Author: "Laurence, Delhaes" - Searchworks@Jio Institute Digital Library Search Results

Author: Erwan Guichoux, Daniela Cota, Aline Marighetto, Sophie Cambos, Laurence Delhaes, Kamel Mohammedi, Samantha Clark, Blandine Gatta-Cherifi, Emilie Chancerel, Esther Viaud, Nicole Etchamendy, and Raphael Enaud
Subjects: Adult, Male, cognition, medicine.medical_specialty, obesity, Adolescent, bariatric surgery, microbiome, Pilot Projects, Gut flora, Article, memory, Feces, Young Adult, Memory improvement, Prevotella, medicine, microbiota, Humans, TX341-641, Microbiome, Prospective Studies, Aged, metagenomics, Nutrition and Dietetics, biology, Bacteria, Working memory, business.industry, Nutrition. Foods and food supply, Fungi, Akkermansia, Middle Aged, biology.organism_classification, medicine.disease, Obesity, Surgery, Gastrointestinal Microbiome, Obesity, Morbid, Female, mycobiota, business, Dysbiosis, Food Science, Mycobiome
Abstract: Patients with obesity are known to exhibit gut microbiota dysbiosis and memory deficits. Bariatric surgery (BS) is currently the most efficient anti-obesity treatment and may improve both gut dysbiosis and cognition. However, no study has investigated association between changes of gut microbiota and cognitive function after BS. We prospectively evaluated 13 obese patients on anthropometric data, memory functions, and gut microbiota-mycobiota before and six months after BS. The Rey Auditory Verbal Learning Test (AVLT) and the symbol span (SS) of the Weschler Memory Scale were used to assess verbal and working memory, respectively. Fecal microbiota and mycobiota were longitudinally analyzed by 16S and ITS2 rRNA sequencing respectively. AVLT and SS scores were significantly improved after BS (AVLT scores: 9.7 ± 1.7 vs. 11.2 ± 1.9, p = 0.02, and SS scores: 9.7 ± 23.0 vs. 11.6 ± 2.9, p = 0.05). An increase in bacterial alpha-diversity, and Ruminococcaceae, Prevotella, Agaricus, Rhodotorula, Dipodascus, Malassezia, and Mucor were significantly associated with AVLT score improvement after BS, while an increase in Prevotella and a decrease in Clostridium, Akkermansia,&nbsp, Dipodascus and Candida were linked to SS scores improvement. We identified several changes in the microbial communities that differ according to the improvement of either the verbal or working memories, suggesting a complex gut-brain-axis that evolves after BS.
Published: 2021

77. Antifungal susceptibility of 182 fusarium species isolates from 20 european centers:Comparison between eucast and gradient concentration strip methods

Author: Marcel Brandenberger, Elisa Rubio, Lise Kristensen, Renaud Piarroux, Anne-Cécile Normand, Boualem Sendid, Erja Chryssanthou, Christine Bonnal, Abdullah M. S. Al-Hatmi, Dirk Stubbe, Arnaud Fekkar, Damien Costa, Arnaud Riat, Sophie Cassaing, Christine Schuttler, Marc Sautour, Sophie Brun, Marion Blaize, Lilia Hasseine, Sébastien Imbert, Laurence Delhaes, Stéphane Ranque, Caroline Mahinc, Sorbonne Université (SU), 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), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), and Sorbonne Université - Faculté de Médecine (SU FM)
Subjects: Fusarium, Antifungal, Veterinary medicine, Posaconazole, Antifungal Agents, medicine.drug_class, Antifungal drugs, Comparison, Microbial Sensitivity Tests, terbinafine, Amphotericin B/pharmacology, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Amphotericin B, medicine, voriconazole, antifungal susceptibility, Pharmacology (medical), [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, EUCAST, Gradient concentration strips, Etest, Pharmacology, Voriconazole, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, Voriconazole/pharmacology, Isavuconazole, ECV, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, posaconazole, amphotericin B, Infectious Diseases, Susceptibility, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Antifungal Agents/pharmacology, Terbinafine, medicine.drug
Abstract: We determined the susceptibility of 182 Fusarium species isolates to five antifungal drugs (amphotericin B, voriconazole, posaconazole, isavuconazole, and terbinafine) by the EUCAST method. Based on the latest taxonomic insights, isolates collected from 20 European centers were distributed into seven complexes and 27 species. The susceptibility was variable, depending on the species. Comparison with the gradient concentration strip method, which was used for 77 isolates, showed essential agreement values for voriconazole, posaconazole, isavuconazole, and amphotericin B of 17%, 91%, 83%, and 70%, respectively.
Published: 2021

78. The Mycobiome: A Neglected Component in the Microbiota-Gut-Brain Axis

Author: Raphaël Enaud, Louise-Eva Vandenborght, Noémie Coron, Thomas Bazin, Renaud Prevel, Thierry Schaeverbeke, Patrick Berger, Michael Fayon, Thierry Lamireau, and Laurence Delhaes
Subjects: brain–gut axis, mycobiome, microbiome, dysbiosis, neurological disorders, psychiatric disorders, fungus, Biology (General), QH301-705.5
Abstract: In recent years, the gut microbiota has been considered as a full-fledged actor of the gut–brain axis, making it possible to take a new step in understanding the pathophysiology of both neurological and psychiatric diseases. However, most of the studies have been devoted to gut bacterial microbiota, forgetting the non-negligible fungal flora. In this review, we expose how the role of the fungal component in the microbiota-gut-brain axis is legitimate, through its interactions with both the host, especially with the immune system, and the gut bacteria. We also discuss published data that already attest to a role of the mycobiome in the microbiota-gut-brain axis, and the impact of fungi on clinical and therapeutic research.
Published: 2018
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79. Population structure and diversity of the pathogenic fungus Aspergillus fumigatus isolated from different sources and geographic origins

Author: Esperanza Duarte-Escalante, Gerardo Zúñiga, Oscar Nava Ramírez, Susana Córdoba, Nicolás Refojo, Roberto Arenas, Laurence Delhaes, and María del Rocío Reyes-Montes
Subjects: Aspergillus fumigatus, AFLP, genetic diversity, polymorphisms, Microbiology, QR1-502, Infectious and parasitic diseases, RC109-216
Abstract: Fifty-five clinical and environmental Aspergillus fumigatus isolates from Mexico, Argentina, France and Peru were analyzed to determine their genetic variability, reproductive system and level of differentiation using amplified fragment length polymorphism markers. The level of genetic variability was assessed by measuring the percentage of polymorphic loci, number of effective alleles, expected heterozygocity and by performing an association index test (I A). The degree of genetic differentiation and variation was determined using analysis of molecular variance at three levels. Using the paired genetic distances, a dendrogram was built to detect the genetic relationship among alleles. Finally, a network of haplotypes was constructed to determine the geographic relationship among them. The results indicate that the clinical isolates have greater genetic variability than the environmental isolates. The I A of the clinical and environmental isolates suggests a recombining population structure. The genetic differentiation among isolates and the dendrogram suggest that the groups of isolates are different. The network of haplotypes demonstrates that the majority of the isolates are grouped according to geographic origin.
Published: 2009
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80. Molecular Typing of Australian Scedosporium Isolates Showing Genetic Variability and Numerous S. aurantiacum

