Publications by authors named "Stephane Bretagne"

100Publications

Risk factors associated with COVID-19-associated pulmonary aspergillosis in ICU patients: a French multicentric retrospective cohort.

Clin Microbiol Infect 2020 Dec 13. Epub 2020 Dec 13.

Université de Paris, Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France; Molecular Mycology Unit, CNRS UMR2000, National Reference Centre for Invasive Mycoses and Antifungals (NRCMA), Institut Pasteur, Paris, France. Electronic address:

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December 2020

Comparison of MultiLocus Sequence Typing (MLST) and Microsatellite Length Polymorphism (MLP) for genotyping.

Comput Struct Biotechnol J 2020 15;18:2890-2896. Epub 2020 Oct 15.

Laboratoire de Parasitologie-Mycologie; AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.

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October 2020

The presence of Pneumocystis jirovecii in critically ill patients with COVID-19.

J Infect 2020 Nov 4. Epub 2020 Nov 4.

Laboratoire de Parasitologie-Mycologie AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Université de Paris, Institut Pasteur, CNRS UMR2000, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques.

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November 2020

Entamoeba histolytica DNA Detection in Serum from Patients with Suspected Amoebic Liver Abscess.

J Clin Microbiol 2020 Sep 22;58(10). Epub 2020 Sep 22.

Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis Lariboisière Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.

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September 2020

Mastomys natalensis, Cricetomys gambianus and Taterillus sp. were found PCR positive for Leishmania major in Burkina Faso, West Africa.

Ann Parasitol 2020 ;66(2):251-254

Unité de Formation et de Recherche en Sciences de la Santé, Université Ouaga I Pr Joseph Ki-Zerbo, Charles de Gaulles street, Ouagadougou 03 BP 7022 Ouaga 03, Burkina Faso.

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July 2020

Prevalence of putative invasive pulmonary aspergillosis in critically ill patients with COVID-19.

Lancet Respir Med 2020 06 20;8(6):e48-e49. Epub 2020 May 20.

Réanimation Médicale et Toxicologique, Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France; Université de Paris, Paris, France; Institut National de la Santé et de la Recherche Médicale, Paris, France.

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June 2020

Genotyping in Human Alveolar Echinococcosis Patients: An EmsB Microsatellite Analysis.

Pathogens 2020 Apr 13;9(4). Epub 2020 Apr 13.

UMR CNRS 6249 Laboratoire Chrono-environnement, Université Franche-Comté, 16 Route de Gray, 25030 Besançon, France.

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April 2020

Anti-Saccharomyces cerevisiae IgG and IgA antibodies are associated with systemic inflammation and advanced disease in hidradenitis suppurativa.

J Allergy Clin Immunol 2020 Aug 13;146(2):452-455.e5. Epub 2020 Feb 13.

Université de Paris, Paris, France; INSERM UMR 1163, Laboratory of Genetic Skin Diseases, Institut Imagine, Paris, France; Department of Dermatology, Hôpital Saint-Louis, APHP, Paris, France. Electronic address:

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August 2020

Failure of multiplex meningitis/encephalitis (ME) NAT during cryptococcal meningitis in solid organ recipients.

Transpl Infect Dis 2020 Aug 11;22(4):e13263. Epub 2020 Jun 11.

Service de Maladies Infectieuses et Tropicales, Centre d'Infectiologie Necker-Pasteur, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France.

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August 2020

Aspergillus flavus malignant external otitis in a diabetic patient: case report and literature review.

Infection 2020 Apr 8;48(2):193-203. Epub 2020 Feb 8.

Service de Maladies Infectieuses Et Tropicales, APHP, Hôpital Bichat-Claude Bernard, 46, rue Henri Huchard, 75018, Paris, France.

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April 2020

Quantification of : Cross-Platform Comparison of One qPCR Assay with Leading Platforms and Six Master Mixes.

J Fungi (Basel) 2019 Dec 26;6(1). Epub 2019 Dec 26.

Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, 75475 Paris, France.

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December 2019

Outbreak-Causing Fungi: Pneumocystis jirovecii.

Mycopathologia 2020 Oct 28;185(5):783-800. Epub 2019 Nov 28.

Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France.

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October 2020

Global guideline for the diagnosis and management of mucormycosis: an initiative of the European Confederation of Medical Mycology in cooperation with the Mycoses Study Group Education and Research Consortium.

