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Saiman L, Waters V, LiPuma JJ, Hoffman LR, Alby K, Zhang SX, Yau YC, Downey DG, Sermet-Gaudelus I, Bouchara JP, Kidd TJ, Bell SC, Brown AW. Practical Guidance for Clinical Microbiology Laboratories: Updated guidance for processing respiratory tract samples from people with cystic fibrosis. Clin Microbiol Rev 2024:e0021521. [PMID: 39158301 DOI: 10.1128/cmr.00215-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024] Open
Abstract
SUMMARYThis guidance presents recommendations for clinical microbiology laboratories for processing respiratory samples from people with cystic fibrosis (pwCF). Appropriate processing of respiratory samples is crucial to detect bacterial and fungal pathogens, guide treatment, monitor the epidemiology of cystic fibrosis (CF) pathogens, and assess therapeutic interventions. Thanks to CF transmembrane conductance regulator modulator therapy, the health of pwCF has improved, but as a result, fewer pwCF spontaneously expectorate sputum. Thus, the collection of sputum samples has decreased, while the collection of other types of respiratory samples such as oropharyngeal and bronchoalveolar lavage samples has increased. To optimize the detection of microorganisms, including Pseudomonas aeruginosa, Staphylococcus aureus, Haemophilus influenzae, and Burkholderia cepacia complex; other less common non-lactose fermenting Gram-negative bacilli, e.g., Stenotrophomonas maltophilia, Inquilinus, Achromobacter, Ralstonia, and Pandoraea species; and yeasts and filamentous fungi, non-selective and selective culture media are recommended for all types of respiratory samples, including samples obtained from pwCF after lung transplantation. There are no consensus recommendations for laboratory practices to detect, characterize, and report small colony variants (SCVs) of S. aureus, although studies are ongoing to address the potential clinical impact of SCVs. Accurate identification of less common Gram-negative bacilli, e.g., S. maltophilia, Inquilinus, Achromobacter, Ralstonia, and Pandoraea species, as well as yeasts and filamentous fungi, is recommended to understand their epidemiology and clinical importance in pwCF. However, conventional biochemical tests and automated platforms may not accurately identify CF pathogens. MALDI-TOF MS provides excellent genus-level identification, but databases may lack representation of CF pathogens to the species-level. Thus, DNA sequence analysis should be routinely available to laboratories for selected clinical circumstances. Antimicrobial susceptibility testing (AST) is not recommended for every routine surveillance culture obtained from pwCF, although selective AST may be helpful, e.g., for unusual pathogens or exacerbations unresponsive to initial therapy. While this guidance reflects current care paradigms for pwCF, recommendations will continue to evolve as CF research expands the evidence base for laboratory practices.
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Affiliation(s)
- Lisa Saiman
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
- Department of Infection Prevention and Control, NewYork-Presbyterian Hospital, New York, New York, USA
| | - Valerie Waters
- Division of Infectious Diseases, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lucas R Hoffman
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Kevin Alby
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Sean X Zhang
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yvonne C Yau
- Division of Microbiology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Damian G Downey
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University, Belfast, Ireland
| | | | - Jean-Philippe Bouchara
- University of Angers-University of Brest, Infections Respiratoires Fongiques, Angers, France
| | - Timothy J Kidd
- Microbiology Division, Pathology Queensland Central Laboratory, The University of Queensland, Brisbane, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Scott C Bell
- The Prince Charles Hospital, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- The Translational Research Institute, Brisbane, Australia
| | - A Whitney Brown
- Cystic Fibrosis Foundation, Bethesda, Maryland, USA
- Inova Advanced Lung Disease and Transplant Program, Inova Fairfax Hospital, Falls Church, Virginia, USA
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Azoicai A, Lupu A, Alexoae MM, Starcea IM, Mocanu A, Lupu VV, Mitrofan EC, Nedelcu AH, Tepordei RT, Munteanu D, Mitrofan C, Salaru DL, Ioniuc I. Lung microbiome: new insights into bronchiectasis' outcome. Front Cell Infect Microbiol 2024; 14:1405399. [PMID: 38895737 PMCID: PMC11183332 DOI: 10.3389/fcimb.2024.1405399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/15/2024] [Indexed: 06/21/2024] Open
Abstract
The present treatments for bronchiectasis, which is defined by pathological dilatation of the airways, are confined to symptom relief and minimizing exacerbations. The condition is becoming more common worldwide. Since the disease's pathophysiology is not entirely well understood, developing novel treatments is critically important. The interplay of chronic infection, inflammation, and compromised mucociliary clearance, which results in structural alterations and the emergence of new infection, is most likely responsible for the progression of bronchiectasis. Other than treating bronchiectasis caused by cystic fibrosis, there are no approved treatments. Understanding the involvement of the microbiome in this disease is crucial, the microbiome is defined as the collective genetic material of all bacteria in an environment. In clinical practice, bacteria in the lungs have been studied using cultures; however, in recent years, researchers use next-generation sequencing methods, such as 16S rRNA sequencing. Although the microbiome in bronchiectasis has not been entirely investigated, what is known about it suggests that Haemophilus, Pseudomonas and Streptococcus dominate the lung bacterial ecosystems, they present significant intraindividual stability and interindividual heterogeneity. Pseudomonas and Haemophilus-dominated microbiomes have been linked to more severe diseases and frequent exacerbations, however additional research is required to fully comprehend the role of microbiome in the evolution of bronchiectasis. This review discusses recent findings on the lung microbiota and its association with bronchiectasis.
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Affiliation(s)
- Alice Azoicai
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Ancuta Lupu
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Monica Mihaela Alexoae
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Iuliana Magdalena Starcea
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Adriana Mocanu
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Vasile Valeriu Lupu
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | | | - Alin Horatiu Nedelcu
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Razvan Tudor Tepordei
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Dragos Munteanu
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Costica Mitrofan
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Delia Lidia Salaru
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Ileana Ioniuc
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
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Burgel PR, Southern KW, Addy C, Battezzati A, Berry C, Bouchara JP, Brokaar E, Brown W, Azevedo P, Durieu I, Ekkelenkamp M, Finlayson F, Forton J, Gardecki J, Hodkova P, Hong G, Lowdon J, Madge S, Martin C, McKone E, Munck A, Ooi CY, Perrem L, Piper A, Prayle A, Ratjen F, Rosenfeld M, Sanders DB, Schwarz C, Taccetti G, Wainwright C, West NE, Wilschanski M, Bevan A, Castellani C, Drevinek P, Gartner S, Gramegna A, Lammertyn E, Landau EEC, Plant BJ, Smyth AR, van Koningsbruggen-Rietschel S, Middleton PG. Standards for the care of people with cystic fibrosis (CF); recognising and addressing CF health issues. J Cyst Fibros 2024; 23:187-202. [PMID: 38233247 DOI: 10.1016/j.jcf.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 01/19/2024]
Abstract
This is the third in a series of four papers updating the European Cystic Fibrosis Society (ECFS) standards for the care of people with CF. This paper focuses on recognising and addressing CF health issues. The guidance was produced with wide stakeholder engagement, including people from the CF community, using an evidence-based framework. Authors contributed sections, and summary statements which were reviewed by a Delphi consultation. Monitoring and treating airway infection, inflammation and pulmonary exacerbations remains important, despite the widespread availability of CFTR modulators and their accompanying health improvements. Extrapulmonary CF-specific health issues persist, such as diabetes, liver disease, bone disease, stones and other renal issues, and intestinal obstruction. These health issues require multidisciplinary care with input from the relevant specialists. Cancer is more common in people with CF compared to the general population, and requires regular screening. The CF life journey requires mental and emotional adaptation to psychosocial and physical challenges, with support from the CF team and the CF psychologist. This is particularly important when life gets challenging, with disease progression requiring increased treatments, breathing support and potentially transplantation. Planning for end of life remains a necessary aspect of care and should be discussed openly, honestly, with sensitivity and compassion for the person with CF and their family. CF teams should proactively recognise and address CF-specific health issues, and support mental and emotional wellbeing while accompanying people with CF and their families on their life journey.
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Affiliation(s)
- Pierre-Régis Burgel
- Respiratory Medicine and Cystic Fibrosis National Reference Center, Cochin Hospital, Assistance Publique Hôpitaux de Paris (AP-HP), Institut Cochin, Inserm U1016, Université Paris-Cité, Paris, France
| | - Kevin W Southern
- Department of Women's and Children's Health, Institute in the Park, Alder Hey Children's Hospital, University of Liverpool, Eaton Road, Liverpool L12 2AP, UK.