Author: Laurence Delhaes, Azian Harun, Sharon C.A. Chen, Quoc Nguyen, Monica Slavin, Christopher H. Heath, Krystyna Maszewska, Catriona Halliday, Vincent Robert, Tania C. Sorrell, and Wieland Meyer
Subjects: Scedosporium prolificans, Scedosporium aurantiacum, Scedosporium apiospermum, molecular epidemiology, ITS-sequencing, ITS-RFLP, Medicine, Infectious and parasitic diseases, RC109-216
Abstract: One hundred clinical isolates from a prospective nationwide study of scedosporiosis in Australia (2003–2005) and 46 additional isolates were genotyped by internal transcribed spacer–restriction fragment length polymorphism (ITS-RFLP) analysis, ITS sequencing, and M13 PCR fingerprinting. ITS-RFLP and PCR fingerprinting identified 3 distinct genetic groups. The first group corresponded to Scedosporium prolificans (n = 83), and the other 2 comprised isolates previously identified as S. apiospermum: one of these corresponded to S. apiospermum (n = 33) and the other to the newly described species S. aurantiacum (n = 30). Intraspecies variation was highest for S. apiospermum (58%), followed by S. prolificans (45%) and S. aurantiacum (28%) as determined by PCR fingerprinting. ITS sequence variation of 2.2% was observed among S. apiospermum isolates. No correlation was found between genotype of strains and their geographic origin, body site from which they were cultured, or colonization versus invasive disease. Twelve S. prolificans isolates from 2 suspected case clusters were examined by amplified fragment length polymorphism analysis. No specific clusters were confirmed.
Published: 2008
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81. Identification of Predictive Markers and Outcomes of Late-onset Pneumocystis jirovecii Pneumonia in Kidney Transplant Recipients

Author: Benjamin Taton, Isabelle Accoceberry, Xavier Iriart, Julie Belliere, Jonathan Visentin, Eléna Charpentier, Arnaud Del Bello, Pierre Merville, Laure Burguet, Marco Gregori, Lionel Couzi, Laurence Delhaes, Stéphane Poirot-Mazères, Nassim Kamar, Hannah Kaminski, Immunology from Concept and Experiments to Translation (ImmunoConcept), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), CHU de Bordeaux Pellegrin [Bordeaux], Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, CHU Toulouse [Toulouse], Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), and 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)
Subjects: 0301 basic medicine, Microbiology (medical), medicine.medical_specialty, Opportunistic infection, medicine.drug_class, Lymphocyte, 030106 microbiology, kidney transplantation, Pneumocystis carinii, Pneumocystis pneumonia, corticosteroid boluses, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Internal medicine, medicine, Humans, 030212 general & internal medicine, Kidney transplantation, Retrospective Studies, Predictive marker, business.industry, Pneumonia, Pneumocystis, lymphopenia, medicine.disease, Transplant Recipients, 3. Good health, Transplantation, Pneumonia, Infectious Diseases, medicine.anatomical_structure, Case-Control Studies, Corticosteroid, business
Abstract: BackgroundIn the era of prophylaxis, Pneumocystis pneumonia (PCP) has become a late-onset opportunistic infection requiring indications for prolonged prophylaxis to be defined. The primary objective of our study was therefore to evaluate risk factors associated with late-onset PCP. The secondary objective was to assess the impact of this infection on graft and patient survival.MethodsWe conducted a French case-control study in Bordeaux and Toulouse center by matching 1 case to 1–2 controls from the same center based on the transplant date and the type of induction treatment.ResultsSeventy cases and 134 controls were included. PCP occurred at a median of 3 years after transplantation. The total lymphocyte count and CD4+ and CD8+ T-lymphocyte values were lower in the cases than in their matched controls on the day of infection and annually up to 4 years earlier. The covariables independently associated with PCP were the total lymphocyte count 1 year before Pneumocystis, mTOR inhibitors used as maintenance immunosuppressive drugs, and the administration of corticosteroid boluses used in acute rejection. A total lymphocyte count threshold ConclusionsPneumocystis pneumonia has dramatic consequences in kidney transplant recipients; a targeted prophylaxis based on simple criteria, such as chronic lymphopenia and/or history of corticosteroid boluses, could be useful to avoid life-threatening complications.
Published: 2021

82. Etest ECVs/ECOFFs for detection of resistance in prevalent and three non-prevalent Candida spp. to triazoles and amphotericin B and Aspergillus spp. to caspofungin: Further assessment of modal variability

Author: Damien Dupont, John D. Turnidge, J Fuller, Maiken Cavling Arendrup, A Forastiero, M Dehais, Emilia Cantón, Hélène Guegan, Nathalie Bourgeois, Ana Espinel-Ingroff, Guillermo Garcia-Effron, Laurence Delhaes, B. Bouteille, Teresa Peláez, J Garcia, Cornelia Lass-Flörl, Jesús Guinea, Arnaud Fekkar, Nelesh P. Govender, Françoise Botterel, Eric Dannaoui, Gloria M. González, R Magobo, Sophie Cassaing, Michaela Lackner, Milène Sasso, Sandrine Houzé, Virginia Commonwealth University (VCU), Hôpital Lapeyronie [Montpellier] (CHU), University of Adelaide, Statens Serum Institut [Copenhagen], CHU Henri Mondor, CHU Limoges, CHU Toulouse [Toulouse], 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), Epidémiosurveillance de protozooses à transmission alimentaire et vectorielle (ESCAPE), 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), CHU Bordeaux [Bordeaux], Hospices Civils de Lyon, Departement de Neurologie (HCL), CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), University of Western Ontario (UWO), Universidad Nacional del Litoral [Santa Fe] (UNL), Hospital Universitario La Paz, Universidad Autonoma de Nuevo Leon [Mexique] (UANL), National Institute for Communicable Diseases [Johannesburg] (NICD), 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 ), Hospital General Universitario 'Gregorio Marañón' [Madrid], 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), Leopold Franzens Universität Innsbruck - University of Innsbruck, Universidad de Oviedo [Oviedo], CHU Henri Mondor [Créteil], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), 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), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), 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 ), Mère et enfant en milieu tropical : pathogènes, système de santé et transition épidémiologique (MERIT - UMR_D 261), and Institut de Recherche pour le Développement (IRD)-Université Paris Cité (UPCité)
Subjects: Posaconazole, [SDV]Life Sciences [q-bio], Aspergillus fumigatus, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Amphotericin B, medicine, Pharmacology (medical), 030212 general & internal medicine, caspofungin, Candida albicans, triazoles, Etest, Candida, Aspergillus spp., Candida, ECOFFS, ECVs, ERG11 mutants, amphotericin B, antifungal resistance, caspofungin, nonprevalent Candida, triazoles, Pharmacology, Voriconazole, ECOFFS, 0303 health sciences, biology, 030306 microbiology, ERG11 mutants, antifungal resistance, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, bacterial infections and mycoses, amphotericin B, Aspergillus spp, nonprevalent Candida, Infectious Diseases, chemistry, ECVs, Caspofungin, Fluconazole, medicine.drug
Abstract: International audience; Susceptibility testing is an important tool in the clinical setting; its utility is based on the availability of categorical endpoints, breakpoints (BPs) or epidemiological cutoff values (ECVs/ECOFFs). CLSI and EUCAST have developed antifungal susceptibility testing, BPs and ECVs for some fungal species. Although the Concentration Gradient Strip BioMerieux Etest is useful for routine testing in the clinical laboratory, ECVs are not available for all agent/species; the lack of clinical data precludes development of BPs. We re-evaluated and consolidated Etest data points from three previous studies, and included new data. We defined ECOFFinder Etest ECVs for three sets of species/agent combinations: fluconazole, posaconazole and voriconazole and 8 Candida spp.; amphotericin B and 3 non-prevalent Candida spp.; and caspofungin and 5 Aspergillus spp. The total of Etest MICs from 23 laboratories (Europe, the Americas, South Africa) included (antifungal agent/dependent): 17,242 Candida albicans, 244 C. dubliniensis, 5,129 C. glabrata species complex (SC), 275 C. guilliermondii (Meyerozyma guilliermondii), 1,133 C. krusei (Pichia kudriavzevii), 933 C. kefyr (Kluyveromyces marxianus), 519 C. lusitaniae (Clavispora lusitaniae), 2,947 C. parapsilosis SC, 2,214 C. tropicalis, 3,212 Aspergillus fumigatus, 232 A. flavus, 181 A. niger, and 267 A. terreus SC isolates. Triazole MICs for 66 confirmed non-wild-type (non-WT) Candida isolates were available (ERG11 point mutations). Distributions fulfilling CLSI ECV criteria were pooled and ECOFFinder Etest ECVs were established for triazoles (9 Candida spp.); amphotericin B (3 less-prevalent Candida spp.) and caspofungin (4 Aspergillus spp.). Etest fluconazole ECVs could be good detectors of Candida non-WT isolates (59/61 Non-WT: 4 of 6 species).
Published: 2021

