (IMTSSA, Marseille), Denis Pons (CHRU Clermont-Ferrand), Denis Filisetti (CHU Strasbourg), Denis Malvy (CHU de Bordeaux), Didier Basset (CHU Montpellier), Didier Jan (CH Laval), Didier Poisson (CHR Orléans), Didier Raffenot (CH Chambéry), Dieudonné Bemba (CH Bondy-Jean Verdier), Dominique Maubon (CHU de Grenoble), Dominique Mazier (CHU Pitié-Salpêtrière, Paris), Dominique Popjora (CH Trousseau, Paris), Dominique Toubas (CHRU de Reims), Dorothée Quino (CHRU Morvan, Brest), Alioune Ndour (INTS, Paris), Ducout Louis (CH de la Côte Basque), Duong Thanh Hai (CHRU Bretonneau), E. Boyer (CH Le Mans), Edgar Ombandza (CH Provins), Edith Mazars (CH de Valenciennes), Elisabeth Buffet (CH de Epernay), Elodie Collin (CHI Robert Ballanger, Aulnay-sous-Bois), Elodie Meynet (CH Annecy Genevois), Emeline Scherer (CHU Besançon, Jean Minjoz), Emilie Fréalle (CH Lille), Emilie Klein (CHU Lariboisière, Paris), Emilie Sitterle (CHU Necker, Paris), Emily Ronez (CHU Lariboisière, Paris), Emmanuel Dutoit (CH Lille), Enrique Casalino (CHU Bichat-Claude Bernard, Paris), Eric Caumes (CHU Pitié-Salpêtrière, Paris), Eric Dannaoui (Hôpital Européen Georges Pompidou, Paris), Eric Gardien (CH de Draguignan, Bordeaux), Eric Kendjo (CHU Pitié-Salpêtrière, Paris),Eric d'Ortenzio (CHU Bichat-Claude Bernard, Paris), Ermanno Candolfi (CHU de Strasbourg), Estelle Perraud-Cateau (CH Poitiers), Eterne Twizeyimana (CH du Cotentin), F. Roblot (CH Poitiers), Fabienne Pateyron (CH Provins), Fabrice Bruneel (CH de Versailles, André Mignot), Fabrice Legros (CNR du paludisme), Fabrice Simon (HIA Laveran), Fakhri Jeddi (CHU Nantes), Farida M. Benaoudia (CH Troyes), Faïzi Ajana (CH Tourcoing), Felix Djossou (CH de Cayenne Andrée Rosemon), Firouze Banisadr (CHRU de Reims), Florent Morio (CHU Nantes), Francis Derouin (Hôpital Saint-Louis, Paris), Francois Moussel (CH François-Quesnay, Mantes-La-Jolie), Francoise Foulet (CHU Henri Mondor), François Peyron (Lyon-Croix-Rousse), Françoise Benoit-Vical (CHU Toulouse), Françoise Botterel (CHU Henri Mondor), Françoise Gayandrieu (CHU Nantes), Françoise Schmitt (CH du Moenchsberg, Mulhouse), Frederic Ariey (CHU Cochin, Paris), Frédéric Grenouillet (CHU Jean Minjoz, Besançon), Frédéric Sorge (CHU Necker), Frédérique Gay (CHU Pitié-Salpêtrière, Paris), Frédérique Foudrinier (CHRU de Reims), G. Courrouble (CH Blois), G. Gallou (CH de Falaise), G. Julienne (CH Belfort), G. Philippon (Centre Médical CMETE, Paris), Gauthier Pean-de-Ponfilly (CHU Lariboisière, Paris), Geneviève Grise (CH d’Elbeuf), Ghania Belkacem Belkadi (CH Tenon), Gilbert Lorre (CHD La Roche-sur-Yon), Gilles Gargala (CHU Rouen), Gilles Nevez (CHRU Morvan, Brest), Gisele Dewulf (CH de Valenciennes), Guillaume Désoubeaux (CHRU Bretonneau, Tours), Guillaume Escriou (CHU Bichat-Claude Bernard, Paris), Guillaume Le Loup (CH Tenon, Paris), Guillaume Menard (HIA Saint-Anne, Toulon), Guy Carroger (CH Jacques Cœur, Bourges), Guy Galeazzi (CH Louis Mourier), Gwénaël le Moal (CH Poitiers), Hana Talabani (CHU