| | - Charlotte Addy
- All Wales Adult Cystic Fibrosis Centre, University Hospital Llandough, Cardiff and Vale University Health Board, Cardiff, UK
| | - Alberto Battezzati
- Clinical Nutrition Unit, Department of Endocrine and Metabolic Medicine, IRCCS Istituto Auxologico Italiano, and ICANS-DIS, Department of Food Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Claire Berry
- Department of Nutrition and Dietetics, Alder Hey Children's NHS Trust, Liverpool, UK
| | - Jean-Philippe Bouchara
- University of Brest, Fungal Respiratory Infections Research Unit, SFR ICAT, University of Angers, Angers, France
| | - Edwin Brokaar
- Department of Pharmacy, Haga Teaching Hospital, The Hague, the Netherlands
| | - Whitney Brown
- Cystic Fibrosis Foundation, Inova Fairfax Hospital, Bethesda, Maryland, USA, Falls Church, VA, USA
| | - Pilar Azevedo
- Cystic Fibrosis Reference Centre-Centro, Hospitalar Universitário Lisboa Norte, Portugal
| | - Isabelle Durieu
- Cystic Fibrosis Reference Center (Constitutif), Service de médecine interne et de pathologie vasculaire, Hospices Civils de Lyon, Hôpital Lyon Sud, RESearch on HealthcAre PErformance (RESHAPE), INSERM U1290, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69373 Lyon Cedex 08, France; ERN-Lung Cystic Fibrosis Network, Frankfurt, Germany
| | - Miquel Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Felicity Finlayson
- Department of Respiratory Medicine, The Alfred Hospital, Melbourne, Australia
| | | | - Johanna Gardecki
- CF Centre at Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Pavla Hodkova
- CF Center at University Hospital Motol, Prague, Czech Republic
| | - Gina Hong
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jacqueline Lowdon
- Clinical Specialist Paediatric Cystic Fibrosis Dietitian, Leeds Children's Hospital, UK
| | - Su Madge
- Royal Brompton Hospital, Part of Guys and StThomas's Hospital, London, UK
| | - Clémence Martin
- Institut Cochin, Inserm U1016, Université Paris-Cité and National Reference Center for Cystic Fibrosis, Hôpital Cochin AP-HP, ERN-Lung CF Network, Paris 75014, France
| | - Edward McKone
- St.Vincent's University Hospital and University College Dublin School of Medicine, Dublin, Ireland
| | - Anne Munck
- Hospital Necker Enfants-Malades, AP-HP, CF Centre, Université Paris Descartes, Paris, France
| | - Chee Y Ooi
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, Faculty of Medicine & Health, Department of Gastroenterology, Sydney Children's Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Lucy Perrem
- Department of Respiratory Medicine, Children's Health Ireland, Dublin, Ireland
| | - Amanda Piper
- Central Clinical School, Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Andrew Prayle
- Child Health, Lifespan and Population Health & Nottingham Biomedical Research Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Felix Ratjen
- Division of Respiratory Medicine, Department of Pediatrics and Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Margaret Rosenfeld
- Department of Pediatrics, Seattle Children's Research Institute, University of Washington School of Medicine, Seattle, WA, USA
| | - Don B Sanders
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Carsten Schwarz
- Division Cystic Fibrosis, CF Center, Clinic Westbrandenburg, HMU-Health and Medical University, Potsdam, Germany
| | - Giovanni Taccetti
- Meyer Children's Hospital IRCCS, Cystic Fibrosis Regional Reference Centre, Italy
| | | | - Natalie E West
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Michael Wilschanski
- Pediatric Gastroenterology Unit, CF Center, Hadassah Medical Center, Jerusalem, Israel
| | - Amanda Bevan
- University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Carlo Castellani
- IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, Genova 16147, Italy
| | - Pavel Drevinek
- Department of Medical Microbiology, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | - Silvia Gartner
- Cystic Fibrosis Unit and Pediatric Pulmonology, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Andrea Gramegna
- Department of Pathophysiology and Transplantation, Respiratory Unit and Adult Cystic Fibrosis Center, Università degli Studi di Milano, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Elise Lammertyn
- Cystic Fibrosis Europe, Brussels, Belgium and the Belgian CF Association, Brussels, Belgium
| | - Eddie Edwina C Landau
- The Graub CF Center, Pulmonary Institute, Schneider Children's Medical Center, Petah Tikva, Israel
| | - Barry J Plant
- Cork Centre for Cystic Fibrosis (3CF), Cork University Hospital, University College Cork, Ireland
| | - Alan R Smyth
- School of Medicine, Dentistry and Biomedical Sciences, Belfast and NIHR Nottingham Biomedical Research Centre, Queens University Belfast, Nottingham, UK
| | | | - Peter G Middleton
- Westmead Clinical School, Department Respiratory & Sleep Medicine, Westmead Hospital, University of Sydney and CITRICA, Westmead, Australia
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Grandhay C, Prétot E, Klaba V, Celle H, Normand AC, Bertrand X, Grenouillet F. Yeast Biodiversity of Karst Waters: Interest of Four Culture Media and an Improved MALDI-TOF MS Database. MICROBIAL ECOLOGY 2024; 87:26. [PMID: 38175217 PMCID: PMC10766713 DOI: 10.1007/s00248-023-02336-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024]
Abstract
Karst aquifers are a significant source of drinking water and highly vulnerable to pollution and microbial contamination. Microbiological regulations for the quality of drinking water mostly focus on bacterial levels and lack guidance concerning fungal contamination. Moreover, there is no standardised microbial analysis methodology for identifying fungi in water. Our main objective was to establish the most effective culture and identification methodology to examine yeast diversity in karst waters. We assessed the comparative efficacy of four culture media (CHROMagar Candida, dichloran glycerol 18% [DG18], dichloran rose Bengal chloramphenicol [DRBC], and SYMPHONY agar) for yeast isolation from karst water samples. Furthermore, we investigated the comprehensiveness of databases used in MALDI-TOF mass spectrometry (MALDI-TOF MS) for identifying environmental yeast species. In total, we analysed 162 water samples, allowing the identification of 2479 yeast isolates. We demonstrate that a combination of four culture media, each with distinct specifications, more efficiently covers a wide range of yeast species in karst water than a combination of only two or three. Supplementation of a MALDI-TOF MS database is also critical for analysing environmental microbial samples and improved the identification of yeast biodiversity. This study is an initial step towards standardising the analysis of fungal biodiversity in karst waters, enabling a better understanding of the significance of this environmental reservoir in relation to public health.
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Affiliation(s)
- Clément Grandhay
- Université de Franche-Comté, CHU Besançon, CNRS, Chrono-environnement, F-25000, Besançon, France
| | - Emma Prétot
- Université de Franche-Comté, CHU Besançon, CNRS, Chrono-environnement, F-25000, Besançon, France
| | - Victor Klaba
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000, Besançon, France
| | - Hélène Celle
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000, Besançon, France
| | - Anne-Cécile Normand
- AP-HP, Groupe Hospitalier La Pitié-Salpêtrière, Service de Parasitologie Mycologie, 75013, Paris, France
| | - Xavier Bertrand
- Université de Franche-Comté, CHU Besançon, CNRS, Chrono-environnement, F-25000, Besançon, France
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000, Besançon, France
| | - Frédéric Grenouillet
- Université de Franche-Comté, CHU Besançon, CNRS, Chrono-environnement, F-25000, Besançon, France.
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000, Besançon, France.
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Agossou M, Inamo J, Ahouansou N, Dufeal M, Provost M, Badaran E, Zouzou A, Awanou B, Dramé M, Desbois-Nogard N. Frequency and Distribution of Broncho-Alveolar Fungi in Lung Diseases in Martinique. J Clin Med 2023; 12:5480. [PMID: 37685550 PMCID: PMC10488106 DOI: 10.3390/jcm12175480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
The microbiota refers to all the microorganisms living in and on the human body; its fungal component is known as the mycobiota. The molecular component (mycobiome) has been linked to certain pulmonary diseases. Morphological fungal examination is still common practice and makes it possible to isolate fungi on direct examination or after sample culture. This study aimed to identify fungi via the genus colonising the respiratory tract in our environment and to evaluate the relationship between identified fungi and underlying diseases. We performed a retrospective study of patients who underwent bronchofiberoscopy and mycological analysis of fluid collected by broncho-alveolar lavage at our centre over a period of 5 years. During the study period, 1588 samples from 1547 patients were analysed (50.7% male, mean age 63.7 ± 14.8 years). Among the 1588 samples, 213 (13.4%) were positive on direct examination, and 1282 (80.8%) were positive after culture. The average number of species detected per sample was 1.4 ± 1.1. For patients with positive fungus, the median was two (ranging from one to seven). At least three fungal species were isolated in 14.4% of samples (17.9% of positive cultures), and at least two were isolated in 41.2% of samples (51.1% of positive cultures). Sterile mycelium was observed in 671 samples (42.28%), while Candida was identified in 607 samples (38.25%), and Geotrichum was identified in 271 samples (17.08%). Moulds were more frequently associated with bronchiectasis, while yeasts were associated with infectious pneumonia. Both moulds and yeasts were less frequent in diffuse interstitial lung disease, and yeast was less frequently present in chronic cough. Although overall, sterile mycelium and Candida were most frequently observed regardless of the underlying disease, there was nonetheless significant variability in the fungal genera between diseases. Fungal spores are highly prevalent in respiratory samples in Martinique. The species present in the samples varied according to the underlying respiratory disease.
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Affiliation(s)
- Moustapha Agossou
- Department of Respiratory Medicine, CHU of Martinique, 97261 Fort-de-France, France; (N.A.); (M.D.); (M.P.); (E.B.); (A.Z.); (B.A.)
| | - Jocelyn Inamo
- Department of Cardiology, CHU of Martinique, 97261 Fort-de-France, France;
| | - Nelly Ahouansou
- Department of Respiratory Medicine, CHU of Martinique, 97261 Fort-de-France, France; (N.A.); (M.D.); (M.P.); (E.B.); (A.Z.); (B.A.)
| | - Marion Dufeal
- Department of Respiratory Medicine, CHU of Martinique, 97261 Fort-de-France, France; (N.A.); (M.D.); (M.P.); (E.B.); (A.Z.); (B.A.)
| | - Mathilde Provost
- Department of Respiratory Medicine, CHU of Martinique, 97261 Fort-de-France, France; (N.A.); (M.D.); (M.P.); (E.B.); (A.Z.); (B.A.)
| | - Elena Badaran
- Department of Respiratory Medicine, CHU of Martinique, 97261 Fort-de-France, France; (N.A.); (M.D.); (M.P.); (E.B.); (A.Z.); (B.A.)
| | - Adel Zouzou
- Department of Respiratory Medicine, CHU of Martinique, 97261 Fort-de-France, France; (N.A.); (M.D.); (M.P.); (E.B.); (A.Z.); (B.A.)
| | - Bérénice Awanou
- Department of Respiratory Medicine, CHU of Martinique, 97261 Fort-de-France, France; (N.A.); (M.D.); (M.P.); (E.B.); (A.Z.); (B.A.)
| | - Moustapha Dramé
- Department of Clinical Research and Innovation, CHU of Martinique, 97261 Fort-de-France, France;
- EpiCliV Research Unit, Faculty of Medicine, University of the French West Indies, 97261 Fort-de-France, France
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Poore TS, Zemanick ET. Infection, Allergy, and Inflammation: The Role of Aspergillus fumigatus in Cystic Fibrosis. Microorganisms 2023; 11:2013. [PMID: 37630573 PMCID: PMC10458351 DOI: 10.3390/microorganisms11082013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Aspergillus fumigatus (Af) is a mold frequently detected in airway samples from people with cystic fibrosis (pwCF). Abnormal airway mucus may allow Af to germinate, resulting in airway infection or an allergic response. While Af is known to increase morbidity in pwCF, individual responses and the degree of impact on lung disease vary. Improved approaches to diagnosis, treatment, and prevention of Af, particularly the persistent Af infection, are needed. This update highlights our current understanding of Af pathophysiology in the CF airway, the effects of Af on pwCF, and areas of research needed to improve clinical outcomes.