83. Risk factors and outcome of pulmonary aspergillosis in critically ill coronavirus disease 2019 patients– a multinational observational study by the European Confederation of Medical Mycology

Author: Sara Volpi, Marc Bourgeois, Mathilde Chamula, Gregor Paul, Jeffrey D. Jenks, Marijke Reynders, Jean-Jacques Tudesq, Marisa H. Miceli, Patricia Muñoz, Stefan Hatzl, Martin Hoenigl, Tobias Lahmer, Paul Bowyer, Sara Gago, Piet Lormans, Lynn Rutsaert, Chiara Robba, Philipp Eller, Peter Zechner, Antonis Rokas, Jonas Frost, Anne-Pauline Bellanger, Jean-Pierre Gangneux, Katrien Lagrou, Jon Salmanton-García, Riina Rautemaa-Richardson, Gustavo H. Goldman, Kauser Jabeen, Simon Feys, Yves Debaveye, Daniele Roberto Giacobbe, Marina Machado, P. Lewis White, Robert Krause, Joerg Steinmann, Laurence Delhaes, Joost Wauters, Juergen Prattes, Matthias Kochanek, Philipp Koehler, Alexander C. Reisinger, Oliver A. Cornely, Paolo Pelosi, Maricela Valerio, Cornelia Lass-Floerl, Niels Van Regenmortel, Matteo Bassetti, Marina Linhofer, and Johan Maertens
Subjects: Microbiology (medical), medicine.medical_specialty, Survival, Critical Illness, Mycology, intensive care unit, survival, law.invention, chemistry.chemical_compound, coronavirus disease 2019, Tocilizumab, law, Risk Factors, Internal medicine, Intensive care, Epidemiology, medicine, Humans, Survival rate, Aged, Invasive Pulmonary Aspergillosis, business.industry, SARS-CoV-2, Hazard ratio, COVID-19, CAPA, General Medicine, Intensive care unit, Intensive Care Units, Infectious Diseases, Aspergillus, chemistry, ICU, coronavirus disease 2019-associated pulmonary aspergillosis, Observational study, Original Article, Pulmonary Aspergillosis, business, Complication
Abstract: Objectives: Coronavirus disease 2019 (COVID-19) -associated pulmonary aspergillosis (CAPA) has emerged as a complication in critically ill COVID-19 patients. The objectives of this multinational study were to determine the prevalence of CAPA in patients with COVID-19 in intensive care units (ICU) and to investigate risk factors for CAPA as well as outcome. Methods: The European Confederation of Medical Mycology (ECMM) conducted a multinational study including 20 centres from nine countries to assess epidemiology, risk factors and outcome of CAPA. CAPA was defined according to the 2020 ECMM/ISHAM consensus definitions. Results: A total of 592 patients were included in this study, including 11 (1.9%) patients with histologically proven CAPA, 80 (13.5%) with probable CAPA, 18 (3%) with possible CAPA and 483 (81.6%) without CAPA. CAPA was diagnosed a median of 8 days (range 0–31 days) after ICU admission predominantly in older patients (adjusted hazard ratio (aHR) 1.04 per year; 95% CI 1.02–1.06) with any form of invasive respiratory support (HR 3.4; 95% CI 1.84–6.25) and receiving tocilizumab (HR 2.45; 95% CI 1.41–4.25). Median prevalence of CAPA per centre was 10.7% (range 1.7%–26.8%). CAPA was associated with significantly lower 90-day ICU survival rate (29% in patients with CAPA versus 57% in patients without CAPA; Mantel–Byar p < 0.001) and remained an independent negative prognostic variable after adjusting for other predictors of survival (HR 2.14; 95% CI 1.59–2.87, p ≤ 0.001). Conclusion: Prevalence of CAPA varied between centres. CAPA was significantly more prevalent among older patients, patients receiving invasive ventilation and patients receiving tocilizumab, and was an independent strong predictor of ICU mortality.
Published: 2021

84. Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis

Author: Perrine, Soret, Louise-Eva, Vandenborght, Florence, Francis, Noémie, Coron, Raphael, Enaud, Marta, Avalos, Thierry, Schaeverbeke, Patrick, Berger, Michael, Fayon, Rodolphe, Thiebaut, Laurence, Delhaes, Dominique, Turck, Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Statistics In System biology and Translational Medicine (SISTM), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)- Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de recherche Cardio-Thoracique de Bordeaux [Bordeaux] (CRCTB), Université Bordeaux Segalen - Bordeaux 2-CHU Bordeaux [Bordeaux]-Institut National de la Santé et de la Recherche Médicale (INSERM), Genoscreen [Lille], Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), CHU Bordeaux [Bordeaux], Aquitaine’s Care and Research organisation for inflammatory and Immune-Mediated diseases [CHU Bordeaux] (FHU ACRONIM), CIC Bordeaux, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Lille, Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Laurence Delhaes has received a research grant from 'Vaincre La Mucoviscidose' (RF20160501626), she is member of ESGHAMI and NGS-MycA working groups of ESCMID and ECCM respectively. Genoscreen Company provided support in the form of Louise-Eva Vandenborght’s salary (AST CT 2016-394)., The Mucofong Investigation Group, Epidémiologie et Biostatistique [Bordeaux], Université Bordeaux Segalen - Bordeaux 2-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Bordeaux Segalen - Bordeaux 2-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), and Bodescot, Myriam
Subjects: 0301 basic medicine, Male, Mycobiota, Cystic Fibrosis, lcsh:Medicine, Cystic fibrosis, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, 0302 clinical medicine, RNA, Ribosomal, 16S, Respiratory function, lcsh:Science, Lung, Respiratory Tract Infections, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Candida, Multidisciplinary, biology, Microbiota, High-Throughput Nucleotide Sequencing, SISTM, medicine.anatomical_structure, Aspergillus, Acute Disease, Disease Progression, Female, Malassezia, Infection, Adult, Article, Microbiology, Scedosporium, 03 medical and health sciences, Young Adult, Pseudomonas, medicine, Humans, lcsh:R, Sputum, Sequence Analysis, DNA, Translational research, biology.organism_classification, medicine.disease, [SDV.MP.MYC] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 030104 developmental biology, 030228 respiratory system, [SDV.MHEP.PSR] Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, lcsh:Q, Respiratory tract
Abstract: Lung infections play a critical role in cystic fibrosis (CF) pathogenesis. CF respiratory tract is now considered to be a polymicrobial niche and advances in high-throughput sequencing allowed to analyze its microbiota and mycobiota. However, no NGS studies until now have characterized both communities during CF pulmonary exacerbation (CFPE). Thirty-three sputa isolated from patients with and without CFPE were used for metagenomic high-throughput sequencing targeting 16S and ITS2 regions of bacterial and fungal rRNA. We built inter-kingdom network and adapted Phy-Lasso method to highlight correlations in compositional data. The decline in respiratory function was associated with a decrease in bacterial diversity. The inter-kingdom network revealed three main clusters organized around Aspergillus, Candida, and Scedosporium genera. Using Phy-Lasso method, we identified Aspergillus and Malassezia as relevantly associated with CFPE, and Scedosporium plus Pseudomonas with a decline in lung function. We corroborated in vitro the cross-domain interactions between Aspergillus and Streptococcus predicted by the correlation network. For the first time, we included documented mycobiome data into a version of the ecological Climax/Attack model that opens new lines of thoughts about the physiopathology of CF lung disease and future perspectives to improve its therapeutic management.
Published: 2020