Cochin, Paris), Hanene Abid (CHU Necker, Paris), Helene Broutier (CHI Robert Ballanger, Aulnay-sous-Bois), Herve Pelloux (CHU de Grenoble), Houria Ichou (CH Louis Mourier), Hugo Laurent (CHU Lariboisière, Paris), Hélène Broutier (CH Meaux), Hélène Lapillonne (CH Trousseau, Paris), Hélène Yera (CHU Cochin, Paris), Hélène savini (HIA Laveran), I. Hermes (CH Saint-Malo), Ilhame Tantaoui (CHU Pitié-Salpêtrière, Paris), Isabelle Poilane (CH Bondy-Jean Verdier), Isabelle Amouroux (Hôpital Antoine-Béclère), Isabelle Mazurier (Hôpitaux Civils de Colmar), Isabelle Salimbeni (CH de Cannes), Isabelle Tawa (Centre Médical CMETE, Paris), J Cuziat (CH Saint-Nazaire), J. Bernard Poux (CH de Val d'Ariège - Foix), J. Heurtet (CH Beauvais), J. Rome (CH de Fougères), J. Truchot (CHU Lariboisière, Paris), J.M. Segalin (CHR Orleans), Jacques Gaillat (CH Annecy Genevois), Jacques Le bras (CHU Bichat-Claude Bernard, Paris), Jacques Thevenot (Centre Médical CMETE, Paris), Jacques Vaucel (CH Saint-Brieuc), Jean Dunand (Hôpital Ambroise Paré), Jean Benjamin Murat (CH de Roanne), Jean Marie Trapateau (CH Angoulême), Jean Yves Peltier (CHI Poissy-st-germain), Jean-Etienne Pilo (HIA Begin), Jean-Francois Magnaval (CHU Toulouse), Jean-François Faucher (CHU Jean Minjoz, Limoge), Jean-Paul Boutin (DESP Sud), Jean-Paul Couaillac (CH de Cahors), Jean-Philippe Breux (CH Cholet), Jean-Pierre Hurst (CH Jacques Monod, Le Havre), Jean-Yves Siriez (CHU Robert Debré, Paris), Jean-philippe Bouchara (CHU Angers), Jerome Clain (CHU Bichat-Claude Bernard, Paris), Jerome Naudin (CHU Robert Debré, Paris), Jordan Leroy (CH Lille), Josette Jehan (CH du Cotentin), Joudia Najid (CHU Pitié-Salpêtrière, Paris), Judith Gorlicki (CHU Lariboisière, Paris), Julie Bonhomme (CHU Côte de Nacre), Julie Brunet (CHU de Strasbourg), Jérome Guinard (CHR Orleans), Karima Cheikh (CHU Henri Mondor), L. Pougnet (HIA Clermont Tonnerre, Brest), Lauren Pull (CHU Robert Debré, Paris), Laurence Millon (CHU Jean Minjoz, Besançon), Laurence Campergue-Mayer (CH Avignon), Laurence Estepa (CH Blois), Laurence Lachaud (CHU Nîmes), Laurent Aaron (CH Jacques Cœur, Bourges), Laurent Bret (CHR Orléans), Laurent Guillaume (CH Blois), Liliane Ciceron (CHU Pitié-Salpêtrière, Paris), Lionnel Bertaux (CNR du paludisme), Lise Musset (Institut Pasteur, Guyane), Louise Basmacyan (CHU Dijon), Loïc Favennec (CHU Rouen), Luce Landraud (CH Louis Mourier), Lucile Cadot (CH Alès - Cévennes), Ludovic de Gentile (CHU Angers), Luis Macias (CHU Bichat-Claude Bernard, Paris), Luu-ly Pham (CHU Kremlin-Bicêtre, Paris), M. Cambon (CHRU Clermont-Ferrand), M.F. Biava (CHU de Nancy), M.H. Kiefer (CH du Moenchsberg), M.P. Carlotti (CNR du paludisme), Madeleine Fontrouge (CH de Gonesse), Marc Pihet (CHU Angers), Marc Thellier (CHU Pitié-Salpêtrière, Paris), Marie-Catherine Receveur (CHU de Bordeaux), Marie-Claire Machouart (CHU de Nancy), Marie-Elisabeth Bougnoux (CHU Necker, Paris), Marie-Laure Bigel (CH François-Quesnay, Mantes-la-Jolie), Marie-Laure Darde (CHU Dupuyrien, Limoges), Marie-Nadège Bachelier (CH Jacques Cœur, Bourges), Marion Almeras (CH Béziers), Marion Leterrier (CHU Nantes), Marion Leterrier (CHD La Roche-sur-Yon), Martin Danis (CHU Pitié-Salpêtrière, Paris), Martin G (CH du Cotentin), Martine Bloch (CH Louis Mourier), Martine Liance (CHU Henri Mondor, Paris), Marylin Madamet (IMTSSA, Marseille), Matthieu Revest (CHU Pontchaillou, Rennes),Matthieu Mechain (CHU de Bordeaux), Maxime Thouvenin (CH Troyes), Mermond Sylvain (Institut Pasteur, Nouméa), Michel Develoux (CH Tenon, Paris), Michel Miegeville (CHU Nantes), Milène Sasso (CHU Nîmes), Mohamed Diaby (CH Vernon), Monique Marty (CH La Rochelle), Monique Greze (CH Albi), Monique Lemoine (CHU Bichat-Claude Bernard, Paris), Mouri Oussama (CHU Pitié-Salpêtrière, Paris), Muriel Cornet (Hôpital Hôtel-Dieu, Paris), Muriel Mimoun Ayache (CH Trousseau), Muriel Nicolas (CHU Pointe-à-Pitre / Abymes), Muriel Roumier (CH Arles), Muriel Silva (CH Jacques Monod), Mylène Penot (CERBA), Myriam Gharbi (CHU Bichat-Claude Bernard, Paris), Nadia Guennouni (CHU Bichat-Claude Bernard, Paris), Nadine Godineau (Hôpital Delafontaine, Saint-Denis), Naima Dahane (CHU Cochin, Paris), Nathalie Bourgeois (CHU Montpellier), Nathalie Desuremain (CH Trousseau, Paris), Nathalie Fauchet (CHI de Créteil), Nathalie Parez (CH Louis Mourier), Nathalie Wilhelm (CH de Cahors), Nawel Ait-Ammar (Hôpital Ambroise Paré), Nayla Nassar (CH Auxerre), Nicolas Argy (CHU Bichat-Claude Bernard, Paris), Nicolas Blondiaux (CH Tourcoing), Nicolas Taudon (CERBA), Nicole Desbois-Nogard (CHU de la Martinique), Noura Hassouni (CHU Necker), Odile Bouret-Dubouis (CH Bretagne Atlantique), Odile Eloy (CH de Versailles, André Mignot), Odile Falguiere (CH Béziers), Odile Fenneteau (CHU Robert Debré, Paris), Olivia Bandin (Hôpital Saint-Camille/Bry-sur-Marne), Olivier Albert (CHU de Bordeaux), Olivier Bouchaud (CH Bobigny-Avicenne), Olivier Patey (CHI Villeneuve St. Georges), Olivier Rogeaux (CH Chambéry), P. Clergeau (CH Sallanches), P. Daumain (CH de Dourdan), P.H. Consigny (Institut Pasteur, Paris), Paméla Chauvin (CHU Toulouse), Pascal Delaunay (CH Universitaire de Nice), Pascal Hazera (CH Saint-Lo), Pascal Houze (Hôpital Saint Louis, Paris), Pascal Millet (CHU de Bordeaux), Pascal Pouedras (CH Bretagne Atlantique), Pascale Penn (CH Le Mans), Patrice Agnamey (CHU Amiens), Patrice Bourrée (CHU Kremlin-Bicêtre, Paris), Patricia Barbut (CH Longjumeau), Patricia Brugel (CH Antibes Juan-Les-Pins), Patricia Roux (CH Saint-Antoine, Paris), Patrick Leguen (HIA Clermont Tonnerre, Brest), Patrick Valayer (CH Notre-Dame de la Miséricorde), Pauline Caraux-Paz (CHI Villeneuve St Georges), Pauline Touroultjupin (CH Cholet), Philippe Abboud (CHU Rouen), Philippe Cormier (CH d’Evry), Philippe Minodier (CH Marseille Nord), Philippe Moskovtchenko (Hôpitaux Civils de Colmar), Philippe Parola (CH Marseille Nord), Philippe Poirier (CHRU Clermont-Ferrand), Philippe Stolidi (CH Aubagne), Pierre Patoz (CH Tourcoing), Pierre