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Affiliation(s)
- T. Spencer Poore
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35223, USA
- UAB Gregory Fleming James Cystic Fibrosis Research Center, Birmingham, AL 35223, USA
| | - Edith T. Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
- Breathing Institute, Children’s Hospital Colorado, Aurora, CO 80045, USA
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Rozaliyani A, Antariksa B, Nurwidya F, Zaini J, Setianingrum F, Hasan F, Nugrahapraja H, Yusva H, Wibowo H, Bowolaksono A, Kosmidis C. The Fungal and Bacterial Interface in the Respiratory Mycobiome with a Focus on Aspergillus spp. Life (Basel) 2023; 13:life13041017. [PMID: 37109545 PMCID: PMC10142979 DOI: 10.3390/life13041017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The heterogeneity of the lung microbiome and its alteration are prevalently seen among chronic lung diseases patients. However, studies to date have primarily focused on the bacterial microbiome in the lung rather than fungal composition, which might play an essential role in the mechanisms of several chronic lung diseases. It is now well established that Aspergillus spp. colonies may induce various unfavorable inflammatory responses. Furthermore, bacterial microbiomes such as Pseudomonas aeruginosa provide several mechanisms that inhibit or stimulate Aspergillus spp. life cycles. In this review, we highlighted fungal and bacterial microbiome interactions in the respiratory tract, with a focus on Aspergillus spp.
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Affiliation(s)
- Anna Rozaliyani
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Budhi Antariksa
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Fariz Nurwidya
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Jamal Zaini
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Findra Setianingrum
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Firman Hasan
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Husna Nugrahapraja
- Life Science and Biotechnology, Bandung Institute of Technology, Bandung 40312, Indonesia
| | - Humaira Yusva
- Magister Program of Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Heri Wibowo
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Anom Bowolaksono
- Department of Biology, Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Indonesia, Depok 16424, Indonesia
| | - Chris Kosmidis
- Manchester Academic Health Science Centre, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M23 9LT, UK
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Noni M, Katelari A, Poulou M, Ioannidis D, Kapasouri EM, Tzetis M, Doudounakis SE, Kanaka-Gantenbein C, Spoulou V. Frequencies of pathogenic CFTR variants in Greek cystic fibrosis patients with allergic bronchopulmonary aspergillosis and Aspergillus fumigatus chronic colonization: A retrospective cohort study. J Mycol Med 2023; 33:101326. [PMID: 36272381 DOI: 10.1016/j.mycmed.2022.101326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022]
Abstract
INTRODUCTION The clinical spectrum of Aspergillus fumigatus diseases in cystic fibrosis (CF) patients, including allergic bronchopulmonary aspergillosis (ABPA) and Aspergillus fumigatus chronic colonization, has recently gained attention due to its association with the progression of lung disease. Our aim was to examine whether there is a difference on pathogenic variant frequencies of the CFTR gene between CF patients with ABPA and those with A. fumigatus chronic colonization. MATERIAL AND METHODS Greek CF patients diagnosed with ABPA and/or A. fumigatus chronic colonization were grouped according to their CFTR genotype. Patients with "minimal" CFTR function were defined as carrying a combination of class I or II pathogenic variants, while patients with "residual" function as carrying at least one class III, IV, V or VI pathogenic variant. RESULTS Fifty-four CF patients were included and all except one were defined as having "minimal" CFTR function. Among the 108 CFTR alleles, 69 (63.9%) of pathogenic variants belonged to class II, and 32 (29.6%) to class I. Five patients had a history of both ABPA and A. fumigatus chronic colonization. No significant difference was detected among patients diagnosed only with ABPA (n = 29) and those who had only a positive history of A. fumigatus chronic colonization (n = 20). The median age of ABPA diagnosis was significantly lower than the median age of A. fumigatus chronic colonization (P = 0.011), while no significant difference was detected on median FEV1% predicted. DISCUSSION No significant differences were detected in the type of CFTR pathogenic variants among patients with ABPA and those with A. fumigatus colonization. Similar studies should be performed in larger CF populations of different ethnic origin to further confirm our results.
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Affiliation(s)
- Maria Noni
- First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, Division of Infectious Diseases, "Aghia Sophia" Children's Hospital, Athens, Greece.
| | - Anna Katelari
- Institute of Child Health, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Myrto Poulou
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Diomidis Ioannidis
- First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, Division of Infectious Diseases, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Efthymia-Maria Kapasouri
- First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, Division of Infectious Diseases, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Maria Tzetis
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Christina Kanaka-Gantenbein
- First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, Division of Infectious Diseases, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Vana Spoulou
- First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, Division of Infectious Diseases, "Aghia Sophia" Children's Hospital, Athens, Greece
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9
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A Multiplex PCR and DNA-Sequencing Workflow on Serum for the Diagnosis and Species Identification for Invasive Aspergillosis and Mucormycosis. J Clin Microbiol 2023; 61:e0140922. [PMID: 36533925 PMCID: PMC9879116 DOI: 10.1128/jcm.01409-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
There has been significant increase in the use of molecular tools for the diagnosis of invasive aspergillosis (IA) and mucormycosis. However, their range of detection may be too limited as species diversity and coinfections are increasing. Here, we aimed to evaluate a molecular workflow based on a new multiplex PCR assay detecting the whole Aspergillus genus and the Mucorales order followed by a species-specific PCR or a DNA-sequencing approach for IA and/or mucormycosis diagnosis and species identification on serum. Performances of the MycoGENIE Aspergillus spp./Mucorales spp. duplex PCR kit were analyzed on a broad range of fungal strains and on sera from high-risk patients prospectively over a 12-month period. The kit allowed the detection of nine Aspergillus species and 10 Mucorales (eight genera) strains assessed. No cross-reactions between the two targets were observed. Sera from 744 patients were prospectively analyzed, including 35 IA, 16 mucormycosis, and four coinfections. Sensitivity varies from 85.7% (18/21) in probable/proven IA to 28.6% (4/14) in COVID-19-associated pulmonary aspergillosis. PCR-positive samples corresponded to 21 A. fumigatus, one A. flavus, and one A. nidulans infections. All the disseminated mucormycosis were positive in serum (14/14), including the four Aspergillus coinfections, but sensitivity fell to 33.3% (2/6) in localized forms. DNA sequencing allowed Mucorales identification in serum in 15 patients. Remarkably, the most frequent species identified was Rhizomucor pusillus (eight cases), whereas it is barely found in fungal culture. This molecular workflow is a promising approach to improve IA and mucormycosis diagnosis and epidemiology.
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10
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Dot Immunobinding Assay for the Rapid Serodetection of Scedosporium/ Lomentospora in Cystic Fibrosis Patients. J Fungi (Basel) 2023; 9:jof9020158. [PMID: 36836272 PMCID: PMC9959861 DOI: 10.3390/jof9020158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
The detection of Scedosporium/Lomentospora is still based on non-standardized low-sensitivity culture procedures. This fact is particularly worrying in patients with cystic fibrosis (CF), where these fungi are the second most common filamentous fungi isolated, because a poor and delayed diagnosis can worsen the prognosis of the disease. To contribute to the discovery of new diagnostic strategies, a rapid serological dot immunobinding assay (DIA) that allows the detection of serum IgG against Scedosporium/Lomentospora in less than 15 min was developed. A crude protein extract from the conidia and hyphae of Scedosporium boydii was employed as a fungal antigen. The DIA was evaluated using 303 CF serum samples (162 patients) grouped according to the detection of Scedosporium/Lomentospora in the respiratory sample by culture, obtaining a sensitivity and specificity of 90.48% and 79.30%, respectively; positive and negative predictive values of 54.81% and 96.77%, and an efficiency of 81.72%. The clinical factors associated with the results were also studied using a univariate and a multivariate analysis, which showed that Scedosporium/Lomentospora positive sputum, elevated anti-Aspergillus serum IgG and chronic Pseudomonas aeruginosa infection were significantly associated with a positive result in DIA, while Staphylococcus aureus positive sputum showed a negative association. In conclusion, the test developed can offer a complementary, rapid, simple and sensitive method to contribute to the diagnosis of Scedosporium/Lomentospora in patients with CF.
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11
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Hong G. Progress and challenges in fungal lung disease in cystic fibrosis. Curr Opin Pulm Med 2022; 28:584-590. [PMID: 36101907 PMCID: PMC9547960 DOI: 10.1097/mcp.0000000000000921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW This review is an overview of the recent progress made for the diagnosis and understanding of fungal lung disease in people with cystic fibrosis (CF), with a focus on Aspergillus fumigatus , the most common filamentous fungus in the CF airway. Currently, the longstanding question of the clinical significance of Aspergillus fumigatus and other fungi in CF respiratory cultures, in the absence of allergy, remains. Clinical criteria and biomarkers are needed to classify fungal lung disease and determine who may warrant therapy. RECENT FINDINGS Several retrospective and prospective studies have described the prevalence of A. fumigatus and other fungi in the CF lung and factors contributing to the changes in fungal epidemiology. Selective fungus culture testing for the detection of fungi in CF sputa has been well studied, yet a standardized fungus culture protocol has yet to be defined. Culture-independent molecular studies and other fungal diagnostic testing have been conducted in the CF population, leading to efforts to better understand the clinical role of these tests. Recent works have aimed to determine whether chronic A. fumigatus colonization is associated with lung disease progression measured by FEV 1 percentage predicted, structural lung disease, lung clearance index and respiratory quality-of-life. However, the existing knowledge gaps remain: definition of a fungal respiratory infection, the association between fungal infection and clinical outcomes, and indications for antifungal therapy. SUMMARY Significant progress has been made for the detection and diagnosis of fungal lung disease. Yet, the role and impact of A. fumigatus and other fungal infections on respiratory health in people with CF remains to be determined.
