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Ravenel K, Guegan H, Gastebois A, Bouchara JP, Gangneux JP, Giraud S. Fungal Colonization of the Airways of Patients with Cystic Fibrosis: the Role of the Environmental Reservoirs. Mycopathologia 2024; 189:19. [PMID: 38407729 DOI: 10.1007/s11046-023-00818-x] [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: 09/25/2023] [Accepted: 11/23/2023] [Indexed: 02/27/2024]
Abstract
Filamentous fungi frequently colonize the airways of patients with cystic fibrosis and may cause severe diseases, such as the allergic bronchopulmonary aspergillosis. The most common filamentous fungi capable to chronically colonize the respiratory tract of the patients are Aspergillus fumigatus and Scedosporium species. Defining the treatment strategy may be challenging, the number of available drugs being limited and some of the causative agents being multiresistant microorganisms. The knowledge of the fungal niches in the outdoor and indoor environment is needed for understanding the origin of the contamination of the patients. In light of the abundance of some of the causative molds in compost, agricultural and flower fields, occupational activities related to such environments should be discouraged for patients with cystic fibrosis (CF). In addition, the microbiological monitoring of their indoor environment, including analysis of air and dust on surfaces, is essential to propose preventive measures aiming to reduce the exposure to environmental molds. Nevertheless, some specific niches were also identified in the indoor environment, in relation with humidity which favors the growth of thermotolerant molds. Potted plants were reported as indoor reservoirs for Scedosporium species. Likewise, Exophiala dermatitidis may be spread in the kitchen via dishwashers. However, genotype studies are still required to establish the link between dishwashers and colonization of the airways of CF patients by this black yeast. Moreover, as nothing is known regarding the other filamentous fungi associated with CF, further studies should be conducted to identify other potential specific niches in the habitat.
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Affiliation(s)
- Kévin Ravenel
- IRF (Infections Respiratoires Fongiques), SFR ICAT 4208, Univ Angers, Univ Brest, Angers, France
| | - Hélène Guegan
- EHESP, IRSET (Institut de Recherche en Santé Environnement et Travail), UMR_S 1085, CHU Rennes, INSERM, Univ Rennes, 35000, Rennes, France
| | - Amandine Gastebois
- IRF (Infections Respiratoires Fongiques), SFR ICAT 4208, Univ Angers, Univ Brest, Angers, France
| | - Jean-Philippe Bouchara
- IRF (Infections Respiratoires Fongiques), SFR ICAT 4208, Univ Angers, Univ Brest, Angers, France
| | - Jean-Pierre Gangneux
- EHESP, IRSET (Institut de Recherche en Santé Environnement et Travail), UMR_S 1085, CHU Rennes, INSERM, Univ Rennes, 35000, Rennes, France
| | - Sandrine Giraud
- IRF (Infections Respiratoires Fongiques), SFR ICAT 4208, Univ Angers, Univ Brest, Angers, France.
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Lemonnier LC, Couroucé A, Cessans M, Petit L, Cardwell JM, Barbazanges P, Toquet MP, Richard EA. Detection of fungi in the airways of horses according to the sample site: a methodological study. Vet Res Commun 2024; 48:345-355. [PMID: 37704768 DOI: 10.1007/s11259-023-10213-y] [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: 06/20/2023] [Accepted: 08/31/2023] [Indexed: 09/15/2023]
Abstract
Fungal detection in equine airways may be performed on either tracheal wash (TW) or bronchoalveolar lavage fluid (BALF) by either cytology or culture. However, method comparisons are sparse. Our objective was to determine the prevalence of fungi in airways of horses according to the sample site and laboratory methodology. Sixty-two adult horses, investigated in the field or referred for respiratory disease, were included. Tracheal wash, and BALF collected separately from both lungs, were collected using a videoendoscope. Fungi were detected in cytologic samples examined by light microscopy, and by fungal culture. Hay was sampled in the field. Prevalence of fungi was of 91.9% in TW and 37.1% in BALF. Fungi were cultured from 82.3% of TW and 20.9% of BALF. Fungal elements were observed cytologically in 69.4% of TW and 22.6% of BALF. In 50% of horses, the same fungi were detected in both TW and hay, but fungi detected in BALF and hay differed in all horses. Poor agreement was found for the detection of fungi between TW and BALF and between fungal culture and cytologic examination (Cohen's kappa coefficient (κ) < 0.20). Moderate agreement was found between cytologic examination of left and right lungs (κ = 0.47). The prevalence of fungi detected cytologically on pooled BALF was significantly different (p = 0.023) than on combined left and right BALF. Fungi were more prevalent in the TW than BALF, and results suggest that hay might not be the primary source of fungi of the lower respiratory tract of horses.