Buffet (INTS, Paris), Pierre Buffet (CHU Pitié-Salpêtrière, Paris), Pierre Flori (CH Saint-Etienne), Pierre Marty (CH Universitaire de Nice), Pierre Mornand (CH Trousseau, Paris), Pinel Claudine (CHU de Grenoble), R. Dahan (CHU de Strasbourg), R. Devallière (CH Saint-Nazaire), R. Mazataud (CH Vitry le François), Rahaf Haj Hamid (CH Louis Mourier), Regis Courtin (CHU Pitié-Salpêtrière, Paris), Renaud Blonde (CHU Robert Debré, Paris), René Nabias (CHI Poissy-st-germain), Roland Fabre (HIA Begin), Rose-Anne Lavergne (CHU Nantes), Roxane Courtois (CH Cholet), Rym Chouk Turki (CHU Henri Mondor), Rémy Durand (CH Bobigny-Avicenne), Réné Nabias (CHU Necker, Paris), Sabah Kubab (CH Corbeil Essonne), Sabine Lasserre (CH Trousseau, Paris), Samia Hamane (Hôpital Saint-Louis, Paris), Sandrine Cojean (CHU Bichat-Claude Bernard, Paris), Sandrine Houze (CHU Bichat-Claude Bernard, Paris), Sophie Matheron (CHU Bichat-Claude Bernard, Paris), Sorya Belaz (CHU Pontchaillou, Rennes), Stephane Jaureguiberry (CHU Pitié-Salpêtrière, Paris), Stephane Ranque (CH de la Timone, Marseille), Stephanie Dulucq (CHU de Bordeaux), Stéphane Bretagne (Hôpital Saint-Louis, Paris), Stéphane Pelleau (Institut Pasteur, Guyane), Stéphane Picot (Hospices Civils de Lyon), Sylvain Clauser (Hôpital Ambroise Paré), Sylviane Chevrier (CHU Pontchaillou, Rennes), Sylviane Dydymski (CHRU Clermont-Ferrand), Sylvie Lariven (CHU Bichat-Claude Bernard, Paris), Sylvie Lhopital (CH Vernon), Sylvie Maurellet Evrard (CHI Villeneuve St Georges), Sylvie Roulaud (CH Angouleme), Sébastien Larréché (HIA Begin), Thi-Hai-Chau Trinh (CHR Orléans), Thierry Ancelle (CHU Cochin, Paris), Thierry Pistone (CHU de Bordeaux), Thomas Hanslik (Hôpital Ambroise Paré), Thomas Guimard (CHD La Roche-sur-Yon), Timothée Klopfenstein (CHU Besançon, Jean Minjoz), Valerie Fuster-Dumas (CHU de Bordeaux), Veronique Blanc-Amrane (CH Antibes Juan-Les-Pins), Veronique Delcey (CHU Lariboisière, Paris), Veronique Sarrasin-Hubert (CHU Bichat-Claude Bernard, Paris), Vincent Foissaud (HIA Percy, Clamart), Virginie Mouton-Rioux (CH Bretagne Atlantique), Virginie Vitrat (CH Annecy Genevois), Véronique Jan-Lasserre (CH Lagny-sur-Marne), Xavier Nicolas (HIA Clermont Tonnerre, Brest), Y. Costa (CH Lagny-sur-Marne), Yassamine Lazrek (Institut Pasteur, Guyane), Yaye Senghor (Hôpital Saint Joseph, Paris), Yohann Le Govic (CHU Angers), Yves Guimard (CH Jacques Cœur, Bourges), Yves Poinsignon (CH Bretagne Atlantique), Claude flamand (Institut Pasteur, Guyane), C.N. guyen (CH Trousseau, Paris), G. Noël (CH Marseille Nord), G. Soula (CH Marseille Nord), J.M.Didier (CH Vesoul), M.F. Raynaud (CH Antibes Juan-Les-Pins), M. Julien (CH Béziers), M. Morillon (HIA Laveran), M.P. Carlotti (IMTSSA), P. Chantelat (CH Vesoul), P. Dussert (CH Belfort), P. Ralaimazava (CH Bobigny-Avicenne), S. Zaouche (CHU Necker, Paris), Élodie Lesteven (CHU Lariboisière, Paris)., Musset, Lise, Centre National de Référence du Paludisme [CHU Pitié-Salpétrière] (CNRpalu), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)