Lancet Infect Dis 2019 12 5;19(12):e405-e421. Epub 2019 Nov 5.

Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India.

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December 2019

Time to and differential time to blood culture positivity for assessing catheter-related yeast fungaemia: A longitudinal, 7-year study in a single university hospital.

Mycoses 2020 Jan 3;63(1):95-103. Epub 2019 Nov 3.

Parasitology-Mycology Laboratory, Lariboisière Saint-Louis Fernand Widal Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.

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January 2020

Corrigendum: Continuous Decline of Seroprevalence in Hospital: A 1997-2014 Longitudinal Study in Paris, France.

Front Microbiol 2018 27;9:2814. Epub 2018 Nov 27.

Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis, Lariboisière, Fernand-Widal, Paris, France.

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November 2018

Failure of voriconazole therapy due to acquired azole resistance in Aspergillus fumigatus in a kidney transplant recipient with chronic necrotizing aspergillosis.

Am J Transplant 2018 09 12;18(9):2352-2355. Epub 2018 Jul 12.

Infectious Diseases Department, Necker Hospital, Public Assistance/Paris Hospitals, University Paris Descartes, Paris, France.

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September 2018

Population Structure of Candida parapsilosis: No Genetic Difference Between French and Uruguayan Isolates Using Microsatellite Length Polymorphism.

Mycopathologia 2018 Apr 16;183(2):381-390. Epub 2017 Nov 16.

Institut Pasteur, CNRS, National Reference Center for Invasive Mycoses and Antifungals, Molecular Mycology Unit, URA, 3012, Paris, France.

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April 2018

A cell impedance-based real-time in vitro assay to assess the toxicity of amphotericin B formulations.

Toxicol Appl Pharmacol 2017 11 1;334:18-23. Epub 2017 Sep 1.

Institut Pasteur, CNRS, Molecular Mycology unit, URA3012 Paris, France; Laboratory of Parasitology-Mycology, Saint-Louis Lariboisière Fernand Widal hospitals, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France; Paris-Diderot, Sorbonne Paris Cité University, Paris, France.

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November 2017

Diversity of Pneumocystis jirovecii Across Europe: A Multicentre Observational Study.

EBioMedicine 2017 Aug 29;22:155-163. Epub 2017 Jun 29.

Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Institut Pasteur, CNRS, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, URA3012, Paris, France.

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August 2017

detection in asymptomatic patients: what does its natural history tell us?

F1000Res 2017 23;6:739. Epub 2017 May 23.

Parasitology-Mycology Laboratory, Lariboisière Saint-Louis Fernand Widal Hospitals, Assistance Publique-Hôpitaux de Paris, Paris, France.

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May 2017

Investigating Clinical Issues by Genotyping of Medically Important Fungi: Why and How?

Clin Microbiol Rev 2017 07;30(3):671-707

Institut Pasteur, Molecular Mycology Unit, National Reference Center for Invasive Mycoses and Antifungals, Paris, France

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July 2017

Predisposing factors and outcome of uncommon yeast species-related fungaemia based on an exhaustive surveillance programme (2002-14).

J Antimicrob Chemother 2017 06;72(6):1784-1793

Institut Pasteur, CNRS, Molecular Mycology Unit, French National Reference Center for Invasive Mycoses & Antifungals, URA3012, Paris, France.

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June 2017

The risk and clinical outcome of candidemia depending on underlying malignancy.

Intensive Care Med 2017 May 20;43(5):652-662. Epub 2017 Mar 20.

Institut Pasteur, Molecular Mycology Unit, French National Reference Center for Invasive Mycoses and Antifungals, CNRS URA3012, 25, rue du Dr. Roux, 75724, Paris Cedex 15, France.

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May 2017

Challenges in microbiological diagnosis of invasive infections.

F1000Res 2017 17;6. Epub 2017 Feb 17.

Parasitology-Mycology Laboratory, Lariboisière Saint-Louis Fernand Widal hospitals, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France; Paris-Diderot, Sorbonne Paris Cité University, Paris, France; Institut Pasteur, CNRS, Molecular Mycology Unit, Reference National Center of Invasive Mycoses and Antifungals, Paris, France.

