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Growing mold together-moving beyond standard cultures in assessing fungi in the CF airway. J Cyst Fibros 2021; 20:191-192. [PMID: 33619013 DOI: 10.1016/j.jcf.2021.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Delhaes L, Touati K, Faure-Cognet O, Cornet M, Botterel F, Dannaoui E, Morio F, Le Pape P, Grenouillet F, Favennec L, Le Gal S, Nevez G, Duhamel A, Borman A, Saegeman V, Lagrou K, Gomez E, Carro ML, Canton R, Campana S, Buzina W, Chen S, Meyer W, Roilides E, Simitsopoulou M, Manso E, Cariani L, Biffi A, Fiscarelli E, Ricciotti G, Pihet M, Bouchara JP. Prevalence, geographic risk factor, and development of a standardized protocol for fungal isolation in cystic fibrosis: Results from the international prospective study "MFIP". J Cyst Fibros 2018; 18:212-220. [PMID: 30348610 DOI: 10.1016/j.jcf.2018.10.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 08/07/2018] [Accepted: 10/01/2018] [Indexed: 01/18/2023]
Affiliation(s)
| | - Kada Touati
- University & CHU of Lille, F-59000 Lille, France
| | - Odile Faure-Cognet
- Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France
| | - Muriel Cornet
- Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France
| | | | | | | | | | | | | | | | | | | | | | - Veroniek Saegeman
- University of Leuven, National Reference center for Mycosis, Belgium
| | - Katrien Lagrou
- University of Leuven, National Reference center for Mycosis, Belgium
| | - Elia Gomez
- Hosital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Madrid, Spain
| | - Maiz-Luis Carro
- Hosital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Madrid, Spain
| | - Rafael Canton
- Hosital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Madrid, Spain
| | | | | | - Sharon Chen
- Molecular Mycology Research Laboratory, Marie Bashir Institute for Biosecurity and Emerging Infections, University of Sydney, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Marie Bashir Institute for Biosecurity and Emerging Infections, University of Sydney, Australia
| | | | | | | | - Lisa Cariani
- Microbiology and Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Milano, Italy
| | - Arianna Biffi
- Microbiology and Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Milano, Italy
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Prigitano A, Esposto MC, Biffi A, De Lorenzis G, Favuzzi V, Koncan R, Lo Cascio G, Barao Ocampo M, Colombo C, Pizzamiglio G, Romanò L, Tortorano AM. Triazole resistance in Aspergillus fumigatus isolates from patients with cystic fibrosis in Italy. J Cyst Fibros 2017; 16:64-69. [DOI: 10.1016/j.jcf.2016.06.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 06/08/2016] [Accepted: 06/13/2016] [Indexed: 10/21/2022]
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Nguyen LDN, Deschaght P, Merlin S, Loywick A, Audebert C, Van Daele S, Viscogliosi E, Vaneechoutte M, Delhaes L. Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation. PLoS One 2016; 11:e0168860. [PMID: 28030619 PMCID: PMC5193350 DOI: 10.1371/journal.pone.0168860] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 12/07/2016] [Indexed: 02/06/2023] Open
Abstract
Introduction and Purpose Propidium monoazide (PMA)-pretreatment has increasingly been applied to remove the bias from dead or damaged cell artefacts, which could impact the microbiota analysis by high-throughput sequencing. Our study aimed to determine whether a PMA-pretreatment coupled with high-throughput sequencing analysis provides a different picture of the airway mycobiome and bacteriome. Results and Discussion We compared deep-sequencing data of mycobiota and microbiota of 15 sputum samples from 5 cystic fibrosis (CF) patients with and without prior PMA-treatment of the DNA-extracts. PMA-pretreatment had no significant effect on the entire and abundant bacterial community (genera expressed as operational taxonomic units (OTUs) with a relative abundance greater than or equal to 1%), but caused a significant difference in the intermediate community (less than 1%) when analyzing the alpha biodiversity Simpson index (p = 0.03). Regarding PMA impact on the airway mycobiota evaluated for the first time here; no significant differences in alpha diversity indexes between PMA-treated and untreated samples were observed. Regarding beta diversity analysis, the intermediate communities also differed more dramatically than the total and abundant ones when studying both mycobiome and bacteriome. Our results showed that only the intermediate (or low abundance) population diversity is impacted by PMA-treatment, and therefore that abundant taxa are mostly viable during acute exacerbation in CF. Given such a cumbersome protocol (PMA-pretreatment coupled with high-throughput sequencing), we discuss its potential interest within the follow-up of CF patients. Further studies using PMA-pretreatment are warranted to improve our “omic” knowledge of the CF airways.
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Affiliation(s)
- Linh Do Ngoc Nguyen
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR 8204, University of Lille, Lille, France
| | - Pieter Deschaght
- Laboratory for Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, Ghent, Belgium
| | - Sophie Merlin
- GenesDiffusion, Douai, France
- PEGASE, Biosciences, Institut Pasteur de Lille, Lille, France
| | - Alexandre Loywick
- GenesDiffusion, Douai, France
- PEGASE, Biosciences, Institut Pasteur de Lille, Lille, France
| | - Christophe Audebert
- GenesDiffusion, Douai, France
- PEGASE, Biosciences, Institut Pasteur de Lille, Lille, France
| | - Sabine Van Daele
- Department of Pediatrics and Genetics, Faculty of Medicine & Health Sciences, Ghent University, Ghent, Belgium
| | - Eric Viscogliosi
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR 8204, University of Lille, Lille, France
| | - Mario Vaneechoutte
- Laboratory for Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, Ghent, Belgium
| | - Laurence Delhaes
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR 8204, University of Lille, Lille, France
- Parasitology-Medical Mycology Department, Regional Hospital Center, Faculty of Medicine, Lille, France
- * E-mail:
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