Subjects: Plasmodium, Epidemiology, FNRCm, MESH: Hospitalization, Mark and recapture, 0302 clinical medicine, MESH: Aged, 80 and over, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Child, 030212 general & internal medicine, MESH: Incidence, MESH: Travel, Imported malaria, media_common, MESH: Aged, MESH: Middle Aged, MESH: Infant, 3. Good health, MESH: Young Adult, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, surveillance, France, Sex ratio, MESH: Medical Record Linkage, MESH: Disease Notification, 030231 tropical medicine, Notifiable disease, MESH: Malaria, capture-recapture, malaria, MESH: Population Surveillance, 03 medical and health sciences, MESH: Cross-Sectional Studies, Virology, parasitic diseases, medicine, media_common.cataloged_instance, European union, MESH: Communicable Diseases, Imported, MESH: Adolescent, MESH: Hospitals, University, MESH: Humans, business.industry, MESH: Child, Preschool, Public Health, Environmental and Occupational Health, MESH: Adult, medicine.disease, Confidence interval, MESH: Male, Metropolitan France, MESH: France, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, travellers, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, MESH: Female, Malaria, Demography
Abstract: Introduction Malaria is a notifiable disease in all European Union and European Economic Area countries except Belgium and France, where only autochthonous malaria is notifiable. Although morbidity caused by malaria has been assessed, little is known about mortality incidence. Objective Our aim was to estimate the number of imported malaria-related deaths in hospital in metropolitan France. Methods We matched individual deaths reported between 1 January 2005 and 31 December 2014 to the French National Reference Centre for malaria (FNRCm) with malaria-related deaths from two other sources: the French National Registry on medical causes of death and the French national hospital discharge database. A capture–recapture method with log-linear modelling was used. Age, sex and place of death stratification were applied to remove heterogeneity. Results The estimated malaria-related deaths in metropolitan France during the study period were 205 (95% confidence interval (CI): 191–219). The annual mean number of malaria-related deaths was estimated at 21 (95% CI: 19–22). The FNRCm malaria-related deaths surveillance had a 38% sensitivity (95% CI: 32–44). Among 161 in-hospital individual malaria-related deaths reported from three data sources, the sex ratio (male to female) was 2.6. Median age of the patients was 57 years, ranging from 1 to 89 years. Conclusion The pertinent finding of this report is that malaria-related death records were significantly less* complete than case records. Therefore, data comparison of imported malaria morbidity and mortality between countries should imperatively be assessed using standard indicators weighted according to the completeness of health surveillance systems.