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February 2017

Fluconazole and Echinocandin Resistance of Correlates Better with Antifungal Drug Exposure Rather than with Mutator Genotype in a French Cohort of Patients Harboring Low Rates of Resistance.

Front Microbiol 2016 23;7:2038. Epub 2016 Dec 23.

Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-WidalParis, France; Université Paris Diderot, Sorbonne Paris CitéParis, France; Unité de Mycologie Moléculaire, Institut Pasteur, Centre National de la Recherche Scientifique, Centre National de Référence Mycoses Invasives et Antifongiques, URA3012Paris, France.

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December 2016

Copy Number Variation of Mitochondrial DNA Genes in Pneumocystis jirovecii According to the Fungal Load in BAL Specimens.

Front Microbiol 2016 12;7:1413. Epub 2016 Sep 12.

Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique - Hôpitaux de ParisParis, France; Sorbonne Paris Cité, Université Paris DiderotParis, France; Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, Institut PasteurParis, France; CNRS URA3012Paris, France.

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September 2016

Performance evaluation of multiplex PCR including Aspergillus-not so simple!

Med Mycol 2017 Jan 23;55(1):56-62. Epub 2016 Sep 23.

Paris-Diderot, Sorbonne Paris Cité University

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January 2017

ECIL guidelines for the diagnosis of Pneumocystis jirovecii pneumonia in patients with haematological malignancies and stem cell transplant recipients.

J Antimicrob Chemother 2016 09 12;71(9):2386-96. Epub 2016 May 12.

Parasitology-Mycology Laboratory, Groupe Hospitalier Lariboisière Saint-Louis Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Diderot, Sorbonne Paris Cité, and Institut Pasteur, Unité de Mycologie Moléculaire, CNRS URA3012, Centre National de Référence Mycoses Invasives et Antifongiques, Paris, France.

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September 2016

Pneumocystis jirovecii pneumonia: still a concern in patients with haematological malignancies and stem cell transplant recipients.

J Antimicrob Chemother 2016 09 12;71(9):2379-85. Epub 2016 May 12.

Department of Haematology, Acute Leukaemia and Stem Cell Transplantation Unit, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium.

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September 2016

New therapeutic strategies for invasive aspergillosis in the era of azole resistance: how should the prevalence of azole resistance be defined?

J Antimicrob Chemother 2016 08;71(8):2075-8

Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France Paris Diderot, Sorbonne Paris Cité University, Paris, France Institut Pasteur, Molecular Mycology Unit, National Reference Centre of Invasive Mycoses and Antifungals, CNRS URA 3012, Paris, France

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August 2016

[Sinonasal fungal infections are not exclusively due to mucorales and Aspergillus!].

Ann Pathol 2016 Aug 27;36(4):245-51. Epub 2016 Jul 27.

Service d'anatomie et cytologie pathologiques, faculté de médecine, université Paris Diderot - Paris 7, AP-HP Lariboisière, 2, avenue Ambroise-Paré, 75475 Paris, France.

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August 2016

Variation in copy number of the 28S rDNA of Aspergillus fumigatus measured by droplet digital PCR and analog quantitative real-time PCR.

J Microbiol Methods 2016 08 14;127:160-163. Epub 2016 Jun 14.

Parasitology-Mycology Laboratory, Lariboisière Saint-Louis Fernand Widal Hospitals, Assistance Publique-Hôpitaux de Paris (AP-HP), France; Université Paris-Diderot, Sorbonne Paris Cité, France; Institut Pasteur, Molecular Mycology Unit, CNRS URA3012, National Reference Center of Invasive Mycoses and Antifungals, France. Electronic address:

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August 2016

Diversity of Pneumocystis jirovecii during Infection Revealed by Ultra-Deep Pyrosequencing.

Front Microbiol 2016 24;7:733. Epub 2016 May 24.

Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique Hôpitaux de Paris, Hôpital Saint-LouisParis, France; Université Paris Diderot, Sorbonne Paris CitéParis, France; Unité de Mycologie Moléculaire, Département de Mycologie, Centre National de Référence Mycoses Invasives et Antifongiques, Institut PasteurParis, France; Centre National de la Recherche Scientifique CNRS URA3012Paris, France.

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June 2016

Seroprevalence of Toxoplasma gondii and direct genotyping using minisequencing in free-range pigs in Burkina Faso.