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Affiliation(s)
- Gina Hong
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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12
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Hughes DA, Rosenthal M, Cuthbertson L, Ramadan N, Felton I, Simmonds NJ, Loebinger MR, Price H, Armstrong-James D, Elborn JS, Cookson WO, Moffatt MF, Davies JC. An invisible threat? Aspergillus positive cultures and co-infecting bacteria in airway samples. J Cyst Fibros 2022; 22:320-326. [PMID: 35871975 DOI: 10.1016/j.jcf.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 11/20/2022]
Abstract
BACKGROUND Aspergillus fumigatus (Af) infection is associated with poor lung health in chronic suppurative lung diseases but often goes undetected. We hypothesised that inhibition of Af growth by Pseudomonas aeruginosa (Pa) increases the frequency of false-negative Af culture in co-infected people. Using a substantial group of cystic fibrosis (CF) airway samples, we assessed the relationship between Af and bacterial pathogens, additionally comparing fungal culture with next-generation sequencing. METHODS Frequency of co-culture was assessed for 44,554 sputum/BAL cultures, from 1,367 CF patients between the years 2010-2020. In a subgroup, Internal Transcribed Spacer-2 (ITS2) fungal sequencing was used to determine sequencing-positive, culture-negative (S+/C-) rates. RESULTS Pa+ samples were nearly 40% less likely (P<0.0001) than Pa- samples to culture Af, an effect that was also seen with some other Gram-negative isolates. This impact varied with Pa density and appeared to be moderated by Staphylococcus aureus co-infection. Sequencing identified Af-S+/C- for 40.1% of tested sputa. Samples with Pa had higher rates of Af-S+/C- (49.3%) than those without (35.7%; RR 1.38 [1.02-1.93], P<0.05). Af-S+/C- rate was not changed by other common bacterial infections. Pa did not affect the S+/C- rates of Candida, Exophiala or Scedosporium. CONCLUSIONS Pa/ Af co-positive cultures are less common than expected in CF. Our findings suggest an Af-positive culture is less likely in the presence of Pa. Interpretation of negative cultures should be cautious, particularly in Pa-positive samples, and a companion molecular diagnostic could be useful. Further work investigating mechanisms, alternative detection techniques and other chronic suppurative lung diseases is needed.
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Affiliation(s)
- Dominic A Hughes
- King's College Hospital NHS Foundation Trust, London, UK; National Heart & Lung Institute, Imperial College London, Emmanuel Kaye Building, 1B Manresa Road, London SW3 6LR, UK.
| | - Mark Rosenthal
- Royal Brompton Hospital, Guy's & St Thomas' Trust, London, UK
| | - Leah Cuthbertson
- National Heart & Lung Institute, Imperial College London, Emmanuel Kaye Building, 1B Manresa Road, London SW3 6LR, UK
| | - Newara Ramadan
- Royal Brompton Hospital, Guy's & St Thomas' Trust, London, UK
| | - Imogen Felton
- Royal Brompton Hospital, Guy's & St Thomas' Trust, London, UK
| | - Nicholas J Simmonds
- National Heart & Lung Institute, Imperial College London, Emmanuel Kaye Building, 1B Manresa Road, London SW3 6LR, UK; Royal Brompton Hospital, Guy's & St Thomas' Trust, London, UK
| | - Michael R Loebinger
- National Heart & Lung Institute, Imperial College London, Emmanuel Kaye Building, 1B Manresa Road, London SW3 6LR, UK; Royal Brompton Hospital, Guy's & St Thomas' Trust, London, UK
| | - Henry Price
- Department of Physics, Imperial College London, UK
| | - Darius Armstrong-James
- Royal Brompton Hospital, Guy's & St Thomas' Trust, London, UK; Department of Infectious Diseases, Imperial College London, UK
| | | | - William O Cookson
- National Heart & Lung Institute, Imperial College London, Emmanuel Kaye Building, 1B Manresa Road, London SW3 6LR, UK
| | - Miriam F Moffatt
- National Heart & Lung Institute, Imperial College London, Emmanuel Kaye Building, 1B Manresa Road, London SW3 6LR, UK
| | - Jane C Davies
- National Heart & Lung Institute, Imperial College London, Emmanuel Kaye Building, 1B Manresa Road, London SW3 6LR, UK; Royal Brompton Hospital, Guy's & St Thomas' Trust, London, UK
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13
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Blomquist A, Inghammar M, Al Shakirchi M, Ericson P, Krantz C, Svedberg M, Lindblad A, Påhlman LI. Persistent Aspergillus fumigatus infection in cystic fibrosis: impact on lung function and role of treatment of asymptomatic colonization-a registry-based case-control study. BMC Pulm Med 2022; 22:263. [PMID: 35790954 PMCID: PMC9258124 DOI: 10.1186/s12890-022-02054-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/27/2022] [Indexed: 11/10/2022] Open
Abstract
Background Aspergillus fumigatus is the most common filamentous fungus isolated from the airways of people with cystic fibrosis (CF). The aim of this study was to investigate how chronic A. fumigatus colonization affects lung function in people with CF, to identify risk factors for colonization, and to evaluate antifungal treatment of asymptomatic Aspergillus colonization.
Methods Data from 2014–2018 was collected from the Swedish CF registry and medical records. Baseline data before the start of A. fumigatus colonization was compared with the two succeeding years to evaluate how colonization and treatment affected lung function and other clinical aspects.
Results A total of 437 patients were included, of which 64 (14.6%) became colonized with A. fumigatus during the study period. Inhaled antibiotics was associated with A. fumigatus colonization (adjusted OR 3.1, 95% CI 1.6–5.9, p < 0.05). Fungal colonization was not associated with a more rapid lung function decline or increased use of IV-antibiotics compared to the non-colonized group, but patients with A. fumigatus had more hospital days, a higher increase of total IgE, and higher eosinophil counts. In the Aspergillus group, 42 patients were considered to be asymptomatic. Of these, 19 patients received antifungal treatment. Over the follow up period, the treated group had a more pronounced decrease in percent predicted Forced Expiratory Volume in one second (ppFEV1) compared to untreated patients (− 8.7 vs − 1.4 percentage points, p < 0.05). Conclusion Inhaled antibiotics was associated with A. fumigatus colonization, but no association was found between persistent A. fumigatus and subsequent lung function decline. No obvious benefits of treating asymptomatic A. fumigatus colonization were demonstrated.
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Affiliation(s)
- Axel Blomquist
- Department of Clinical Sciences Lund, Section for Infection Medicine, Skåne University Hospital, Lund University, BMC B14, 221 84, Lund, Sweden
| | - Malin Inghammar
- Department of Clinical Sciences Lund, Section for Infection Medicine, Skåne University Hospital, Lund University, BMC B14, 221 84, Lund, Sweden
| | - Mahasin Al Shakirchi
- Stockholm Cystic Fibrosis Centre, Karolinska University Hospital Huddinge, Department of Clinical Science, Intervention and Technology, Division of Paediatrics, Karolinska Institute, Stockholm, Sweden
| | - Petrea Ericson
- Department of Respiratory Medicine, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Christina Krantz
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Marcus Svedberg
- Department of Paediatrics, Institute of Clinical Science at The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anders Lindblad
- Department of Paediatrics, Institute of Clinical Science at The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lisa I Påhlman
- Department of Clinical Sciences Lund, Section for Infection Medicine, Skåne University Hospital, Lund University, BMC B14, 221 84, Lund, Sweden. .,Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.
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14
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de Dios Caballero J, Cantón R, Ponce-Alonso M, García-Clemente MM, Gómez G. de la Pedrosa E, López-Campos JL, Máiz L, del Campo R, Martínez-García MÁ. The Human Mycobiome in Chronic Respiratory Diseases: Current Situation and Future Perspectives. Microorganisms 2022; 10:810. [PMID: 35456861 PMCID: PMC9029612 DOI: 10.3390/microorganisms10040810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/04/2022] [Accepted: 04/09/2022] [Indexed: 12/15/2022] Open
Abstract
Microbes play an important role in the pathogenesis of chronic lung diseases, such as chronic obstructive pulmonary disease, cystic fibrosis, non-cystic fibrosis bronchiectasis, and asthma. While the role of bacterial pathogens has been extensively studied, the contribution of fungal species to the pathogenesis of chronic lung diseases is much less understood. The recent introduction of next-generation sequencing techniques has revealed the existence of complex microbial lung communities in healthy individuals and patients with chronic respiratory disorders, with fungi being an important part of these communities' structure (mycobiome). There is growing evidence that the components of the lung mycobiome influence the clinical course of chronic respiratory diseases, not only by direct pathogenesis but also by interacting with bacterial species and with the host's physiology. In this article, we review the current knowledge on the role of fungi in chronic respiratory diseases, which was obtained by conventional culture and next-generation sequencing, highlighting the limitations of both techniques and exploring future research areas.
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Affiliation(s)
- Juan de Dios Caballero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Rafael Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Manuel Ponce-Alonso
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Marta María García-Clemente
- Department of Pneumology, Central Asturias University Hospital, 33011 Oviedo, Spain;
- Principality Asturias Health Research Institute (ISPA), 33011 Oviedo, Spain
| | - Elia Gómez G. de la Pedrosa
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - José Luis López-Campos
- Medical-Surgical Unit for Respiratory Diseases (CIBERES), Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, University of Seville, 41013 Sevilla, Spain;
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
| | - Luis Máiz
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, Ramón y Cajal University Hospital, 28034 Madrid, Spain
| | - Rosa del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Miguel Ángel Martínez-García
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
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15
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Piechowiak MB, Brown AW, Aryal S, Katugaha SB. Lung nodules due to Candida parapsilosis in a person with cystic fibrosis. BMJ Case Rep 2021; 14:e245441. [PMID: 34972773 PMCID: PMC8720950 DOI: 10.1136/bcr-2021-245441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2021] [Indexed: 11/04/2022] Open
Abstract
We present the first reported case of Candida parapsilosis pulmonary infection presenting as lung nodules. The patient is a 31-year-old man with cystic fibrosis (CF) colonised with multidrug-resistant Escherichia coli and increased frequency of pulmonary exacerbations in the preceding months. While on intravenous antibiotics for a pulmonary exacerbation, he developed bilateral pulmonary nodules. Bronchoalveolar lavage cultures grew C. parapsilosis He was initially treated with dual antifungal therapy, voriconazole and micafungin. Discontinuation of voriconazole due to transaminitis resulted in the development of new nodules, and isavuconazonium was added. Repeat imaging revealed no progression of disease. Micafungin was eventually discontinued. Monotherapy with isavuconazonium is planned for 1 year post lung transplant. In the CF population, C. parapsilosis may be an opportunistic pathogen. The case highlights that frequent CF exacerbations and antibiotic exposure increase the risk for opportunistic infections including Candida species and the implications for lung transplantation in this setting.