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Affiliation(s)
- L C Lemonnier
- CISCO-ONIRIS, Department of Equine Internal Medicine, University Veterinary Teaching Hospital, Oniris, 44300, Nantes, France.
| | - A Couroucé
- CISCO-ONIRIS, Department of Equine Internal Medicine, University Veterinary Teaching Hospital, Oniris, 44300, Nantes, France
- Université de Caen Normandie, BIOTARGEN UR7450, F-14000, Caen, France
| | - M Cessans
- CISCO-ONIRIS, Department of Equine Internal Medicine, University Veterinary Teaching Hospital, Oniris, 44300, Nantes, France
| | - L Petit
- LABÉO (Frank Duncombe), 1 route de Rosel, 14053, Caen, France
| | - J M Cardwell
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, Hertfordshire, UK
| | - P Barbazanges
- CISCO-ONIRIS, Department of Equine Internal Medicine, University Veterinary Teaching Hospital, Oniris, 44300, Nantes, France
| | - M -P Toquet
- Université de Caen Normandie, BIOTARGEN UR7450, F-14000, Caen, France
- LABÉO (Frank Duncombe), 1 route de Rosel, 14053, Caen, France
| | - E A Richard
- Université de Caen Normandie, BIOTARGEN UR7450, F-14000, Caen, France
- LABÉO (Frank Duncombe), 1 route de Rosel, 14053, Caen, France
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O'Dea AL, Feng R, Glaser LJ, Kubrak C, Rubenstein RC, Dorgan DJ, Hadjiliadis D, Kawut SM, Hong G. The Clinical Association between Aspergillus fumigatus and Respiratory Outcomes in Adolescents and Adults with Cystic Fibrosis. Ann Am Thorac Soc 2023; 20:984-992. [PMID: 36800434 DOI: 10.1513/annalsats.202210-852oc] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/17/2023] [Indexed: 02/19/2023] Open
Abstract
Rationale: The clinical significance of Aspergillus fumigatus (Af) detection in the absence of allergic bronchopulmonary aspergillosis in cystic fibrosis (CF) airways remains unclear. Yet, some clinicians initiate antifungal therapy for Af-positive respiratory cultures out of concern for infection in people with CF. Objectives: To determine the association between the presence of Af and respiratory outcomes in individuals with CF. Methods: We conducted a prospective longitudinal cohort study of 206 adults and adolescents (age 14 yr and older) with CF and collected sputum for selective fungus culture. We assessed clinical outcome measurements, including patient-reported outcomes (measured by the Cystic Fibrosis Questionnaire-Revised), spirometry, and number of pulmonary exacerbations (PEx) for a 1-year period. We used mixed-effects linear models to determine the association between positive Af culture results, defined as Af detection in sputum culture at the study visit, with both respiratory domain score and forced expiratory volume in 1 second (FEV1) percent predicted, adjusted for confounders. Mixed-effects Poisson regression models were employed to examine the association between positive Af culture results and PEx events. We explored the association between Af history, defined as Af detection at baseline or within 2 years of enrollment, and respiratory outcomes. Results: Af prevalence was 10.3% (95% confidence interval [CI], 6.8, 15.7) at baseline. Forty-eight (23.3%; 95% CI, 17.7, 29.7) participants had at least one Af-positive culture result during the study period. Positive Af culture result was not associated with lower respiratory domain score. However, Af history was associated with a 6.48-point lower respiratory domain score, reflective of worse respiratory quality of life (95% CI, -11.96, -0.99; P = 0.02). Positive Af culture result was associated with a 2.54% lower FEV1 percent predicted (95% CI, -4.64, -0.44; P = 0.02) and a 1.71-fold increase in severe PEx incidence (95% CI, 1.05, 2.76; P = 0.03). Conclusions: Positive Af culture result was not associated with lower patient-reported, respiratory-related quality of life. Yet, positive Af culture result was associated with both lower FEV1 percent predicted and increased frequency of severe PEx warranting intravenous antibiotics in adolescents and adults with CF. Future studies are required to better understand the direct role of Af in lung disease progression in CF.