Int J Food Microbiol 2016 Aug 16;230:10-5. Epub 2016 Apr 16.

Laboratoire de Parasitologie-Mycologie, Groupe hospitalier Saint Louis Lariboisière, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France. Electronic address:

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August 2016

Comparison of Nonculture Blood-Based Tests for Diagnosing Invasive Aspergillosis in an Animal Model.

J Clin Microbiol 2016 Apr 20;54(4):960-6. Epub 2016 Jan 20.

San Antonio Center for Medical Mycology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA South Texas Veterans Health Care System, San Antonio, Texas, USA.

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April 2016

[Cryptococcus where they are not expected: Five case reports of extra-cerebral and extra-pulmonary cryptococcosis].

Ann Pathol 2015 Dec 18;35(6):479-85. Epub 2015 Nov 18.

Unité d'histopathologie humaine et modèles animaux, Institut Pasteur, 28, rue du Dr.-Roux, 75724 Paris, France; Université Paris Descartes, PRES Sorbonne Paris Cité, 75006 Paris, France.

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December 2015

Typing Candida Species Using Microsatellite Length Polymorphism and Multilocus Sequence Typing.

Methods Mol Biol 2016 ;1356:199-214

Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, 25 rue du Dr. Roux, 75724, Paris cedex 15, France.

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May 2016

Absence of Fungal Spore Internalization by Bronchial Epithelium in Mouse Models Evidenced by a New Bioimaging Approach and Transmission Electronic Microscopy.

Am J Pathol 2015 Sep 10;185(9):2421-30. Epub 2015 Jul 10.

Unit of Molecular Mycology, Institut Pasteur, Paris, France; Paris Diderot University, Bio Sorbonne Paris Cité, Paris, France; Parasitology-Mycology Service, Hôpital St Louis, AP-HP, Paris, France.

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September 2015

Cutaneous Invasive Aspergillosis: Retrospective Multicenter Study of the French Invasive-Aspergillosis Registry and Literature Review.

Medicine (Baltimore) 2015 Jul;94(26):e1018

Dermatology Department, UPEC (CB, SI-H-O, OC); Mycology and Parasitology Department (FF); Pathology Department, AP-HP, Henri Mondor Hospital, Créteil (NO); Pasteur Institute, National Reference Center for Invasive Mycoses and Antifungals, Paris (KS, OL, SB); Skin Cancer Unit, Nantes University Hospital (GQ); Infectious Diseases and Tropical Medicine Department, AP-HP, Necker-Enfants malades Hospital, Necker-Pasteur Infectious Diseases Center, IHU Imagine, Paris (OL); Université Paris Descartes (NO, OL); Université Paris-Est-Créteil UPEC, Créteil (OC); Mycology and Parasitology Department, AP-HP, Saint Louis Hospital, Paris (SB); Université Paris Diderot (SB); INSERM Centre d'Investigation Clinique, Créteil, (OC); and EA EpidermE, UPEC, Créteil, France (SI-H-O, OC).

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July 2015

New Short Tandem Repeat-Based Molecular Typing Method for Pneumocystis jirovecii Reveals Intrahospital Transmission between Patients from Different Wards.

PLoS One 2015 1;10(5):e0125763. Epub 2015 May 1.

Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France; Université Paris-Diderot, Sorbonne Cité, Paris, France; Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses invasives et Antifongiques, Paris, France; CNRS URA3012, Paris, France.

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January 2016

Importance of operational factors in the reproducibility of Aspergillus galactomannan enzyme immune assay.

PLoS One 2015 10;10(4):e0124044. Epub 2015 Apr 10.

Laboratoire de Parasitologie-Mycologie, Groupe hospitalier Lariboisière-Saint Louis, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; CNRS URA3012, Paris, France; Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, Paris, France.

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April 2016

Utility of adding Pneumocystis jirovecii DNA detection in nasopharyngeal aspirates in immunocompromised adult patients with febrile pneumonia.

Med Mycol 2015 Apr 30;53(3):241-7. Epub 2014 Dec 30.

Laboratoire de Parasitologie et de Mycologie, APHP, Hôpital Saint Louis Université Paris Diderot, Sorbonne Paris Cité CNRS URA3012 Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, Paris, France

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April 2015

Worrisome trends in incidence and mortality of candidemia in intensive care units (Paris area, 2002-2010).