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Affiliation(s)
| | - Anne Whitney Brown
- Adult Cystic Fibrosis Program, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - Shambhu Aryal
- Adult Cystic Fibrosis Program, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - Shalika Basnayake Katugaha
- Adult Cystic Fibrosis Program, Inova Fairfax Hospital, Falls Church, Virginia, USA
- Division of Infectious Diseases, Baptist Health, Jacksonville, Florida, USA
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16
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Bao JR, Master RN, Jones RS, Clark RB, Moore EC, Shier KL. Recovery and Its Dynamics of Filamentous Fungi from Clinical Specimen Cultures: An Extensive Study. Microbiol Spectr 2021; 9:e0008021. [PMID: 34346747 PMCID: PMC8552699 DOI: 10.1128/spectrum.00080-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/15/2021] [Indexed: 12/01/2022] Open
Abstract
The culture method remains vital in diagnosing fungal infections, but extensive data-based evaluation of the method, especially for filamentous fungi (molds), is minimal. The purpose of this study was to characterize mold recoveries from fungal cultures and the impact of media and incubation duration. Clinical specimens for fungal cultures were submitted primarily from the eastern and central United States, and mold isolation data were prospectively collected and analyzed. A total of 1,821 molds in 59 genera were isolated from 1,687 positive specimens, accounting for approximately 5.6% of our cohort of 30,000 fungal cultures. Within 2 weeks, nearly 90% of molds and 97.3% of Aspergillus fumigatus complex were recovered (>95% confidence interval [CI]). All Mucorales fungi were recovered within 11 days of incubation. The recovery peak time was day 3 for Mucorales fungi, day 4 for hyaline molds, day 5 for dematiaceous molds, and day 7 for Onygenales fungi. The recovery of Histoplasma capsulatum and Trichophyton species in the fourth week of incubation reveals that a 3-week incubation time is insufficient. Inhibitory mold agar was the best medium for recovering all mold types among all tested specimen types, yielding nearly 78% of mold growth overall, indicating the necessity of selective medium for fungal cultures. IMPORTANCE Fungal culture is the gold standard method of diagnosing fungal infections, but important information, such as the impact of media and incubation times on fungal recovery, is not well documented. This study addressed these gaps using extensive data-based evaluation focused on molds. We identified the best medium types and incubation times for better fungal culture practice. We analyzed 1,821 molds from 1,687 positive specimens in our cohort of approximately 30,000 fungal cultures. Mold recovery peaked between 3 and 7 days of incubation, dependent upon the type of mold. Some well-defined fungal pathogens, such as Histoplasma capsulatum and Trichophyton species, were isolated in the fourth week of incubation. Inhibitory mold agar was identified as the best medium for recovering all mold types among all tested specimen sources. As we are aware, this is the largest study of fungal culture methods and supports 4 weeks of incubation for optimal mold recovery.
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Affiliation(s)
- Jian R. Bao
- Quest Diagnostics Nichols Institute, Chantilly, Virginia, USA
| | | | - Robert S. Jones
- Quest Diagnostics Nichols Institute, Chantilly, Virginia, USA
| | | | | | - Kileen L. Shier
- Quest Diagnostics Nichols Institute, Chantilly, Virginia, USA
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17
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Francis F, Enaud R, Soret P, Lussac-Sorton F, Avalos-Fernandez M, Bui S, Fayon M, Thiébaut R, Delhaes L. New Insights in Microbial Species Predicting Lung Function Decline in CF: Lessons from the MucoFong Project. J Clin Med 2021; 10:jcm10163725. [PMID: 34442021 PMCID: PMC8396880 DOI: 10.3390/jcm10163725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/09/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022] Open
Abstract
Several predictive models have been proposed to understand the microbial risk factors associated with cystic fibrosis (CF) progression. Very few have integrated fungal airways colonisation, which is increasingly recognized as a key player regarding CF progression. To assess the association between the percent predicted forced expiratory volume in 1 s (ppFEV1) change and the fungi or bacteria identified in the sputum, 299 CF patients from the “MucoFong” project were included and followed-up with over two years. The relationship between the microorganisms identified in the sputum and ppFEV1 course of patients was longitudinally analysed. An adjusted linear mixed model analysis was performed to evaluate the effect of a transient or chronic bacterial and/or fungal colonisation at inclusion on the ppFEV1 change over a two-year period. Pseudomonas aeruginosa, Achromobacter xylosoxidans, Stenotrophomonas maltophilia, and Candida albicans were associated with a significant ppFEV1 decrease. No significant association was found with other fungal colonisations. In addition, the ppFEV1 outcome in our model was 11.26% lower in patients presenting with a transient colonisation with non-pneumoniae Streptococcus species compared to other patients. These results confirm recently published data and provide new insights into bacterial and fungal colonisation as key factors for the assessment of lung function decline in CF patients.
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Affiliation(s)
- Florence Francis
- CHU de Bordeaux, Department of Public Health, F-33000 Bordeaux, France; (F.F.); (R.T.)
- Bordeaux Population Health Research Center, Univ. Bordeaux, Inserm, UMR 1219, F-33000 Bordeaux, France; (P.S.); (M.A.-F.)
| | - Raphael Enaud
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33000 Bordeaux, France; (R.E.); (F.L.-S.); (S.B.); (M.F.)
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000 Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC 1401, F-33000 Bordeaux, France
| | - Perrine Soret
- Bordeaux Population Health Research Center, Univ. Bordeaux, Inserm, UMR 1219, F-33000 Bordeaux, France; (P.S.); (M.A.-F.)
- INRIA SISTM Team, F-33405 Talence, France
- Laboratoire Servier, 50 Rue Carnot, 92284 Suresnes, France
| | - Florian Lussac-Sorton
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33000 Bordeaux, France; (R.E.); (F.L.-S.); (S.B.); (M.F.)
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000 Bordeaux, France
- CHU de Bordeaux, Service de Parasitologie-Mycologie, F-33000 Bordeaux, France
| | - Marta Avalos-Fernandez
- Bordeaux Population Health Research Center, Univ. Bordeaux, Inserm, UMR 1219, F-33000 Bordeaux, France; (P.S.); (M.A.-F.)
- INRIA SISTM Team, F-33405 Talence, France
| | | | - Stéphanie Bui
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33000 Bordeaux, France; (R.E.); (F.L.-S.); (S.B.); (M.F.)
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000 Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC 1401, F-33000 Bordeaux, France
| | - Michael Fayon
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33000 Bordeaux, France; (R.E.); (F.L.-S.); (S.B.); (M.F.)
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000 Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC 1401, F-33000 Bordeaux, France
| | - Rodolphe Thiébaut
- CHU de Bordeaux, Department of Public Health, F-33000 Bordeaux, France; (F.F.); (R.T.)
- Bordeaux Population Health Research Center, Univ. Bordeaux, Inserm, UMR 1219, F-33000 Bordeaux, France; (P.S.); (M.A.-F.)
- INRIA SISTM Team, F-33405 Talence, France
| | - Laurence Delhaes
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33000 Bordeaux, France; (R.E.); (F.L.-S.); (S.B.); (M.F.)
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000 Bordeaux, France
- CHU de Bordeaux, Service de Parasitologie-Mycologie, F-33000 Bordeaux, France
- Correspondence: ; Tel.: +33-05-47-30-27-50
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Hong G, Desai S, Moss RB, Eschenhagen P, Quon BS, Schwarz C. Clinician variability in the diagnosis and treatment of aspergillus fumigatus-related conditions in cystic fibrosis: An international survey. J Cyst Fibros 2021; 21:136-142. [PMID: 34332906 DOI: 10.1016/j.jcf.2021.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/07/2021] [Accepted: 07/14/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND The diagnosis and treatment of Aspergillus fumigatus (Af)-related conditions remain a challenge in cystic fibrosis (CF) due to overlapping features of disease and absence of clinical guidelines for Af-related conditions outside of ABPA. OBJECTIVE To investigate the differences of clinical practice in the diagnosis and management of Af-related conditions in CF. METHODS We conducted an international survey to CF clinicians to ascertain the screening, diagnostic, and treatment practices for Af-related conditions in CF. Respondents were grouped into geographical regions and regional comparisons using chi-square tests of independence or Fisher's tests were performed. RESULTS A total of 319 survey responses from 35 countries were analyzed. We observed differences in use and frequency of fungus culture, Aspergillus-specific IgE and IgG, skin prick testing, and pulmonary function testing as screening for Af-related conditions between the geographical regions. ABPA and Aspergillus bronchitis diagnostic criteria selection differed by region; significantly greater proportion of United States (US) and Canadian clinicians were unable to define Aspergillus bronchitis compared to Europe and other regions. Decision to treat ABPA was uniform across regions, but the consideration of Aspergillus bronchitis as a clinical disease warranting therapy differed between regions. The use of glucocorticoid and itraconazole was the first-line treatment of ABPA among clinicians; however, prednisone monotherapy was more common in US and Canada. CONCLUSIONS Significant variability in the diagnosis and management of Aspergillus-related conditions in CF was observed. Future studies are necessary to better harmonize the approach to Af-related disease in CF.