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Affiliation(s)
- Anna L O'Dea
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine
| | - Rui Feng
- Center for Clinical Epidemiology and Biostatistics, and
| | - Laurel J Glaser
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Christina Kubrak
- Division of Allergy and Pulmonary Medicine, Department of Pediatrics, Washington University School of Medicine in Saint Louis, St. Louis, Missouri; and
| | - Ronald C Rubenstein
- Division of Allergy and Pulmonary Medicine, Department of Pediatrics, Washington University School of Medicine in Saint Louis, St. Louis, Missouri; and
| | - Daniel J Dorgan
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine
| | - Denis Hadjiliadis
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Steven M Kawut
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine
- Center for Clinical Epidemiology and Biostatistics, and
| | - Gina Hong
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine
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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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O’Connor JB, Wagner BD, Harris JK, Frank DN, Clabots DE, Laguna TA. Detection and identification of fungi in the lower airway of children with and without cystic fibrosis. Front Microbiol 2023; 14:1119703. [PMID: 36846802 PMCID: PMC9948248 DOI: 10.3389/fmicb.2023.1119703] [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: 12/09/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction Airway infection and inflammation lead to the progression of obstructive lung disease in persons with cystic fibrosis (PWCF). However, cystic fibrosis (CF) fungal communities, known drivers of CF pathophysiology, remain poorly understood due to the shortcomings of traditional fungal culture. Our objective was to apply a novel small subunit rRNA gene (SSU-rRNA) sequencing approach to characterize the lower airway mycobiome in children with and without CF. Methods Bronchoalveolar lavage fluid (BALF) samples and relevant clinical data were collected from pediatric PWCF and disease control (DC) subjects. Total fungal load (TFL) was measured using quantitative PCR, and SSU-rRNA sequencing was used for mycobiome characterization. Results were compared across groups, and Morisita-Horn clustering was performed. Results 161 (84%) of the BALF samples collected had sufficient load for SSU-rRNA sequencing, with amplification being more common in PWCF. BALF from PWCF had increased TFL and increased neutrophilic inflammation compared to DC subjects. PWCF exhibited increased abundance of Aspergillus and Candida, while Malassezia, Cladosporium, and Pleosporales were prevalent in both groups. CF and DC samples showed no clear differences in clustering when compared to each other or to negative controls. SSU-rRNA sequencing was used to profile the mycobiome in pediatric PWCF and DC subjects. Notable differences were observed between the groups, including the abundance of Aspergillus and Candida. Discussion Fungal DNA detected in the airway could represent a combination of pathogenic fungi and environmental exposure (e.g., dust) to fungus indicative of a common background signature. Next steps will require comparisons to airway bacterial communities.