85. CT evaluation of hyperattenuating mucus to diagnose allergic bronchopulmonary aspergillosis in the special condition of cystic fibrosis

Author: John Refait, Michael Fayon, Laurence Delhaes, Julie Macey, Stéphanie Bui, Patrick Berger, Gaël Dournes, François Laurent, Centre de recherche Cardio-Thoracique de Bordeaux [Bordeaux] (CRCTB), and Université Bordeaux Segalen - Bordeaux 2-CHU Bordeaux [Bordeaux]-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0301 basic medicine, Pulmonary and Respiratory Medicine, medicine.medical_specialty, Adolescent, Cystic Fibrosis, [SDV]Life Sciences [q-bio], Consensus criteria, Gastroenterology, Cystic fibrosis, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, medicine, Humans, Child, Retrospective Studies, Bronchiectasis, medicine.diagnostic_test, business.industry, Aspergillosis, Allergic Bronchopulmonary, Gold standard (test), medicine.disease, Mucus, 3. Good health, 030104 developmental biology, 030228 respiratory system, Pediatrics, Perinatology and Child Health, Biomarker (medicine), Allergic bronchopulmonary aspergillosis, Tomography, X-Ray Computed, Chest radiograph, business
Abstract: Background Mucus plugging (MP), central bronchiectasis (CB), and consolidation/atelectasia (CA) are conventional CT signs to diagnose allergic bronchopulmonary aspergillosis (ABPA) in cystic fibrosis (CF). Hyperattenuating mucus (HAM) has recently been described and may improve diagnostic accuracy. The goal of our study was to compare HAM versus conventional CT signs to diagnose ABPA in CF. Secondary objectives were to determine the optimal threshold of HAM quantitatively and to assess the diagnostic value of HAM using chest radiograph (CXR). Methods The study was retrospective and included 137 patients with CF, aged >6-year-old. The presence of HAM, CB, MP and CA were determined by two radiologists in consensus. HAM was quantified using an absolute mean density value (AMD) and a ratio between mucus and paraspinal muscle (DRM). Sensitivity (Se), Specificity (Sp) and Youden's J-index were calculated. The Cystic Fibrosis Conference Consensus criteria were chosen as Gold Standard. Results 23 out of 137 CF patients had ABPA. Using CT, the most sensitive structural alteration was MP (Se = 91%), followed by CB (Se = 87%) and CA (Se = 70%) whereas specificities were 28%, 19% and 58%, respectively. Conversely, HAM had the highest specificity (Sp = 100%) whereas Se was 69%. HAM had the highest Youden's J-index (p 78 HU (Se/Sp = 71%/98%) and DRM > 1.3 (Se/Sp = 82%/97%). HAM was unseen using CXR (Se = 0%). Conclusion HAM is the most specific CT biomarker of ABPA in CF, with good sensitivity. Our study suggests that characterization of mucus density may improve the accuracy of imaging criteria to diagnose ABPA early.
Published: 2019

86. Clinical Origin and Species Distribution of Fusarium spp. Isolates Identified by Molecular Sequencing and Mass Spectrometry: A European Multicenter Hospital Prospective Study

Author: Damien Costa, Abdullah M. S. Al-Hatmi, Marcel Brandenberger, Renaud Piarroux, Christine Schuttler, Anne-Cécile Normand, Elisa Rubio, Lilia Hasseine, Sophie Cassaing, Laurence Delhaes, Lise Kristensen, Caroline Mahinc, Arnaud Fekkar, Sébastien Imbert, Stéphane Ranque, Sophie Brun, Ann Packeu, Juliette Guitard, Boualem Sendid, C. Bonnal, Arnaud Riat, Marc Sautour, Erja Chryssanthou, CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Hôpital Avicenne [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Radboud University Medical Center [Nijmegen], Karolinska Institutet [Stockholm], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Centre Hospitalier Universitaire de Nice (CHU Nice), Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), CHU Rouen, Normandie Université (NU), CIC - CHU Bichat, Institut National de la Santé et de la Recherche Médicale (INSERM), 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), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), University of Barcelona, Instituto de Salud Global - Institute For Global Health [Barcelona] (ISGlobal), CHU de Bordeaux Pellegrin [Bordeaux], Geneva University Hospitals and Geneva University, CHU Lille, Aarhus University Hospital, Centre de Recherche Saint-Antoine (CRSA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), CHU Saint-Antoine [AP-HP], Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), 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), Service de Parasitologie - Mycologie [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre Hospitalier Universitaire de Saint-Etienne (CHU de Saint-Etienne), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Service de Parasitologie - Mycologie [CHU Saint-Antoine], Gestionnaire, Hal Sorbonne Université, Service de parasitologie - mycologie [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Radboud University Medical Centre [Nijmegen, The Netherlands], CHU Toulouse [Toulouse], 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)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), and Centre d'Immunologie et de Maladies Infectieuses (CIMI)
Subjects: Microbiology (medical), Fusariosis, Fusarium, Species complex, MALDI ToF mass spectrometry, [SDV]Life Sciences [q-bio], Species distribution, fusariosis, mALDI ToF mass spectrometry, Plant Science, Computational biology, Biology, Mass spectrometry, DNA sequencing, 03 medical and health sciences, DNA database, medicine, lcsh:QH301-705.5, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Fusarium species complex, 030306 microbiology, medicine.disease, biology.organism_classification, 3. Good health, elongation factor, [SDV] Life Sciences [q-bio], Elongation factor, lcsh:Biology (General), Identification (biology)
Abstract: Fusarium spp. are widespread environmental fungi as well as pathogens that can affect plants, animals and humans. Yet the epidemiology of human fusariosis is still cloudy due to the rapidly evolving taxonomy. The Mass Spectrometry Identification database (MSI) has been developed since 2017 in order to allow a fast, accurate and free-access identification of fungi by matrix-assisted laser desorption ionization—time of flight (MALDI-TOF) mass spectrometry. Taking advantage of the MSI database user network, we aim to study the species distribution of Fusarium spp. isolates in an international multicenter prospective study. This study also allowed the assessment of the abilities of miscellaneous techniques to identify Fusarium isolates at the species level. The identification was performed by PCR-sequencing and phylogenic-tree approach. Both methods are used as gold standard for the evaluation of mass spectrometry. Identification at the species complex was satisfactory for all the tested methods. However, identification at the species level was more challenging and only 32% of the isolates were correctly identified with the National Center for Biotechnology Information (NCBI) DNA database, 20% with the Bruker MS database and 43% with the two MSI databases. Improvement of the mass spectrometry database is still needed to enable precise identification at the species level of any Fusarium isolates encountered either in human pathology or in the environment.
Published: 2021

87. Pulmonary Aspergillosis in Critically Ill Coronavirus Disease 2019 Patients– A Multinational Observational Study by the European Confederation of Medical Mycology