Intensive Care Med 2014 Sep 6;40(9):1303-12. Epub 2014 Aug 6.

Unité de Mycologie Moléculaire, Centre National de Référence Mycologie et Antifongiques, Institut Pasteur, Paris, France,

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September 2014

Longer incubation times for yeast fungemia: importance for presumptive treatment.

Diagn Microbiol Infect Dis 2014 Oct 20;80(2):119-21. Epub 2014 May 20.

Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, Paris, France; Université Paris Diderot- Paris 7, Service de Parasitologie-Mycologie, Hôpital Saint-Louis, APHP, Créteil, France.

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October 2014

Incidence and risk factors of Legionella pneumophila pneumonia during anti-tumor necrosis factor therapy: a prospective French study.

Chest 2013 Sep;144(3):990-998

Université Paris Descartes, Sorbonne Paris Cité, IHU Imagine, APHP, Hôpital Necker Enfants malades, Centre d'Infectiologie Necker Pasteur, Service de maladies infectieuses et tropicales, Paris. Electronic address:

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September 2013

Aerosolized liposomal amphotericin B: prediction of lung deposition, in vitro uptake and cytotoxicity.

Int J Pharm 2012 Oct 17;436(1-2):106-10. Epub 2012 Jul 17.

Faculty of Pharmacy, Paris-Sud XI University, UMR CNRS 8612, IFR 141, 5 rue J.B. Clément, 92296 Chatenay-Malabry, France.

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October 2012

Azole preexposure affects the Aspergillus fumigatus population in patients.

Antimicrob Agents Chemother 2012 Sep 18;56(9):4948-50. Epub 2012 Jun 18.

Institut Pasteur, Unité de mycologie moléculaire, Paris, France.

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September 2012

High prevalence of triazole resistance in Aspergillus fumigatus, especially mediated by TR/L98H, in a French cohort of patients with cystic fibrosis.

J Antimicrob Chemother 2012 Aug 11;67(8):1870-3. Epub 2012 May 11.

Département de Parasitologie et Mycologie Médicale, Université de Nantes, Nantes Atlantique Universités, EA1155-IICiMed, Faculté de Pharmacie, Nantes, France.

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August 2012

Association between circulating DNA, serum (1->3)-β-D-glucan, and pulmonary fungal burden in Pneumocystis pneumonia.

Clin Infect Dis 2012 Jul 20;55(2):e5-8. Epub 2012 Apr 20.

Laboratoire de Parasitologie-Mycologie, Hôpital Henri Mondor (AP-HP), Créteil, France.

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July 2012

Temporal similarity between Candida albicans genotypes in a Tunisian neonatal intensive care unit suggests several nosocomial cross-contamination episodes.

DNA Cell Biol 2012 Jul 15;31(7):1161-6. Epub 2012 Feb 15.

Unité de Recherche UR 02SP13, Laboratoire de Parasitologie-Mycologie, Ministère de la Santé Publique, Sousse, Tunisie.

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July 2012

Variation of B1 gene and AF146527 repeat element copy numbers according to Toxoplasma gondii strains assessed using real-time quantitative PCR.

J Clin Microbiol 2012 Apr 18;50(4):1452-4. Epub 2012 Jan 18.

Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Chenevier-Mondor, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France.

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April 2012

Candida spp. with acquired echinocandin resistance, France, 2004-2010.

Emerg Infect Dis 2012 Jan;18(1):86-90

Centre National de Référence Mycologie et Antifongiques, Unité de Mycologie Moléculaire, CNRS URA3012, 25, Rue du Dr. Roux, 75724 Paris Cedex 15, France.

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January 2012

Clinical significance of quantifying Pneumocystis jirovecii DNA by using real-time PCR in bronchoalveolar lavage fluid from immunocompromised patients.

J Clin Microbiol 2012 Feb 7;50(2):227-31. Epub 2011 Dec 7.

Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Chenevier-Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France.

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February 2012

Contribution of uniformly 13C-enriched sterigmatocystin to the study of its pulmonary metabolism.

Rapid Commun Mass Spectrom 2011 Oct;25(19):2704-10

UMR BIPAR, U-PEC, AFSSA, ENVA, Faculté de Médecine, Créteil Cedex F-94010, France.

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October 2011