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Affiliation(s)
- John B. O’Connor
- Division of Pulmonary and Sleep Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States,*Correspondence: John B. O’Connor, ✉
| | - Brandie D. Wagner
- University of Colorado School of Medicine, Aurora, CO, United States,Colorado School of Public Health, University of Colorado Denver, Aurora, CO, United States
| | - J. Kirk Harris
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Daniel N. Frank
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Diana E. Clabots
- University of Colorado School of Medicine, Aurora, CO, United States,Department of Internal Medicine, Palmetto General Hospital, Hialeah, FL, United States
| | - Theresa A. Laguna
- Division of Pulmonary and Sleep Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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6
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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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Zhao Z, Song J, Yang C, Yang L, Chen J, Li X, Wang Y, Feng J. Prevalence of Fungal and Bacterial Co-Infection in Pulmonary Fungal Infections: A Metagenomic Next Generation Sequencing-Based Study. Front Cell Infect Microbiol 2021; 11:749905. [PMID: 34790588 PMCID: PMC8591235 DOI: 10.3389/fcimb.2021.749905] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/18/2021] [Indexed: 01/08/2023] Open
Abstract
With the widespread use of antibacterial drugs and increasing number of immunocompromised patients, pulmonary fungal infections are becoming more common. However, the incidence of pulmonary fungal and bacterial co-infection is rarely reported. In this study, 119 patients definitively diagnosed with pulmonary fungal infections between July 2018 and March 2020 were assessed using metagenomic next-generation sequencing (mNGS) as well as traditional pathogen detection to gauge the incidence of fungal and bacterial co-infection and evaluate the associated risk factors. We found that of the 119 patients with fungal infections, 48 (40.3%) had pulmonary fungal and bacterial co-infection. We identified immunocompromised status and the presence of one or more pulmonary cavities as risk factors associated with fungal and bacterial co-infection. The most commonly isolated fungi species were Aspergillus, Pneumocystis, and Rhizopus. The most commonly isolated bacterial species were Pseudomonas aeruginosa, Acinetobacter baumannii, and Stenotrophomonas maltophilia. Seventy-nine (66.4%) patients had received empirical antibiotic treatment before their pathogenic test results became available, and 41.7% (fungal infection group) and 38.7% (fungal and bacterial co-infection group) of the patients had their antibacterial drug dosage changed accordingly. This mNGS-based study showed that the incidence of fungal and bacterial co-infection is significant. Our research outcomes can, thus, guide the use of antibacterial drugs in the treatment of clinical fungal infections.
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Affiliation(s)
- Zhan Zhao
- Respiratory Department, Tianjin Medical University General Hospital, Tianjin, China
| | - Junxiu Song
- Respiratory Department, Tianjin Medical University General Hospital, Tianjin, China
| | - Changqing Yang
- Respiratory Department, Tianjin Medical University General Hospital, Tianjin, China
| | - Lei Yang
- Respiratory Department, Tianjin Medical University General Hospital, Tianjin, China
| | - Jie Chen
- Guangzhou Sagene Biotechnology Company, Limited, Guangzhou, China
| | - Xinhui Li
- Guangzhou Sagene Biotechnology Company, Limited, Guangzhou, China
| | - Yubao Wang
- Institute of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Jing Feng
- Respiratory Department, Tianjin Medical University General Hospital, Tianjin, China
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8
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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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10
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Scedosporium and Lomentospora infections in lung transplant recipients. CURRENT FUNGAL INFECTION REPORTS 2021. [DOI: 10.1007/s12281-021-00416-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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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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12
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Kitisin T, Ampawong S, Muangkaew W, Sukphopetch P. Phenomic profiling of a novel sibling species within the Scedosporium complex in Thailand. BMC Microbiol 2021; 21:42. [PMID: 33563219 PMCID: PMC7874643 DOI: 10.1186/s12866-021-02105-5] [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: 11/03/2020] [Accepted: 01/18/2021] [Indexed: 11/16/2022] Open
Abstract
Background Scedosporium species are a group of pathogenic fungi, which can be found worldwide around high human-impacted areas. Infections of Scedosporium have been reported in several immunocompromised and immunocompetent patients with a high mortality rate. Recently, we have isolated and identified several Scedosporium strains during an environmental survey in Thailand. Results We describe the isolate, TMMI-012, possibly a new species isolated from soils in the Chatuchak public park, Bangkok, Thailand. TMMI-012 is phylogenetically related to the Scedosporium genus and is a sibling to S. boydii but shows distinct morphological and pathological characteristics. It is fast growing and highly resistant to antifungal drugs and abiotic stresses. Pathological studies of in vitro and in vivo models confirm its high virulence and pathogenicity. Conclusion TMMI-012 is considered a putative novel Scedosporium species. The high antifungal resistance of TMMI-012 compared with its sibling, Scedosporium species is likely related to its clinical impact on human health.