Published: 2020
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40. Absence of association between Plasmodium falciparum small sub-unit ribosomal RNA gene mutations and in vitro decreased susceptibility to doxycycline

Author: Jacques Lebras, François Nosten, Bruno Pradines, Tiphaine Gaillard, Chirapat Wangsing, Véronique Hubert, Sandrine Houzé, Nathalie Wurtz, Sébastien Briolant, Kanlaya Sriprawat, UL, SIMPA, Hôpital d'Instruction des Armées Sainte Anne, Service de Santé des Armées, Institut de Recherches Biomédicales des Armées, Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence du Paludisme, Hôpital Bichat - Claude Bernard, Mère et enfant en milieu tropical : pathogènes, système de santé et transition épidémiologique (MERIT - UMR_D 216), Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5), PRES Sorbonne Paris Cité, Mahidol University [Bangkok], University of Oxford, Direction Interarmées du Service de Santé, Laboratoire de Parasitologie [Cayenne, Guyane française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), This study was supported by the Délégation Générale pour l’Armement (Grant number 10CO405) and the Institut national de Veille sanitaire (CNR paludisme). The Shoklo Malaria Research Unit is part of the Mahidol Oxford University Research Unit, supported by The Wellcome Trust of Great Britain., French National Reference Centre for Imported Malaria Study Group : Ahmed Aboubacar, Patrice Agnamey, Faïza Ajana, Roger Amira, Nicolas Argy, Sonia Baumard, Pauline Bellanger, Dieudonné Bemba, Jean Beytout, Marie-Laure Bigel, Martine Bloch, Richard Bonnet, Alice Borel, Olivier Bouchaud, Catherine Branger, Fabrice Bruneel, Monique Cambon, Daniel Camus, Enrique Casalino, Jérome Clain, Sandrine Cojean, Bernadette Cuisenier B, Ludovic De Gentile, Jean-Marie Delarbre, Anne Delaval, Rémy Durand, Emmanuel Dutoit, Odile Eloy, Jean-François Faucher, Albert Faye, Odile Fenneteau, Denis Filisetti, Christian Fulleda, Nadine Godineau, Frédéric Grenouillet, Jean-Pierre Hurst, Houria Ichou, Elizabeth Klein E, Sylvie Lariven, Magalie Lefevre, Monique Lemoine, Olivier Lesens, Caroline Lohmann, Daniel Lusina, Marie-Claude Machouart, Robert Mary, Sophie Matheron, Denis Mechali, Audrey Merrens, Laurence Millon, Sébastien Monnier, Emmanuel Mortier, François Moussel, Olivier Pageot, Nathalie Parez, Pierre Patoz, Alexander Pfaff, Marc Pihet, Jean-Etienne Pilo, Isabelle Poilane, Denis Pons, Marie Poupart, Marc Prevel, Lauren Pull, Christophe Rapp, Alexandre Rivier, Emily Ronez, Daniel Rotten, Anne-Laure Simonet, Jean-Yves Siriez, Christophe Strady, Audrey Therby, Michel Thibault, Maxime Thouvenin, Dominique Toubas., INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), University of Oxford [Oxford], Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes ( URMITE ), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes ( URMITE ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -IFR48, INSB-INSB-Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -IFR48, INSB-INSB-Centre National de la Recherche Scientifique ( CNRS ), Mère et enfant face aux infections tropicales ( MERIT - UMR_D 216 ), Institut de Recherche pour le Développement ( IRD ) -Université Paris Descartes - Paris 5 ( UPD5 ), Laboratoire de parasitologie [Cayenne], Réseau International des Instituts Pasteur ( RIIP ) -Réseau International des Instituts Pasteur ( RIIP ), Fédération des Laboratoires, Hôpital d'instruction des armées Sainte-Anne, Service de Parasitologie Mycologie [AP-HP