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Affiliation(s)
- Gina Hong
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Sameer Desai
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Richard B Moss
- Center of Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Patience Eschenhagen
- Department of Pediatric Pneumology, Immunology and Intensive Care Medicine, CF Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Bradley S Quon
- Department of Pediatric Pneumology, Immunology and Intensive Care Medicine, CF Center, Charité-Universitätsmedizin Berlin, Berlin, Germany; Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Carsten Schwarz
- Department of Pediatric Pneumology, Immunology and Intensive Care Medicine, CF Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
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Abstract
In the past three decades, fungal respiratory colonization and fungal respiratory infections increasingly raised concern in cystic fibrosis (CF). Reasons for this are a better knowledge of the pathogenicity of fungi, whereby detection is sought in more and more CF centers, but also improvement of detection methods. However, differences in fungal detection rates within and between geographical regions exist and indicate the need for standardization of mycological examination of respiratory secretions. The still existing lack of standardization also complicates the assessment of fungal pathogenicity, relevance of fungal detection and risk factors for fungal infections. Nevertheless, numerous studies have now been conducted on differences in detection methods, epidemiology, risk factors, pathogenicity and therapy of fungal diseases in CF. Meanwhile, some research groups now have classified fungal disease entities in CF and developed diagnostic criteria as well as therapeutic guidelines.The following review presents an overview on fungal species relevant in CF. Cultural detection methods with their respective success rates as well as susceptibility testing will be presented, and the problem of increasing azole resistance in Aspergillus fumigatus will be highlighted. Next, current data and conflicting evidence on the epidemiology and risk factors for fungal diseases in patients with CF will be discussed. Finally, an overview of fungal disease entities in CF with their current definitions, diagnostic criteria and therapeutic options will be presented.
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Recognition of Diagnostic Gaps for Laboratory Diagnosis of Fungal Diseases: Expert Opinion from the Fungal Diagnostics Laboratories Consortium (FDLC). J Clin Microbiol 2021; 59:e0178420. [PMID: 33504591 DOI: 10.1128/jcm.01784-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fungal infections are a rising threat to our immunocompromised patient population, as well as other nonimmunocompromised patients with various medical conditions. However, little progress has been made in the past decade to improve fungal diagnostics. To jointly address this diagnostic challenge, the Fungal Diagnostics Laboratory Consortium (FDLC) was recently created. The FDLC consists of 26 laboratories from the United States and Canada that routinely provide fungal diagnostic services for patient care. A survey of fungal diagnostic capacity among the 26 members of the FDLC was recently completed, identifying the following diagnostic gaps: lack of molecular detection of mucormycosis; lack of an optimal diagnostic algorithm incorporating fungal biomarkers and molecular tools for early and accurate diagnosis of Pneumocystis pneumonia, aspergillosis, candidemia, and endemic mycoses; lack of a standardized molecular approach to identify fungal pathogens directly in formalin-fixed paraffin-embedded tissues; lack of robust databases to enhance mold identification with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; suboptimal diagnostic approaches for mold blood cultures, tissue culture processing for Mucorales, and fungal respiratory cultures for cystic fibrosis patients; inadequate capacity for fungal point-of-care testing to detect and identify new, emerging or underrecognized, rare, or uncommon fungal pathogens; and performance of antifungal susceptibility testing. In this commentary, the FDLC delineates the most pressing unmet diagnostic needs and provides expert opinion on how to fulfill them. Most importantly, the FDLC provides a robust laboratory network to tackle these diagnostic gaps and ultimately to improve and enhance the clinical laboratory's capability to rapidly and accurately diagnose fungal infections.
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21
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Fungal Infection and Inflammation in Cystic Fibrosis. Pathogens 2021; 10:pathogens10050618. [PMID: 34069863 PMCID: PMC8157353 DOI: 10.3390/pathogens10050618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/14/2022] Open
Abstract
Fungi are frequently recovered from lower airway samples from people with cystic fibrosis (CF), yet the role of fungi in the progression of lung disease is debated. Recent studies suggest worsening clinical outcomes associated with airway fungal detection, although most studies to date are retrospective or observational. The presence of fungi can elicit a T helper cell type 2 (Th-2) mediated inflammatory reaction known as allergic bronchopulmonary aspergillosis (ABPA), particularly in those with a genetic atopic predisposition. In this review, we discuss the epidemiology of fungal infections in people with CF, risk factors associated with development of fungal infections, and microbiologic approaches for isolation and identification of fungi. We review the spectrum of fungal disease presentations, clinical outcomes after isolation of fungi from airway samples, and the importance of considering airway co-infections. Finally, we discuss the association between fungi and airway inflammation highlighting gaps in knowledge and future research questions that may further elucidate the role of fungus in lung disease progression.
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Bui S, Dournes G, Fayon M, Bouchet S, Burgel PR, Macey J, Murris M, Delhaes L. [Allergic Broncho-Pulmonary Aspergillosis (ABPA) in cystic fibrosis: Mechanisms, diagnosis and therapeutic options]. Rev Mal Respir 2021; 38:466-476. [PMID: 33926779 DOI: 10.1016/j.rmr.2021.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/28/2021] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Fungal aspergillosis colonization and allergic bronchopulmonary aspergillosis (ABPA) can have a strong impact on the prognosis in cystic fibrosis (CF). We conducted round table discussions involving French experts from pediatric and adult centers caring for patients with CF, microbiologists, radiologists and pharmacists. The aim was to explore the current state of knowledge on: the pathophysiological mechanisms of Aspergillus and other micromycetes infections in CF (such as Scedosporium sp.), and on the clinico-biological diagnosis of ABPA. In perspective, the experts explored the role of imaging in the diagnosis of APBA, specifically CT and MRI; as well as the role of bronchoscopy in the management. We also reviewed the therapeutic management, including different corticosteroid regimens, antifungals and anti-IgE antibodies. CONCLUSION The diagnosis of ABPA in CF should be based on more standardized biological assays and imaging to optimize treatment and follow-up.
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Affiliation(s)
- S Bui
- CRCM pédiatrique, Centre d'investigation clinique (CIC 1401), hôpital Pellegrin-Enfants, CHU de Bordeaux, Bordeaux, France.
| | - G Dournes
- Service de radiologie, hôpital Haut L'Evêque, CHU de Bordeaux, Bordeaux, France
| | - M Fayon
- CRCM pédiatrique, Centre d'investigation clinique (CIC 1401), hôpital Pellegrin-Enfants, CHU de Bordeaux, Bordeaux, France
| | - S Bouchet
- Service de pharmacologie, hôpital Pellegrin, CHU de Bordeaux, Bordeaux, France
| | - P R Burgel
- CRCM Adultes, AP-HP, hôpital Cochin, Paris, France
| | - J Macey
- CRCM adultes, hôpital Haut L'Evêque, CHU de Bordeaux, Bordeaux, France
| | - M Murris
- CRCM adultes, hôpital Larrey, CHU de Toulouse, Toulouse, France
| | - L Delhaes
- Service de parasitologie, CHU de Bordeaux, hôpital Pellegrin, Bordeaux, France
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Papon N, Bouchara JP. Improving and standardizing protocols for cystic fibrosis routine microbiology. J Cyst Fibros 2021; 20:e67-e68. [PMID: 33879418 DOI: 10.1016/j.jcf.2021.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 10/21/2022]
Affiliation(s)
- Nicolas Papon
- Univ Angers, Université de Bretagne Occidentale, SFR 4208 ICAT, Host-Pathogen Interactions Study Group (GEIHP, EA 3142), Angers, France.
| | - Jean-Philippe Bouchara
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalier Universitaire, Angers, France.
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Mills R, Rautemaa-Richardson R, Wilkinson S, Patel L, Maitra A, Horsley A. Impact of airway Exophiala spp. on children with cystic fibrosis. J Cyst Fibros 2021; 20:702-707. [PMID: 33775601 DOI: 10.1016/j.jcf.2021.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Isolation of Exophiala species from sputum samples has become increasingly reported in Cystic Fibrosis (CF). However, the clinical significance of Exophiala spp. with regards to the paediatric CF population is unknown. METHODS A case control study was undertaken to compare CF children with and without chronic Exophiala spp. in their sputum samples. Demographic and clinical data were collected retrospectively for each case from the date of Exophiala isolation and for 12 months preceding isolation. Each case was compared to three age and year-matched controls. To determine the effect of Exophiala on clinical course, patients were then followed for 12 months post isolation. RESULTS In total, 27 of 244 eligible paediatric CF patients (11%) isolated Exophiala spp. on more than one occasion. There were no significant differences in the key clinical parameters: spirometry, mean number of intravenous (IV) antibiotic days and body mass index (BMI), between cases and controls (p = 0.91, p = 0.56 and p = 0.63 respectively). A higher proportion of cases isolated Candida spp. (67% vs 21%, p < 0.0001) and Aspergillus fumigatus (37% vs 26%, p = 0.37). There was no clinically significant difference in spirometry, mean number of IV antibiotic days and BMI in cases pre and post Exophiala spp. isolation. Posaconazole was the only drug used that successfully eradicated Exophiala. CONCLUSION Despite the frequent isolation of Exophiala spp. in this cohort, in most patients it is not associated with significant clinical deterioration. It does however seem to be associated with isolation of other fungi.
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Affiliation(s)
- Rowena Mills
- Mycology Reference Centre Manchester, ECMM Centre of Excellence for Medical Mycology and the Department of Infectious Diseases, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, UK; Paediatric Respiratory Department, Royal Manchester Children's Hospital, Manchester University Hospital NHS Foundation Trust, Manchester, UK; Department of General Paediatrics, Birmingham Children's Hospital, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Riina Rautemaa-Richardson
- Mycology Reference Centre Manchester, ECMM Centre of Excellence for Medical Mycology and the Department of Infectious Diseases, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, UK; Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Stuart Wilkinson
- Paediatric Respiratory Department, Royal Manchester Children's Hospital, Manchester University Hospital NHS Foundation Trust, Manchester, UK
| | - Latifa Patel
- Paediatric Respiratory Department, Royal Manchester Children's Hospital, Manchester University Hospital NHS Foundation Trust, Manchester, UK
| | - Anirban Maitra
- Paediatric Respiratory Department, Royal Manchester Children's Hospital, Manchester University Hospital NHS Foundation Trust, Manchester, UK
| | - Alex Horsley
- Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Adult Cystic Fibrosis Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, UK.