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Affiliation(s)
- T Kitisin
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - S Ampawong
- Department of Tropical Pathology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - W Muangkaew
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - P Sukphopetch
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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13
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Patel D, Dacanay KC, Pashley CH, Gaillard EA. Comparative Analysis of Clinical Parameters and Sputum Biomarkers in Establishing the Relevance of Filamentous Fungi in Cystic Fibrosis. Front Cell Infect Microbiol 2021; 10:605241. [PMID: 33553007 PMCID: PMC7862329 DOI: 10.3389/fcimb.2020.605241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/04/2020] [Indexed: 11/13/2022] Open
Abstract
Background The relationship between fungal culture (FC) positivity and airway inflammation in CF is largely unknown. Identifying the clinical significance of filamentous fungi in CF using both clinical parameters and biomarkers may change our antimicrobial therapeutic strategies. Objectives To investigate the clinical characteristics and airway biomarker profile in relation to the detection of filamentous fungi in respiratory samples obtained from CF patients. Methods A prospective cohort study over 24 months, including children and adults with CF. Participants provided sputum and/or bronchoalveolar lavage samples, which underwent processing for bacterial and fungal culture, leukocyte differential cell count and biomarker analysis for neutrophil elastase (NE), interleukin-8 (IL-8), galactomannan and tumor necrosis factor receptor type 2 (TNF-R2). We performed FC using neat sputum plugs, an approach shown to be more sensitive compared to routine laboratory testing. Results Sixty-one patients provided 76 respiratory samples (72 sputum and 4 BAL). Median age was 17 years (range 6 months-59 years). FC positivity was noted in 49% of the cohort. FC positivity was greater during pulmonary exacerbation compared to the stable state (67 versus 50%). Participants aged 5-30 years had a lower FEV1 within the FC positive group. A significant association between FC positivity and non-tuberculosis mycobacterial (NTM) culture was observed on non-parametric testing (p = 0.022) and regression analysis (p = 0.007). Exposure to indoor mold was a predictor for FC positivity (p = 0.047). There was a trend towards increased lung clearance index (LCI), bronchiectasis and intravenous antibiotic use in the FC positive group. There was no significant difference in biomarkers between FC positive and negative patients. Conclusion Aspergillus. fumigatus is the commonest filamentous fungi cultured from CF airways. We found no difference in the airway biomarker profile between FC positive and negative patients. The role of galactomannan and TNFR2 as fungal specific biomarkers in CF remains uncertain. FC positivity is associated with a lower FEV1 in younger patients, a lower LCI, NTM positivity, bronchiectasis, and intravenous antibiotic exposure. Larger trials are needed to determine the role of galactomannan and TNF-R2 as potential fungal biomarkers in CF.