Hôpital Bichat - Claude Bernard], AP-HP - Hôpital Bichat - Claude Bernard [Paris], Shoklo Malaria Research Unit [Mae Sot, Thailand] (Faculty of Tropical Medicine), Mahidol University [Bangkok]-Mahidol Oxford Tropical Medicine Research Unit (MORU), University of Oxford [Oxford]-Mahidol University [Bangkok]-Wellcome Trust-University of Oxford [Oxford]-Wellcome Trust, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris]-Université Paris Descartes - Paris 5 (UPD5), Unité de Recherche en Biologie et Epidémiologie Parasitaires, Institut de Médecine Tropicale du Service de Santé des Armées-Centre National de la Recherche Scientifique (CNRS), Groupe d'Etude des Interactions Hôte-Parasite (GEIHP), and Université d'Angers (UA)
Subjects: Genes, Protozoan, Drug Resistance, Drug resistance, Molecular marker, chemistry.chemical_compound, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, [ SDV.IMM ] Life Sciences [q-bio]/Immunology, MESH: Doxycycline, Malaria, Falciparum, ComputingMilieux_MISCELLANEOUS, MESH: Plasmodium falciparum, MESH: Inhibitory Concentration 50, Doxycycline, Quinine, biology, MESH: Malaria, Falciparum, 3. Good health, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Genes, Protozoan, MESH: Drug Resistance, [SDV.IMM]Life Sciences [q-bio]/Immunology, medicine.drug, [SDV.IMM] Life Sciences [q-bio]/Immunology, pfssrRNA, Plasmodium falciparum, Antimalarials, Inhibitory Concentration 50, In vitro, parasitic diseases, MESH: Genes, rRNA, medicine, Humans, [SDV.EE.SANT] Life Sciences [q-bio]/Ecology, environment/Health, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, 16S rRNA, Gene, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, MESH: Humans, Research, Genes, rRNA, Ribosomal RNA, biology.organism_classification, medicine.disease, Virology, Small ribosomal sub-unit RNA gene, MESH: Antimalarials, Malaria, chemistry, Artesunate, Parasitology, Anti-malarial
Abstract: International audience; Background: Doxycycline is an antibiotic used in combination with quinine or artesunate for malaria treatment or alone for malaria chemoprophylaxis. Recently, one prophylactic failure has been reported, and several studies have highlighted in vitro doxycycline decreased susceptibility in Plasmodium falciparum isolates from different areas. The genetic markers that contribute to detecting and monitoring the susceptibility of P. falciparum to doxycycline, the pfmdt and pftetQ genes, have recently been identified. However, these markers are not sufficient to explain in vitro decreased susceptibility of P. falciparum to doxycycline. In this paper, the association between polymorphism of the small sub-unit ribosomal RNA apicoplastic gene pfssrRNA (PFC10_API0057) and in vitro susceptibilities of P. falciparum isolates to doxycycline were investigated.Methods: Doxycycline IC50 determinations using the hypoxanthine uptake inhibition assay were performed on 178 African and Thai P. falciparum isolates. The polymorphism of pfssrRNA was investigated in these samples by standard PCR followed by sequencing.Results: No point mutations were found in pfssrRNA in the Thai or African isolates, regardless of the determined IC50 values.Conclusions: The pfssrRNA gene is not associated with in vitro decreased susceptibility of P. falciparum to doxycycline. Identifying new in vitro molecular markers associated with reduced susceptibility is needed, to survey the emergence of doxycycline resistance.
Published: 2015
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