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25
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Magee LC, Louis M, Khan V, Micalo L, Chaudary N. Managing Fungal Infections in Cystic Fibrosis Patients: Challenges in Clinical Practice. Infect Drug Resist 2021; 14:1141-1153. [PMID: 33790585 PMCID: PMC7998013 DOI: 10.2147/idr.s267219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 02/25/2021] [Indexed: 12/31/2022] Open
Abstract
Cystic Fibrosis (CF) is an autosomal recessive disease characterized by a mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) protein. Impairment of the CFTR protein in the respiratory tract results in the formation of thick mucus, development of inflammation, destruction of bronchial tissue, and development of bacterial or fungal infections over time. CF patients are commonly colonized and/or infected with fungal organisms, Candida albicans or Aspergillus fumigatus, with prevalence rates ranging from 5% to 78% in the literature. Risk factors for acquiring fungal organisms include older age, coinfection with Pseudomonas aeruginosa, prolonged use of oral and inhaled antibiotics, and lower forced expiratory volume (FEV1). There are limited data available to differentiate between contamination, colonization, and active infection. Furthermore, the pathogenicity of colonization is variable in the literature as some studies report a decline in lung function associated with fungal colonization whereas others showed no difference. Limited data are available for the eradication of fungal colonization and the treatment of active invasive aspergillosis in adult CF patients. In this review article, we discuss the challenges in clinical practice and current literature available for laboratory findings, clinical diagnosis, and treatment options for fungal infections in adult CF patients.
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Affiliation(s)
- Lauren C Magee
- Department of Pharmacy, Virginia Commonwealth University Health System, Richmond, VA, USA
| | - Mariam Louis
- Department of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Jacksonville, FL, USA
| | - Vaneeza Khan
- Division of Pulmonary Disease and Critical Care Medicine, Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Lavender Micalo
- Division of Pulmonary Disease and Critical Care Medicine, Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Nauman Chaudary
- Division of Pulmonary Disease and Critical Care Medicine, Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
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26
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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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Renner S, Nachbaur E, Jaksch P, Dehlink E. Update on Respiratory Fungal Infections in Cystic Fibrosis Lung Disease and after Lung Transplantation. J Fungi (Basel) 2020; 6:jof6040381. [PMID: 33371198 PMCID: PMC7766476 DOI: 10.3390/jof6040381] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/08/2020] [Accepted: 12/16/2020] [Indexed: 12/19/2022] Open
Abstract
Cystic fibrosis is the most common autosomal-recessive metabolic disease in the Western world. Impaired trans-membrane chloride transport via the cystic fibrosis transmembrane conductance regulator (CFTR) protein causes thickened body fluids. In the respiratory system, this leads to chronic suppurative cough and recurrent pulmonary infective exacerbations, resulting in progressive lung damage and respiratory failure. Whilst the impact of bacterial infections on CF lung disease has long been recognized, our understanding of pulmonary mycosis is less clear. The range and detection rates of fungal taxa isolated from CF airway samples are expanding, however, in the absence of consensus criteria and univocal treatment protocols for most respiratory fungal conditions, interpretation of laboratory reports and the decision to treat remain challenging. In this review, we give an overview on fungal airway infections in CF and CF-lung transplant recipients and focus on the most common fungal taxa detected in CF, Aspergillus fumigatus, Candida spp., Scedosporium apiospermum complex, Lomentospora species, and Exophiala dermatitidis, their clinical presentations, common treatments and prophylactic strategies, and clinical challenges from a physician’s point of view.
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Affiliation(s)
- Sabine Renner
- Division of Pediatric Pulmonology, Allergology and Endocrinology, Department of Pediatrics and Adolescent Medicine, Associated National Center in the European Reference Network on Rare Respiratory Diseases ERN-LUNG and the European Reference Network on Transplantation in Children, ERN TRANSPLANT-CHILD, Medical University of Vienna, 1090 Vienna, Austria; (S.R.); (E.N.)
| | - Edith Nachbaur
- Division of Pediatric Pulmonology, Allergology and Endocrinology, Department of Pediatrics and Adolescent Medicine, Associated National Center in the European Reference Network on Rare Respiratory Diseases ERN-LUNG and the European Reference Network on Transplantation in Children, ERN TRANSPLANT-CHILD, Medical University of Vienna, 1090 Vienna, Austria; (S.R.); (E.N.)
| | - Peter Jaksch
- Division of Thoracic Surgery, Medical University of Vienna, 1090 Vienna, Austria;
| | - Eleonora Dehlink
- Division of Pediatric Pulmonology, Allergology and Endocrinology, Department of Pediatrics and Adolescent Medicine, Associated National Center in the European Reference Network on Rare Respiratory Diseases ERN-LUNG and the European Reference Network on Transplantation in Children, ERN TRANSPLANT-CHILD, Medical University of Vienna, 1090 Vienna, Austria; (S.R.); (E.N.)
- Correspondence:
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28
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Risk factors for respiratory Aspergillus fumigatus in German Cystic Fibrosis patients and impact on lung function. Sci Rep 2020; 10:18999. [PMID: 33149181 PMCID: PMC7643137 DOI: 10.1038/s41598-020-75886-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/23/2020] [Indexed: 01/01/2023] Open
Abstract
Airway inflammation and chronic lung infections in cystic fibrosis (CF) patients are mostly caused by bacteria, e.g. Pseudomonas aeruginosa (PA). The role of fungi in the CF lung is still not well elucidated, but evidence for a harmful and complex role is getting stronger. The most common filamentous fungus in CF is Aspergillus fumigatus (AF). Age and continuous antibiotic treatment have been discussed as risk factors for AF colonisation but did not differentiate between transient and persistent AF colonisation. Also, the impact of co-colonisation of PA and AF on lung function is still under investigation. Data from patients with CF registered in the German Cystic Fibrosis Registry database in 2016 and 2017 were retrospectively analysed, involving descriptive and multivariate analysis to assess risk factors for transient or persistent AF colonisation. Age represented an independent risk factor for persistent AF colonisation. Prevalence was low in children less than ten years, highest in the middle age and getting lower in higher age (≥ 50 years). Continuous antibiotic lung treatment was significantly associated with AF prevalence in all age groups. CF patients with chronic PA infection had a lower lung function (FEV1%predicted), which was not influenced by an additional AF colonisation. AF colonisation without chronic PA infection, however, was significantly associated with a lower function, too. Older age up to 49 years and continuous antibiotic use were found to be the main risk factors for AF permanent colonisation. AF might be associated with decrease of lung function if not disguised by chronic PA infection.
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Bonnet P, Le Gal S, Calderon E, Delhaes L, Quinio D, Robert-Gangneux F, Ramel S, Nevez G. Pneumocystis jirovecii in Patients With Cystic Fibrosis: A Review. Front Cell Infect Microbiol 2020; 10:571253. [PMID: 33117730 PMCID: PMC7553083 DOI: 10.3389/fcimb.2020.571253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022] Open
Abstract
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.
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Affiliation(s)
- Pierre Bonnet
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, Brest, France
| | - Solène Le Gal
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, Brest, France.,Groupe d'Etude des Interactions Hôte-Pathogène (ER, GEIHP), Université d'Angers, Université de Brest, Brest, France
| | - Enrique Calderon
- CIBER de Epidemiologia y Salud Publica and Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, Seville, Spain
| | - Laurence Delhaes
- Laboratory of Parasitology and Mycology, Bordeaux University Hospital, Bordeaux, France Inserm U1045 - University of Bordeaux, Bordeaux, France
| | - Dorothée Quinio
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, Brest, France
| | - Florence Robert-Gangneux
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé Environnement Travail), UMR_S 1085, Rennes, France
| | - Sophie Ramel
- Centre de Ressources et de Compétences de la Mucoviscidose, Fondation Ildys, Roscoff, France
| | - Gilles Nevez
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, Brest, France.,Groupe d'Etude des Interactions Hôte-Pathogène (ER, GEIHP), Université d'Angers, Université de Brest, Brest, France
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Soret P, Vandenborght LE, Francis F, Coron N, Enaud R, Avalos M, Schaeverbeke T, Berger P, Fayon M, Thiebaut R, Delhaes L. Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis. Sci Rep 2020; 10:3589. [PMID: 32108159 PMCID: PMC7046743 DOI: 10.1038/s41598-020-60015-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
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.
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Affiliation(s)
- Perrine Soret
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
- INRIA SISTM Team, F-33405, Talence, France
| | - Louise-Eva Vandenborght
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- Genoscreen Society, 59000, Lille, France
| | - Florence Francis
- CHU Bordeaux, Department of Public Health, F-33000, Bordeaux, France
| | - Noémie Coron
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
- CHU de Bordeaux: Laboratoire de Parasitologie-Mycologie, Univ. Bordeaux, F-33000, Bordeaux, France
| | - Raphael Enaud
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC, 1401, Bordeaux, France
| | - Marta Avalos
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
- INRIA SISTM Team, F-33405, Talence, France
| | | | - Patrick Berger
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
| | - Michael Fayon
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC, 1401, Bordeaux, France
| | - Rodolphe Thiebaut
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
- INRIA SISTM Team, F-33405, Talence, France
- CHU Bordeaux, Department of Public Health, F-33000, Bordeaux, France
| | - Laurence Delhaes
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France.
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France.
- CHU de Bordeaux: Laboratoire de Parasitologie-Mycologie, Univ. Bordeaux, F-33000, Bordeaux, France.
- CHU de Bordeaux, CRCM Pédiatrique, CIC, 1401, Bordeaux, France.
- University and CHU of Lille, F-59000, Lille, France.
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Martín-Gómez MT. Taking a look on fungi in cystic fibrosis: More questions than answers. Rev Iberoam Micol 2020; 37:17-23. [PMID: 31928888 DOI: 10.1016/j.riam.2019.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/21/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023] Open
Abstract
Cystic fibrosis (CF) is one of the most frequent recessive inherited diseases in western countries. Advances in medical care have led to a substantial increase in the life expectancy of CF patients. Survival beyond adolescence has permitted to see fungi not only as late colonizers, but also as potential pathogens responsible of allergic reactions and chronic infections related to lung function deterioration. The role of fungi, nevertheless, has been overlooked until recently. As a result, a number of questions on their epidemiology, clinical significance, or diagnosis, among others, remain unanswered. Besides more in depth studies about the extent of the deleterious effect of fungi on the CF host, new technologies may provide the key to understand its pathogenic role, its interaction with other microbial components of the respiratory microbiota, and should pave the way to define subsets of patients at risk who would benefit from specific therapy. This review is intended to provide a quick overview on what we know about the presence of fungi in the CF airway and its repercussion in the host, and to point out some of the many knowledge gaps needed to understand and advance in the management of fungi in the airway of CF subjects.