Author: Marc Bourgeois, Martin Hoenigl, Oliver A. Cornely, Philipp Koehler, Mathilde Chamula, Tobias Lahmer, Marijke Reynders, Stefan Hatzl, Lynn Rutsaert, Kauser Jabeen, Piet Lormans, Juergen Prattes, Jon Salmanton-García, Simon Feys, Johan Maertens, Alexander C. Reisinger, Maricela Valerio, Katrien Lagrou, Laurence Delhaes, Niels Van Regenmortel, Joost Wauters, Matteo Bassetti, Joerg Steinmann, Riina Rautemaa-Richardson, and Daniele Roberto Giacobbe
Subjects: medicine.medical_specialty, Coronavirus disease 2019 (COVID-19), business.operation, Declaration, Conflict of interest, Octapharma, Intensive care, Political science, Family medicine, Honorarium, medicine, Observational study, business, Declaration of Helsinki
Abstract: Background: Coronavirus disease 2019 (COVID-19) associated pulmonary aspergillosis (CAPA) has emerged as a complication in critically ill COVID-19 patients. To determine the prevalence of CAPA in patients with COVID-19 in intensive care units (ICU) and to investigate risk factors for CAPA as well as outcome. Methods: The European Confederation of Medical Mycology (ECMM) conducted a multinational study including 20 centers from nine different countries to assess epidemiology, risk factors, treatment and outcome of CAPA. CAPA was defined according to ECMM/ISHAM consensus definitions. Findings: A total of 592 patients were included in this study, including 11 (1.9%) patients with histologically proven CAPA, 80 (13.5%) patients with probable CAPA, 18 (3%) with possible CAPA and 483 (81.6%) without CAPA. CAPA was diagnosed a median of 8 days (range 0-31) after ICU admission predominantly in older patients [adjusted hazard ratio (aHR) 1.04 per year] with any form of invasive respiratory support (HR 3.4) and receiving tocilizumab (HR 2.45). Median prevalence of CAPA per center was 10.7% (range 1.7% - 26.8%). CAPA was associated with significantly lower 90-day ICU survival rate (29% in patients with CAPA versus 57% in patients without CAPA; Mantel-Byar p
Published: 2021

88. Increased Fecal Calprotectin is Associated with Worse Gastrointestinal Symptoms and Quality of Life Scores in Children with Cystic Fibrosis

Author: Fabien Beaufils, Michael Fayon, Raphaël Enaud, Stéphanie Bui, Laurence Delhaes, Thierry Lamireau, Emmanuel Mas, H. Clouzeau, François Galode, M. Mittaine, Martin Addra, Centre de recherche Cardio-Thoracique de Bordeaux [Bordeaux] (CRCTB), Université Bordeaux Segalen - Bordeaux 2-CHU Bordeaux [Bordeaux]-Institut National de la Santé et de la Recherche Médicale (INSERM), Aquitaine’s Care and Research organisation for inflammatory and Immune-Mediated diseases [CHU Bordeaux] (FHU ACRONIM), CHU Bordeaux [Bordeaux], CIC Bordeaux, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche en Santé Digestive (IRSD ), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), CHU Toulouse [Toulouse], Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Admin, Oskar, and Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)
Subjects: medicine.medical_specialty, Nausea, lcsh:Medicine, Gastroenterology, Cystic fibrosis, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, Article, 03 medical and health sciences, 0302 clinical medicine, Bloating, [SDV.MHEP.PED] Life Sciences [q-bio]/Human health and pathology/Pediatrics, Quality of life, 030225 pediatrics, Internal medicine, gas, intestinal inflammation, Medicine, [SDV.MHEP.PED]Life Sciences [q-bio]/Human health and pathology/Pediatrics, business.industry, lcsh:R, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, General Medicine, pancreatic insufficiency, medicine.disease, nausea, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, humanities, 3. Good health, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Vomiting, Biomarker (medicine), [SDV.MHEP.PSR] Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, 030211 gastroenterology & hepatology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, reflux, Calprotectin, medicine.symptom, business, Dysbiosis
Abstract: In cystic fibrosis (CF), cystic fibrosis transmembrane regulator (CFTR) dysfunction leads to digestive disorders that promote intestinal inflammation and dysbiosis enhancing gastrointestinal symptoms. In pancreatic insufficiency CF patients, both intestinal inflammation and dysbiosis, are associated with an increase in the fecal calprotectin (FC) level. However, associations between the FC level, gastrointestinal symptoms, and quality of life (QoL) remain poorly studied. We aimed to assess such associations in pancreatic insufficiency CF children. The FC level was measured in pancreatic insufficiency CF children&rsquo, s stool samples. Children and their parents completed two questionnaires: The Gastrointestinal Symptoms Scales 3.0-PedsQLTM and the Quality of Life Pediatric Inventory 4.0-PedsQLTM. Lower scores indicated worse symptomatology or QoL. Thirty-seven CF children were included. A FC level above 250 &micro, g/g was associated with worse gastrointestinal symptoms and QoL scores. The FC level was inversely correlated with several gastrointestinal scores assessed by children (i.e., Total, &ldquo, Heart Burn Reflux&rdquo, &ldquo, Nausea and Vomiting&rdquo, and &ldquo, Gas and Bloating&rdquo, ). Several QoL scores were correlated with gastrointestinal scores. The FC level was weakly associated with clinical parameters. Some gastrointestinal and QoL scores were related to disease severity associated parameters. In CF, the FC level, biomarker previously related to intestinal inflammation and dysbiosis, was associated with worse digestive symptoms and QoL scores.
Published: 2020

89. 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

90. Reply

Author: Louise-Eva Vandenborght, Raphaël Enaud, Charlotte Urien, Noémie Coron, Pierre-Olivier Girodet, Stéphanie Ferreira, Patrick Berger, and Laurence Delhaes
Subjects: Immunology, Immunology and Allergy
Published: 2020

91. Review for 'The Mycobiomes and Bacteriomes of Sputum, Saliva, and Home Dust'

Author: Laurence Delhaes
Subjects: Saliva, business.industry, Medicine, Sputum, medicine.symptom, business, Mycobiome, Microbiology
Published: 2020

92. Type 2-high asthma is associated with a specific indoor mycobiome and microbiome

Author: Raphaël Enaud, Patrick Berger, Laurence Delhaes, Louise-Eva Vandenborght, Pierre-Olivier Girodet, Charlotte Urien, Stéphanie Ferreira, and Noémie Coron
Subjects: 0301 basic medicine, Male, Endotype, Exacerbation, V3-V4, Variable 3-variable 4 of the 16S rRNA encoding gene, microbiome, Severity of Illness Index, 0302 clinical medicine, Immunology and Allergy, Type 2 asthma, IL, Interleukin, OTU, Operational taxonomic unit, DNA, Fungal, medicine.diagnostic_test, ICS, Inhaled corticosteroid, T2, Type 2, Microbiota, Indoor environment, Dust, Middle Aged, ERS, European Respiratory Society, LABA, Long acting beta2 agonist, STB, Stable state, Air Pollution, Indoor, Female, medicine.symptom, EDC, Electrostatic Dust Collector, Environmental Monitoring, Spirometry, severe asthma, VRC, Voriconazole, Adult, DNA, Bacterial, BAL, Bronchoalveolar lavage, SA, Severe asthma, COBRA, Cohort of Bronchial obstruction and Asthma, Immunology, BMI, Body mass index, qPCR, Quantitative polymerase chain reaction, Article, EXA, Exacerbation of asthma, 03 medical and health sciences, mycobiome, medicine, ITS2, Internal transcribed spacer 2, Humans, Microbiome, FeNO, Asthma, Aged, business.industry, Sputum, medicine.disease, respiratory tract diseases, PERMANOVA, Permutational multivariate analysis of variance, 030104 developmental biology, 030228 respiratory system, NGS, Next generation sequencing, Metagenomics, PCoA, principal coordinates analysis, Exhaled nitric oxide, LAMA, Long acting muscarinic antagonist, OCS, Oral corticosteroid, business, FeNO, Fraction of exhaled nitric oxide, LDA, Linear discriminant analysis
Abstract: Background The links between microbial environmental exposures and asthma are well documented, but no study has combined deep-sequencing results from pulmonary and indoor microbiomes of asthmatic patients with spirometry, clinical and endotype parameters. Objective The goal of this study was to investigate the links between indoor microbial exposures and pulmonary microbial communities and to document the role of microbial exposures on inflammatory and clinical outcomes of patients with severe asthma (SA). Methods Fifty-five SA patients from the national COBRA cohort were enrolled for analyzing their indoor microbial flora through the use of electrostatic dust collectors (EDCs). Among these patients, 22 were able to produce sputa during stable or pulmonary exacerbation periods and had complete pairs of EDC and sputum samples, both collected and analysed. We used amplicon targeted metagenomics to compare microbial communities from EDC and sputum samples of patients according to type 2 (T2)-asthma endotypes. Results Compared to patients with T2-low SA, patients with T2-high SA exhibited an increase in bacterial alpha-diversity and a decrease in fungal alpha-diversity of their indoor microbial floras, the latter being significantly correlated with FeNO levels. The beta-diversity of the EDC mycobiome significantly clustered according to T2 endotypes. Moreover, the proportion of fungal taxa in common between sputum and EDC samples was significantly higher when patients exhibited acute exacerbation. Conclusion These results illustrated, for the first time, a potential association between the indoor mycobiome and clinical features of SA patients, which should renew interest in deciphering the interactions between indoor environment, fungi, and host in asthma., Graphical abstract, Capsule summary. This study is the first to date that investigates both the endogenous and the exogenous mycobiomes and microbiomes of asthmatic patients and reveals associations between indoor microbial communities, exacerbation, and T2 of severe asthma.
Published: 2020