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Affiliation(s)
- Deepa Patel
- Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom.,Paediatric Respiratory Department, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Keith Chester Dacanay
- Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom.,Institute for Lung Health, NIHR Respiratory Biomedical Research Center, Leicester, United Kingdom
| | - Catherine H Pashley
- Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom.,Institute for Lung Health, NIHR Respiratory Biomedical Research Center, Leicester, United Kingdom
| | - Erol A Gaillard
- Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom.,Paediatric Respiratory Department, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom.,Institute for Lung Health, NIHR Respiratory Biomedical Research Center, Leicester, United Kingdom
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14
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COVID-19-Associated Invasive Aspergillosis: Data from the UK National Mycology Reference Laboratory. J Clin Microbiol 2020; 59:JCM.02136-20. [PMID: 33087440 PMCID: PMC7771443 DOI: 10.1128/jcm.02136-20] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/17/2020] [Indexed: 12/21/2022] Open
Abstract
COVID-19-associated pulmonary aspergillosis (CAPA) was recently reported as a potential infective complication affecting critically ill patients with acute respiratory distress syndrome following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, with incidence rates varying from 8 to 33% depending on the study. However, definitive diagnosis of CAPA is challenging. Standardized diagnostic algorithms and definitions are lacking, clinicians are reticent to perform aerosol-generating bronchoalveolar lavages for galactomannan testing and microscopic and cultural examination, and questions surround the diagnostic sensitivity of different serum biomarkers. COVID-19-associated pulmonary aspergillosis (CAPA) was recently reported as a potential infective complication affecting critically ill patients with acute respiratory distress syndrome following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, with incidence rates varying from 8 to 33% depending on the study. However, definitive diagnosis of CAPA is challenging. Standardized diagnostic algorithms and definitions are lacking, clinicians are reticent to perform aerosol-generating bronchoalveolar lavages for galactomannan testing and microscopic and cultural examination, and questions surround the diagnostic sensitivity of different serum biomarkers. Between 11 March and 14 July 2020, the UK National Mycology Reference Laboratory received 1,267 serum and respiratory samples from 719 critically ill UK patients with COVID-19 and suspected pulmonary aspergillosis. The laboratory also received 46 isolates of Aspergillus fumigatus from COVID-19 patients (including three that exhibited environmental triazole resistance). Diagnostic tests performed included 1,000 (1-3)-β-d-glucan and 516 galactomannan tests on serum samples. The results of this extensive testing are presented here. For a subset of 61 patients, respiratory specimens (bronchoalveolar lavage specimens, tracheal aspirates, and sputum samples) in addition to serum samples were submitted and subjected to galactomannan testing, Aspergillus-specific PCR, and microscopy and culture. The incidence of probable/proven and possible CAPA in this subset of patients was approximately 5% and 15%, respectively. Overall, our results highlight the challenges in biomarker-driven diagnosis of CAPA, especially when only limited clinical samples are available for testing, and the importance of a multimodal diagnostic approach involving regular and repeat testing of both serum and respiratory samples.
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15
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Martin-Souto L, Buldain I, Areitio M, Aparicio-Fernandez L, Antoran A, Bouchara JP, Martin-Gomez MT, Rementeria A, Hernando FL, Ramirez-Garcia A. ELISA Test for the Serological Detection of Scedosporium/ Lomentospora in Cystic Fibrosis Patients. Front Cell Infect Microbiol 2020; 10:602089. [PMID: 33324582 PMCID: PMC7726441 DOI: 10.3389/fcimb.2020.602089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/28/2020] [Indexed: 12/19/2022] Open
Abstract
The detection and diagnosis of the opportunistic fungi Scedosporium spp. and Lomentospora prolificans still relies mainly on low-sensitive culture-based methods. This fact is especially worrying in Cystic Fibrosis (CF) patients in whom these fungal species are frequently isolated and may increase the risk of suffering from an infection or other health problems. Therefore, with the purpose of developing a serologic detection method for Scedosporium/Lomentospora, four different Scedosporium boydii protein extracts (whole cell protein extract, secretome, total cell surface and conidial surface associated proteins) were studied by ELISA to select the most useful for IgG detection in sera from CF patients. The four extracts were able to discriminate the Scedosporium/Lomentospora-infected from Aspergillus-infected and non-infected patients. However, the whole cell protein extract was the one selected, as it was the one with the highest output in terms of protein concentration per ml of fungal culture used, and its discriminatory capacity was the best. The ELISA test developed was then assayed with 212 sera from CF patients and it showed to be able to detect Scedosporium spp. and Lomentospora prolificans with very high sensitivity and specificity, 86%–100% and 93%–99%, respectively, depending on the cut-off value chosen (four values were proposed A450nm= 0.5837, A450nm= 0.6042, A450nm= 0.6404, and A450nm= 0.7099). Thus, although more research is needed to reach a standardized method, this ELISA platform offers a rapid, low-cost and easy solution to detect these elusive fungi through minimally invasive sampling, allowing the monitoring of the humoral response to fungal presence.