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32
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Fungal Infections and ABPA. Respir Med 2020. [DOI: 10.1007/978-3-030-42382-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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33
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Bouchara JP, Le Govic Y, Kabbara S, Cimon B, Zouhair R, Hamze M, Papon N, Nevez G. Advances in understanding and managing Scedosporium respiratory infections in patients with cystic fibrosis. Expert Rev Respir Med 2019; 14:259-273. [PMID: 31868041 DOI: 10.1080/17476348.2020.1705787] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Considered for a long time to be exclusively responsible for chronic localized infections, fungi of the genus Scedosporium have recently received a renewed interest because of their recognition as common colonizing agents of the respiratory tract of patients with cystic fibrosis, and of the description of severe disseminated infections in patients undergoing lung transplantation. Recently, several studies have been carried out on these opportunistic pathogens, which led to some advances in the understanding of their pathogenic mechanisms and in the biological diagnosis of the airway colonization/respiratory infections caused by these fungi.Areas covered: From a bibliographic search on the Pubmed database, we summarize the current knowledge about the taxonomy of Scedosporium species, the epidemiology of these fungi and their pathogenic mechanisms, and present the improvements in the detection of the airway colonization and diagnosis of Scedosporium respiratory infections, the difficulties in their therapeutic management, and the antifungal drugs in development.Expert opinion: As described in this review, many advances have been made regarding the taxonomy and ecology of Scedosporium species or the molecular determinants of their pathogenicity, but also in the management of Scedosporium infections, particularly by improving the biological diagnostic and publishing evidence for the efficacy of combined therapy.
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Affiliation(s)
- Jean-Philippe Bouchara
- Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA 3142), UNIV Angers, UNIV Brest, SFR 4208 ICAT, Angers, France
| | - Yohann Le Govic
- Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA 3142), UNIV Angers, UNIV Brest, SFR 4208 ICAT, Angers, France
| | - Samar Kabbara
- Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA 3142), UNIV Angers, UNIV Brest, SFR 4208 ICAT, Angers, France
| | - Bernard Cimon
- Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA 3142), UNIV Angers, UNIV Brest, SFR 4208 ICAT, Angers, France
| | - Rachid Zouhair
- Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA 3142), UNIV Angers, UNIV Brest, SFR 4208 ICAT, Angers, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Liban
| | - Nicolas Papon
- Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA 3142), UNIV Angers, UNIV Brest, SFR 4208 ICAT, Angers, France
| | - Gilles Nevez
- Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA 3142), UNIV Angers, UNIV Brest, Brest, France
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Savant AP, McColley SA. Cystic fibrosis year in review 2018, part 1. Pediatr Pulmonol 2019; 54:1117-1128. [PMID: 31106528 DOI: 10.1002/ppul.24361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/28/2019] [Accepted: 04/29/2019] [Indexed: 12/14/2022]
Abstract
Cystic fibrosis research and case reports were robust in the year 2018. This report summarizes research and cases related to Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) modulator therapies, inflammation and infection, epidemiology and the physiologic, and imaging assessment of disease.
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Affiliation(s)
- Adrienne P Savant
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Stanley Manne Children's Research Institute, Chicago, Illinois.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Susanna A McColley
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Stanley Manne Children's Research Institute, Chicago, Illinois.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
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Fiscarelli EV, Ricciotti G, Rossitto M, Pompilio A, Tuccio Guarna Assanti V, Lucidi V. A cystic fibrosis child with lung function decline. J Cyst Fibros 2019; 18:e62-e64. [PMID: 31300282 DOI: 10.1016/j.jcf.2019.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/25/2019] [Accepted: 06/27/2019] [Indexed: 10/26/2022]
Abstract
Respiratory infections are a major threat to cystic fibrosis patients. Besides bacteria, many fungi colonize the cystic fibrosis respiratory tract where an important fungal biota has been described. We report here the case of a 7-year-old cystic fibrosis child with pulmonary exacerbation and Arthrographis kalrae isolated from bronchoalveolar lavage fluid. To the best of our knowledge, this is the first reported case of lung infection due to Arhtrographis kalrae in a cystic fibrosis pediatric patient.
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Affiliation(s)
- Ersilia Vita Fiscarelli
- Laboratory Department, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy.
| | - Gabriella Ricciotti
- Laboratory Department, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy
| | - Martina Rossitto
- Laboratory Department, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy
| | - Arianna Pompilio
- Department of Medical, Oral and Biotechnological Sciences, and Center of Excellence on Aging and Translational Medicine, "G. d'Annunzio" University of Chieti-Pescara, Italy
| | | | - Vincenzina Lucidi
- Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy
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36
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Interactions between Aspergillus fumigatus and Pulmonary Bacteria: Current State of the Field, New Data, and Future Perspective. J Fungi (Basel) 2019; 5:jof5020048. [PMID: 31212791 PMCID: PMC6617096 DOI: 10.3390/jof5020048] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/10/2019] [Accepted: 06/10/2019] [Indexed: 12/14/2022] Open
Abstract
Aspergillus fumigatus and Pseudomonas aeruginosa are central fungal and bacterial members of the pulmonary microbiota. The interactions between A. fumigatus and P. aeruginosa have only just begun to be explored. A balance between inhibitory and stimulatory effects on fungal growth was observed in mixed A. fumigatus-P. aeruginosa cultures. Negative interactions have been seen for homoserine-lactones, pyoverdine and pyochelin resulting from iron starvation and intracellular inhibitory reactive oxidant production. In contrast, several types of positive interactions were recognized. Dirhamnolipids resulted in the production of a thick fungal cell wall, allowing the fungus to resist stress. Phenazines and pyochelin favor iron uptake for the fungus. A. fumigatus is able to use bacterial volatiles to promote its growth. The immune response is also differentially regulated by co-infections.
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37
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Hedayati MT, Tavakoli M, Maleki M, Heidari S, Mortezaee V, Gheisari M, Hassanzad M, Mirenayat MS, Mahdaviani SA, Pourabdollah M, Velayati AA, Vakili M, Abastabar M, Haghani I, Jafarzadeh J, Hedayati N, Seyedmousavi S, Alastruey-Izquierdo A. Fungal epidemiology in cystic fibrosis patients with a special focus on Scedosporium species complex. Microb Pathog 2019; 129:168-175. [PMID: 30742949 DOI: 10.1016/j.micpath.2019.02.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 02/04/2023]
Abstract
In this present study, for the first time, we evaluated the cystic fibrosis (CF) patients for the Scedosporium species and their antifungal susceptibility against eight antifungal agents. During one-year period, 90 Sputum samples were collected from Iranian CF patients. All samples were evaluated by direct microscopic examination, culture onto four different media including Malt extract agar, Inhibitory mold agar, Brain Heart Infusion and Scedo-Select III. The mold isolated fungi were identified by PCR-Sequencing of ITS and β-tubulin genes. In-vitro antifungal susceptibility was performed according to the Clinical & Laboratory Standards Institute (CLSI) M38-A2 guidelines. Out of 90 CF patients, 47 (52.2%) were male. The age of the patients ranged from 1 to 34 years (median of 15.84 ± 7.41 years). Overall, 3 (3.3%) cases were positive for Scedosporium spp. of which two isolates were characterized as Scedosporium boydii and one isolate as S. ellipsoideum. Among Aspergillus genus, A. flavus (29.4%) was the most prevalent species followed by A. tubingensis (24.7%), A. niger (17.0%) and A. fumigatus (14.5%). The minimum effective concentration ranges of micafungin, anidulafungin, and caspofungin were 0.008-0.031 μg/mL, 0.0625-0.25 μg/mL, and 0.0625-0.25 μg/mL, respectively. All isolates of Scedosporium species showed high minimum inhibitory concentration to the triazoles tested, except voriconazole. Our results showed that A. flavus and Scedosporium species are the most prevalent molds isolated from CF patient populations in Iran. Our findings have also showed that Scedo-Select III can be used as a reliable culture media for isolation of Scedosporium spp. in clinical samples.
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Affiliation(s)
- Mohammad T Hedayati
- Invasive Fungi Research Center, Mazandaran University of Medical Sciences, Sari, Iran; Department of Medical Mycology, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahin Tavakoli
- Student Research Committee, Invasive Fungi Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Maedeh Maleki
- Student Research Committee, Invasive Fungi Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Somaye Heidari
- Invasive Fungi Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Vida Mortezaee
- Student Research Committee, Invasive Fungi Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Maryam Gheisari
- Student Research Committee, Invasive Fungi Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Maryam Hassanzad
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Maryam Sadat Mirenayat
- Lung Transplantation Research Center (LTRC), National Research Institute of Tuberculosis and Lung Diseases (NIRTLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Alireza Mahdaviani
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mihan Pourabdollah
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Akbar Velayati
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahshid Vakili
- Student Research Committee, Invasive Fungi Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahdi Abastabar
- Invasive Fungi Research Center, Mazandaran University of Medical Sciences, Sari, Iran; Department of Medical Mycology, Mazandaran University of Medical Sciences, Sari, Iran
| | - Iman Haghani
- Invasive Fungi Research Center, Mazandaran University of Medical Sciences, Sari, Iran; Department of Medical Mycology, Mazandaran University of Medical Sciences, Sari, Iran
| | - Jalal Jafarzadeh
- Student Research Committee, Invasive Fungi Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Newsha Hedayati
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Seyedmojtaba Seyedmousavi
- Invasive Fungi Research Center, Mazandaran University of Medical Sciences, Sari, Iran; Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA; Medical Mycology Reference Laboratory, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Alastruey-Izquierdo
- Center of Expertise in Microbiology, Infection Biology and Antimicrobial Pharmacology, Tehran, Iran
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