93. Severe toxoplasmosis imported from tropical Africa in immunocompetent patients: A case series

Author: Marie-Laure Dardé, Benjamin Rossi, F. Ajana, Paul Loubet, Anne-Sophie Deleplancque, Boualem Sendid, Eric Senneville, Sandrine Houzé, Laurence Delhaes, Jordan Leroy, Denis Malvy, Hélène Yera, and Frédéric Gabriel
Subjects: Adult, Male, Pediatrics, medicine.medical_specialty, Cerebellar Ataxia, 030231 tropical medicine, Serology, IDLIC, 03 medical and health sciences, 0302 clinical medicine, Communicable Diseases, Imported, parasitic diseases, Genotype, Medicine, Humans, 030212 general & internal medicine, Myositis, Africa South of the Sahara, biology, business.industry, Zoonosis, Public Health, Environmental and Occupational Health, Chorioretinitis, Toxoplasma gondii, medicine.disease, biology.organism_classification, Toxoplasmosis, 3. Good health, Infectious Diseases, Etiology, France, business, Immunocompetence, Toxoplasma
Abstract: Background Toxoplasmosis is a zoonosis caused by the protozoan Toxoplasma gondii. In immunocompetent patients the infection is usually benign. However, cases of severe and even lethal primo-infections are regularly reported in South America. In contrast, data from tropical Africa are fragmentary. Methods Data for French cases of severe toxoplasmosis acquired between 2013 and 2018, in tropical Africa and among immunocompetent patients were collected retrospectively in 2018. Results Four male patients with a mean age of 34-years were identified. All infections originated in West or Central Africa. The clinical presentations were heterogeneous: two patients had severe disseminated toxoplasmosis, of which one presented with chorioretinitis associated with myositis and the other with febrile pneumopathy; one patient presented with post-infectious acute cerebellar ataxia and the final case had general symptoms and skin manifestations. The diagnosis of acute toxoplasmosis was confirmed by serology in four patients. Molecular diagnosis confirmed T. gondii infection in three patients with Africa 1 as the dominant genotype. The infection was cured with anti-infective treatment in all four patients. Ocular sequelae were reported in the two patients with chorioretinitis. Conclusions Imported cases of severe toxoplasmosis in immunocompetent patients are rare in France. However, this aetiology should be evoked rapidly in a patient with a severe infectious syndrome who has recently visited or originated from tropical Africa.
Published: 2020

94. Pneumocystis jiroveciiin Patients With Cystic Fibrosis: A Review

Author: Pierre Bonnet, Solène Le Gal, Enrique Calderon, Laurence Delhaes, Dorothée Quinio, Florence Robert-Gangneux, Sophie Ramel, Gilles Nevez, Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP), Université d'Angers (UA), Laboratoire de Parasitologie et Mycologiede [CHRU Brest], Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), SFR UA 4208 Interactions Cellulaires et Applications Thérapeutiques (ICAT), Hospital Universitario Virgen del Rocío [Sevilla], Aquitaine’s Care and Research organisation for inflammatory and Immune-Mediated diseases [CHU Bordeaux] (FHU ACRONIM), CHU Bordeaux [Bordeaux], Centre de recherche Cardio-Thoracique de Bordeaux [Bordeaux] (CRCTB), Université Bordeaux Segalen - Bordeaux 2-CHU Bordeaux [Bordeaux]-Institut National de la Santé et de la Recherche Médicale (INSERM), 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 ), Fondation ILDYS (ILDYS), Chard-Hutchinson, Xavier, Université d'Angers (UA)-Université de Rennes 1 (UR1), and 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 )
Subjects: 0301 basic medicine, Cystic Fibrosis, medicine.medical_treatment, [SDV]Life Sciences [q-bio], lcsh:QR1-502, Disease, Pneumocystis carinii, Pneumocystis pneumonia, Cystic fibrosis, lcsh:Microbiology, Organ transplantation, genomic diversity, cystic fibrosis, Cellular and Infection Microbiology, Child, Lung, Pneumocystis jirovecii, biology, Pneumonia, Pneumocystis, 3. Good health, [SDV] Life Sciences [q-bio], Infectious Diseases, medicine.symptom, Brazil, Adult, Microbiology (medical), medicine.medical_specialty, Pneumocystis primary infection, Mini Review, 030106 microbiology, Immunology, Microbiology, Asymptomatic, 03 medical and health sciences, medicine, Pneumocystispneumonia, microbiota, lung transplantation, Humans, Lung transplantation, Risk factor, business.industry, Pneumocystisprimary infection, Infant, medicine.disease, biology.organism_classification, 030104 developmental biology, pulmonary colonization, business
Abstract: Réseau Muco Ouest., Pneumocystis pneumonia (PCP) remains the most frequent AIDS-defining illness in developed countries. This infection also occurs in non-AIDS immunosuppressed patients, e.g., those who have undergone an organ transplantation. Moreover, mild Pneumocystis jirovecii infections related to low pulmonary fungal burden, frequently designated as pulmonary colonization, occurs in patients with chronic pulmonary diseases, e.g., cystic fibrosis (CF). Indeed, this autosomal recessive disorder alters mucociliary clearance leading to bacterial and fungal colonization of the airways. This mini-review compiles and discusses available information on P. jirovecii and CF. It highlights significant differences in the prevalence of P. jirovecii pulmonary colonization in European and Brazilian CF patients. It also describes the microbiota associated with P. jirovecii in CF patients colonized by P. jirovecii. Furthermore, we have described P. jirovecii genomic diversity in colonized CF patients. In addition of pulmonary colonization, it appears that PCP can occur in CF patients specifically after lung transplantation, thus requiring preventive strategies. In other respects, Pneumocystis primary infection is a worldwide phenomenon occurring in non-immunosuppressed infants within their first months. The primary infection is mostly asymptomatic but it can also present as a benign self-limiting infection. It probably occurs in the same manner in CF infants. Nonetheless, two cases of severe Pneumocystis primary infection mimicking PCP in CF infants have been reported, the genetic disease appearing in these circumstances as a risk factor of PCP while the host-pathogen interaction in older children and adults with pulmonary colonization remains to be clarified.
Published: 2020

95. The airway microbiota in cystic fibrosis: a complex fungal and bacterial community--implications for therapeutic management.

