title: Aerially transmitted human fungal pathogens: what can we learn from metagenomics and comparative genomics?
abstract: In the last few decades, aerially transmitted human fungal pathogens have been increasingly recognized to impact the clinical course of chronic pulmonary diseases, such as asthma, cystic fibrosis or chronic obstructive pulmonary disease. Thanks to recent development of culture-free high-throughput sequencing methods, the metagenomic approaches are now appropriate to detect, identify and even quantify prokaryotic or eukaryotic microorganism communities inhabiting human respiratory tract and to access the complexity of even low-burden microbe communities that are likely to play a role in chronic pulmonary diseases. In this review, we explore how metagenomics and comparative genomics studies can alleviate fungal culture bottlenecks, improve our knowledge about fungal biology, lift the veil on cross-talks between host lung and fungal microbiota, and gain insights into the pathogenic impact of these aerially transmitted fungi that affect human beings. We reviewed metagenomic studies and comparative genomic analyses of carefully chosen microorganisms, and confirmed the usefulness of such approaches to better delineate biology and pathogenesis of aerially transmitted human fungal pathogens. Efforts to generate and efficiently analyze the enormous amount of data produced by such novel approaches have to be pursued, and will potentially provide the patients suffering from chronic pulmonary diseases with a better management. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012).
authors.affiliation: Biology & Diversity of Emerging Eukaryotic Pathogens (BDEEP), Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR8204, IFR142, Lille Pasteur Institute, Lille Nord de France University (EA4547), Lille, France; Parasitology-Medical Mycology Department, Faculty of Pharmacy, Lille, France.
authors.forename: Cécile-Marie
authors.initials: CM
authors.lastname: Aliouat-Denis
authors.affiliation: Biology & Diversity of Emerging Eukaryotic Pathogens (BDEEP), Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR8204, IFR142, Lille Pasteur Institute, Lille Nord de France University (EA4547), Lille, France; Parasitology-Medical Mycology Department, Faculty of Pharmacy, Lille, France.
authors.forename: Magali
authors.initials: M
authors.lastname: Chabé
authors.affiliation: Biology & Diversity of Emerging Eukaryotic Pathogens (BDEEP), Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR8204, IFR142, Lille Pasteur Institute, Lille Nord de France University (EA4547), Lille, France; Parasitology-Medical Mycology Department, Regional Hospital Center, Faculty of Medicine, Lille, France. Electronic address: Laurence.Delhaes@pasteur-lille.fr.
authors.forename: Laurence
authors.initials: L
authors.lastname: Delhaes
authors.affiliation: Biology & Diversity of Emerging Eukaryotic Pathogens (BDEEP), Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR8204, IFR142, Lille Pasteur Institute, Lille Nord de France University (EA4547), Lille, France; Parasitology-Medical Mycology Department, Regional Hospital Center, Faculty of Medicine, Lille, France.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Dei-Cas
mesh_terms: D000391:Air Microbiology; D055028:Comparative Genomic Hybridization; D003550:Cystic Fibrosis / Q000150:complications / Q000382:microbiology; D019143:Evolution, Molecular; D005658:Fungi / Q000235:genetics* / Q000472:pathogenicity; D016681:Genome, Fungal; D006801:Humans; D008168:Lung / Q000382:microbiology; D056186:Metagenomics; D064307:Microbiota; D025202:Molecular Diagnostic Techniques; D009172:Mycology / Q000379:methods; D009181:Mycoses / Q000382:microbiology / Q000635:transmission*; D029424:Pulmonary Disease, Chronic Obstructive / Q000382:microbiology; D012130:Respiratory Hypersensitivity / Q000382:microbiology; D012141:Respiratory Tract Infections / Q000382:microbiology / Q000635:transmission; D013045:Species Specificity; D013183:Sputum / Q000382:microbiology; D014774:Virulence
keywords: Aspergillus; Chronic pulmonary diseases; Enfermedades pulmonares crónicas; Fungi; Hongos; Lung; Metagenomics; Metagenómica; Microbiota; Next-generation sequencing; Pneumocystis; Pulmón; Secuenciación de nueva generación