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Affiliation(s)
- Leire Martin-Souto
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Idoia Buldain
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Maialen Areitio
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Leire Aparicio-Fernandez
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Aitziber Antoran
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jean-Philippe Bouchara
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), SFR ICAT 4208, Institut de Biologie en Santé-IRIS, Centre Hospitalier Universitaire, Angers, France
| | | | - Aitor Rementeria
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Fernando L Hernando
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Andoni Ramirez-Garcia
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Leioa, Spain
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16
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Keown K, Reid A, Moore JE, Taggart CC, Downey DG. Coinfection with Pseudomonas aeruginosa and Aspergillus fumigatus in cystic fibrosis. Eur Respir Rev 2020; 29:29/158/200011. [PMID: 33208485 DOI: 10.1183/16000617.0011-2020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/16/2020] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Cystic fibrosis (CF) lung disease is characterised by mucus stasis, chronic infection and inflammation, causing progressive structural lung disease and eventual respiratory failure. CF airways are inhabited by an ecologically diverse polymicrobial environment with vast potential for interspecies interactions, which may be a contributing factor to disease progression. Pseudomonas aeruginosa and Aspergillus fumigatus are the most common bacterial and fungal species present in CF airways respectively and coinfection results in a worse disease phenotype. METHODS In this review we examine existing expert knowledge of chronic co-infection with P. aeruginosa and A. fumigatus in CF patients. We summarise the mechanisms of interaction and evaluate the clinical and inflammatory impacts of this co-infection. RESULTS P. aeruginosa inhibits A. fumigatus through multiple mechanisms: phenazine secretion, iron competition, quorum sensing and through diffusible small molecules. A. fumigatus reciprocates inhibition through gliotoxin release and phenotypic adaptations enabling evasion of P. aeruginosa inhibition. Volatile organic compounds secreted by P. aeruginosa stimulate A. fumigatus growth, while A. fumigatus stimulates P. aeruginosa production of cytotoxic elastase. CONCLUSION A complex bi-directional relationship exists between P. aeruginosa and A. fumigatus, exhibiting both mutually antagonistic and cooperative facets. Cross-sectional data indicate a worsened disease state in coinfected patients; however, robust longitudinal studies are required to derive causality and to determine whether interspecies interaction contributes to disease progression.
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Affiliation(s)
- Karen Keown
- Royal Belfast Hospital for Sick Children, Belfast Health and Social Care Trust, Belfast, UK.,Wellcome Wolfson Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Alastair Reid
- Royal Belfast Hospital for Sick Children, Belfast Health and Social Care Trust, Belfast, UK
| | - John E Moore
- Northern Ireland Public Health Laboratory, Dept of Bacteriology, Belfast City Hospital, Belfast, UK
| | - Clifford C Taggart
- Wellcome Wolfson Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Damian G Downey
- Wellcome Wolfson Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
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17
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Borman AM, Fraser M, Schilling W, Jones G, Pearl R, Linton CJ, Johnson EM. Exophiala campbellii causing a subcutaneous palmar cyst in an otherwise healthy UK resident. Med Mycol Case Rep 2020; 29:43-45. [PMID: 32817812 PMCID: PMC7424171 DOI: 10.1016/j.mmcr.2020.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 11/19/2022] Open
Abstract
Exophiala is a ubiquitous genus encompassing more than forty species, a number of which have been associated with superficial or systemic infections in humans, and other hot- or cold-blooded animals. Here we report a human case of subcutaneous mycotic cyst caused by Exophiala campbellii. To our knowledge, this is only the third reported human infection caused by E. campbellii, all three of which involved subcutaneous nodules in patients who had resided in the United Kingdom.