Author: Laurence Delhaes, Sébastien Monchy, Emilie Fréalle, Christine Hubans, Julia Salleron, Sylvie Leroy, Anne Prevotat, Frédérick Wallet, Benoit Wallaert, Eduardo Dei-Cas, Telesphore Sime-Ngando, Magali Chabé, and Eric Viscogliosi
Subjects: Medicine, Science
Abstract: BackgroundGiven the polymicrobial nature of pulmonary infections in patients with cystic fibrosis (CF), it is essential to enhance our knowledge on the composition of the microbial community to improve patient management. In this study, we developed a pyrosequencing approach to extensively explore the diversity and dynamics of fungal and prokaryotic populations in CF lower airways.Methodology and principal findingsFungi and bacteria diversity in eight sputum samples collected from four adult CF patients was investigated using conventional microbiological culturing and high-throughput pyrosequencing approach targeting the ITS2 locus and the 16S rDNA gene. The unveiled microbial community structure was compared to the clinical profile of the CF patients. Pyrosequencing confirmed recently reported bacterial diversity and observed complex fungal communities, in which more than 60% of the species or genera were not detected by cultures. Strikingly, the diversity and species richness of fungal and bacterial communities was significantly lower in patients with decreased lung function and poor clinical status. Values of Chao1 richness estimator were statistically correlated with values of the Shwachman-Kulczycki score, body mass index, forced vital capacity, and forced expiratory volume in 1 s (p = 0.046, 0.047, 0.004, and 0.001, respectively for fungal Chao1 indices, and p = 0.010, 0.047, 0.002, and 0.0003, respectively for bacterial Chao1 values). Phylogenetic analysis showed high molecular diversities at the sub-species level for the main fungal and bacterial taxa identified in the present study. Anaerobes were isolated with Pseudomonas aeruginosa, which was more likely to be observed in association with Candida albicans than with Aspergillus fumigatus.ConclusionsIn light of the recent concept of CF lung microbiota, we viewed the microbial community as a unique pathogenic entity. We thus interpreted our results to highlight the potential interactions between microorganisms and the role of fungi in the context of improving survival in CF.
Published: 2012
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96. Microplanktonic community structure in a coastal system relative to a Phaeocystis bloom inferred from morphological and tag pyrosequencing methods.

Author: Sébastien Monchy, Jean-David Grattepanche, Elsa Breton, Dionigia Meloni, Giovanna Sanciu, Magali Chabé, Laurence Delhaes, Eric Viscogliosi, Télesphore Sime-Ngando, and Urania Christaki
Subjects: Medicine, Science
Abstract: BACKGROUND: Massive phytoplankton blooms, like the recurrent Phaeocystis proliferation observed every year in the Eastern English Channel (EEC), have a significant influence on the overall planktonic community structure and their food web dynamics. As well as being an important area for local fisheries, the EEC is an ideal ecosystem for work on microbial diversity. This is because, although its environmental context is relatively complex, it is reasonably well understood due to several years of monitoring and morphological observations of its planktonic organisms. The objective of our study was to better understand the under-explored microbial eukaryotic diversity relative to the Phaeocystis bloom. METHODOLOGY AND PRINCIPAL FINDINGS: The community structure of microplankton (diatoms, haptophytes, ciliates and dinoflagellates) was studied through morphological observations and tag pyrosequencing. During the annual Phaeocystis spring bloom, the phytoplankton biomass increased by 34-fold, while the microzooplankton biomass showed a 4-fold increase, representing on average about 4.6% of the biomass of their phytoplankton prey. Tag pyrosequencing unveiled an extensive diversity of Gymnodiniaceae, with G. spirale and G. fusiformis representing the most abundant reads. An extended diversity of Phaeocystales, with partial 18S rDNA genes sequence identity as low as 85% was found, with taxa corresponding to P. globosa, but also to unknown Phaeocystaceae. CONCLUSIONS: Morphological analyses and pyrosequencing were generally in accordance with capturing frequency shifts of abundant taxa. Tag pyrosequencing allowed highlighting the maintenance of microplankton diversity during the Phaeocystis bloom and the increase of the taxa presenting low number of reads (minor taxa) along with the dominant ones in response to biotic and/or abiotic changing conditions. Although molecular approaches have enhanced our perception on diversity, it has come to light that the challenge of modelling and predicting ecological change requires the use of different complementary approaches, to link taxonomic data with the functional roles of microbes in biogeochemical cycles.
Published: 2012
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97. Developing collaborative works for faster progress on fungal respiratory infections in cystic fibrosis

Author: Gilles Nevez, Joerg Steinmann, Laurence Delhaes, Ludovic Duvaux, Jean-Philippe Bouchara, Wieland Meyer, Ludwig Sedlacek, Maxime Fleury, Nicolas Papon, Loïc Favennec, Patrick Vandeputte, Javier Pemán, Amandine Gastebois, Françoise Botterel, Jose A. Vazquez, Stéphane Ranque, Sharon C.-A. Chen, Ana Alastruey-Izquierdo, Solène Le Gal, Craig Williams, Marie-Elisabeth Bougnoux, Carsten Schwarz, Françoise Symoens, Estrella Martin Mazuelos, Guillermo Quindós, Thomas Dugé de Bernonville, Josep Cano, Amparo Solé, Amandine Rougeron, Sandrine Giraud, María Teresa Martín-Gómez, Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP), Université d'Angers (UA), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), University of Sheffield [Sheffield], Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, Anofel Cryptosporidium National Network, 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), Service de Microbiologie, Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de Parasitologie et de Mycologie [Lille], Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Centre de recherche Cardio-Thoracique de Bordeaux [Bordeaux] (CRCTB), Université Bordeaux Segalen - Bordeaux 2-CHU Bordeaux [Bordeaux]-Institut National de la Santé et de la Recherche Médicale (INSERM), Appareil Digestif Environnement Nutrition (ADEN ), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Augusta University, University System of Georgia (USG), The Westmead Institute for Medical Research, Centre for Infectious Disease and Microbiology (CIDM), Hôpital de la Cavale Blanche - CHRU Brest (CHU - BREST ), APP1031943, National Health and Medical Research Council, 2010/IC1003, Vaincre la Mucoviscidose, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Groupe d'Etude des Interactions Hôte-Parasite (GEIHP), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Groupe d’Etude des Interactions Hôte-Pathogène, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), 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 ), and Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de la Recherche Agronomique (INRA)
Subjects: Microbiological Techniques, 0301 basic medicine, medicine.medical_specialty, Antifungal Agents, Cystic Fibrosis, biological diagnosis, 030106 microbiology, Medizin, Context (language use), Disease, Drug resistance, Cystic fibrosis, pathogenic mechanisms, cystic fibrosis, Scedosporium, 03 medical and health sciences, fungal respiratory infections, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Drug Resistance, Multiple, Fungal, medicine, Humans, Microbiome, Intensive care medicine, Respiratory Tract Infections, Genotyping, treatment, business.industry, Fungi, Genomics, General Medicine, medicine.disease, 3. Good health, Infectious Diseases, Mycoses, Scedosporium species, Identification (biology), business
Abstract: International audience; Cystic fibrosis (CF) is the major genetic inherited disease in Caucasian populations. The respiratory tract of CF patients displays a sticky viscous mucus, which allows for the entrapment of airborne bacteria and fungal spores and provides a suitable environment for growth of microorganisms, including numerous yeast and filamentous fungal species. As a consequence, respiratory infections are the major cause of morbidity and mortality in this clinical context. Although bacteria remain the most common agents of these infections, fungal respiratory infections have emerged as an important cause of disease. Therefore, the International Society for Human and Animal Mycology (ISHAM) has launched a working group on Fungal respiratory infections in Cystic Fibrosis (Fri-CF) in October 2006, which was subsequently approved by the European Confederation of Medical Mycology (ECMM). Meetings of this working group, comprising both clinicians and mycologists involved in the follow-up of CF patients, as well as basic scientists interested in the fungal species involved, provided the opportunity to initiate collaborative works aimed to improve our knowledge on these infections to assist clinicians in patient management. The current review highlights the outcomes of some of these collaborative works in clinical surveillance, pathogenesis and treatment, giving special emphasis to standardization of culture procedures, improvement of species identification methods including the development of nonculture-based diagnostic methods, microbiome studies and identification of new biological markers, and the description of genotyping studies aiming to differentiate transient carriage and chronic colonization of the airways. The review also reports on the breakthrough in sequencing the genomes of the main Scedosporium species as basis for a better understanding of the pathogenic mechanisms of these fungi, and discusses treatment options of infections caused by multidrug resistant microorganisms, such as Scedosporium and Lomentospora species and members of the Rasamsonia argillacea species complex.
Published: 2018

98. Fungal and Bacterial Diversity of Airway Microbiota in Adults with Cystic Fibrosis: Concordance Between Conventional Methods and Ultra-Deep Sequencing, and Their Practical use in the Clinical Laboratory

Author: Benoit Wallaert, Franziska A. Stressmann, Françoise Botterel, Kenneth D. Bruce, Cécile Angebault, J. M. Costa, Odile Cabaret, Laurence Delhaes, and Frédéric Wallet
Subjects: Adult, DNA, Bacterial, Microbiological Techniques, 0301 basic medicine, medicine.medical_specialty, Cystic Fibrosis, Veterinary (miscellaneous), Respiratory System, 030106 microbiology, Plant Science, DNA, Ribosomal, Applied Microbiology and Biotechnology, Microbiology, Cystic fibrosis, Young Adult, 03 medical and health sciences, Medical microbiology, RNA, Ribosomal, 16S, DNA, Ribosomal Spacer, RNA, Ribosomal, 18S, medicine, Cluster Analysis, Humans, Internal transcribed spacer, DNA, Fungal, Phylogeny, Bacteria, biology, Microbiota, Fungi, Sputum, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Ribosomal RNA, medicine.disease, 16S ribosomal RNA, biology.organism_classification, Agricultural and Biological Sciences (miscellaneous), Terminal restriction fragment length polymorphism, 030104 developmental biology, Female, medicine.symptom, Agronomy and Crop Science, Polymorphism, Restriction Fragment Length, Follow-Up Studies
Abstract: Given the complexity of the airway microbiota in the respiratory tract of cystic fibrosis (CF) patients, it seems crucial to compile the most exhaustive and exact list of the microbial communities inhabiting CF airways. The aim of the present study was to compare the bacterial and fungal diversity of sputa from adult CF patients during non-exacerbation period by culture-based and molecular methods, and ultra-deep-sequencing (UDS). Sputum samples from four CF patients were cultured and analysed by DNA extractions followed by terminal restriction fragment length polymorphism analysis through resolution of bacterial ribosomal gene (rDNA) fragments, and cloning plus sequencing of part of fungal rRNA genes. These approaches were compared with UDS method targeting 16S rDNA gene and the internal transcribed spacer (ITS) 2 region of rDNA. A total of 27 bacterial and 18 fungal genera were detected from the four patients. Five (18%) and 3 (16%) genera were detected by culture for bacteria and fungi, respectively, 9 (33%) and 3 (16%) by first generation sequencing (FGS) methods, and 26 (96%) and 18 (100%) by UDS. The mean number of genera detected by UDS per patient was statistically higher than by culture or FGS methods. Patients with severe airway disease as assessed by standard spirometry exhibited a reduced fungal and bacterial diversity. UDS approach evaluates more extensively the diversity of fungal and bacterial flora compared with cultures. However, it currently remains difficult to routinely use UDS mainly because of the lack of standardization, and the current cost of this method.
Published: 2017

99. 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

100. Detección y genotipificación de Pneumocystis jirovecii en muestras de pacientes mexicanos VIH positivos y negativos

Author: Fernando Rosalío Morales-Villarreal, Francisca Hernández-Hernández, Fabiola Ramírez-Corona, Laurence Delhaes, Amanda Alcántara-Mojica, Edith Sánchez-Paredes, Erika Córdova-Martínez, and Sigfrido Sierra-Galván
Subjects: Adult, Male, Genotype, Negative control, Early detection, HIV Infections, Pneumocystis carinii, Polymerase Chain Reaction, Young Adult, Pneumocystis jirovecii, Medicine, Humans, In patient, Prospective Studies, Mexico, Phylogeny, Aged, biology, business.industry, Pneumonia, Pneumocystis, Healthy subjects, General Medicine, Middle Aged, biology.organism_classification, Molecular biology, Cross-Sectional Studies, Child, Preschool, Transplant patient, Female, business, Nested polymerase chain reaction, Phylogenetic relationship
Abstract: espanolIntroduccion: Pneumocystis jirovecii es un hongo atipico detectado particularmente en pacientes VIH-positivos o con trasplante. Objetivo: Detectar y genotipificar Pneumocystis jirovecii en muestras de pacientes de dos hospitales de la ciudad de Mexico. Metodo: Fueron procesadas 89 muestras respiratorias, correspondientes a 53 pacientes (30 VIH positivos y 23 VIH negativos) con sintomatologia respiratoria y 11 personas sanas incluidas como control negativo. El DNA fue extraido y amplificado por PCR anidada de la region del espaciador transcrito interno, obteniendo un fragmento en cada ronda (de 693 y 550 pb). Los genotipos y su relacion filogenetica fueron determinados por secuenciacion del fragmento de 550 pb. Resultados: Cuarenta y ocho muestras de 30 pacientes VIH-positivos provenian de un solo hospital, de las cuales 11 (36.6 %) fueron positivas a Pneumocystis jirovecii. Ninguna fue positiva en pacientes VIH-negativos o personas sanas. Los haplotipos detectados con mayor frecuencia fueron Eg y Em. Conclusiones: La frecuencia de infeccion por Pneumocystis jirovecii fue alta en la poblacion mexicana estudiada. El genotipo mas frecuente fue diferente a los reportados en otros paises. Es necesario encauzar este problema de salud hacia la deteccion temprana de esta infeccion. EnglishIntroduction: Pneumocystis jirovecii is an atypical fungus particularly detected in HIV-positive or transplant patients. Objective: To detect and genotype Pneumocystis jirovecii in patient samples from two hospitals in Mexico City. Method: Eighty-nine respiratory tract samples, corresponding to 53 patients (30 HIV-positive and 23 HIV-negative) with respiratory symptoms and to 11 healthy individuals included as negative control, were processed. DNA was extracted from the ITS region and amplified by nested polymerase chain reaction from the internal transcribed spacer, with one fragment being obtained at each round (693 and 550 bp). Genotypes and their phylogenetic relationship were determined by sequencing the 550 bp fragment. Results: Forty-eight samples from 30 HIV-positive patients were received from a single hospital, out of which 11 (36.6 %) were positive for Pneumocystis jirovecii. No sample was positive in HIV-negative patients or healthy subjects. The most frequently detected haplotypes were Eg and Em. Conclusions: The frequency of Pneumocystis jirovecii infection was high in the studied Mexican population. The most common genotype was different from those reported in other countries. It is necessary to address this health problem through early detection of this infection.
Published: 2019

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