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Affiliation(s)
- Andrew M. Borman
- UK National Mycology Reference Laboratory, Public Health England, Science Quarter, Southmead Hospital, Bristol, BS10 5NB, United Kingdom
- Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, EX4 4QD, United Kingdom
- Corresponding author. UK National Mycology Reference Laboratory, Public Health England, Science Quarter, Southmead Hospital, Bristol, BS10 5NB, United Kingdom.
| | - Mark Fraser
- UK National Mycology Reference Laboratory, Public Health England, Science Quarter, Southmead Hospital, Bristol, BS10 5NB, United Kingdom
| | - William Schilling
- Royal Sussex County Hospital, Brighton and Sussex University Hospitals NHS Trust, Eastern Road, Brighton, BN2 5BE, United Kingdom
| | - Gillian Jones
- Royal Sussex County Hospital, Brighton and Sussex University Hospitals NHS Trust, Eastern Road, Brighton, BN2 5BE, United Kingdom
| | - Robert Pearl
- Queen Victoria Hospital NHS Foundation Trust, Holtye Road, East Grinstead, West Sussex, RH19 3DZ, United Kingdom
| | - Christopher J. Linton
- UK National Mycology Reference Laboratory, Public Health England, Science Quarter, Southmead Hospital, Bristol, BS10 5NB, United Kingdom
| | - Elizabeth M. Johnson
- UK National Mycology Reference Laboratory, Public Health England, Science Quarter, Southmead Hospital, Bristol, BS10 5NB, United Kingdom
- Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, EX4 4QD, United Kingdom
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18
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Gitelman I. Saliva-controlled sputum culture (SSC) - A high value diagnostic tool for deep pulmonary infections. J Microbiol Methods 2020; 179:105986. [PMID: 32622844 DOI: 10.1016/j.mimet.2020.105986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/27/2020] [Accepted: 06/15/2020] [Indexed: 11/30/2022]
Abstract
A major obstacle to prompt diagnosis of fungal pulmonary infections is that deep sputum samples are scarce, yet are frequently rejected if they contain saliva. We show that including saliva controls unfailingly distinguishes oropharyngeal flora from pulmonary fungi, thus preserving valuable samples for analysis, expediting diagnoses and improving patient care.
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Affiliation(s)
- Inna Gitelman
- Department of Cell Biology and Physiology, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel.
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19
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Cuthbertson L, Felton I, James P, Cox MJ, Bilton D, Schelenz S, Loebinger MR, Cookson WOC, Simmonds NJ, Moffatt MF. The fungal airway microbiome in cystic fibrosis and non-cystic fibrosis bronchiectasis. J Cyst Fibros 2020; 20:295-302. [PMID: 32540174 PMCID: PMC8048771 DOI: 10.1016/j.jcf.2020.05.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 02/08/2023]
Abstract
The prevalence of fungal disease is increasing in CF and non-CF bronchiectasis. Effective management of fungal disease requires an understanding of the mycobiome. Culture methods alone are inadequate for the accurate diagnosis of fungal disease. Our study provides a framework to characterize fungal airway disease using NGS. NGS can improve detection and clinical management of fungal infections.
Background The prevalence of fungal disease in cystic fibrosis (CF) and non-CF bronchiectasis is increasing and the clinical spectrum is widening. Poor sensitivity and a lack of standard diagnostic criteria renders interpretation of culture results challenging. In order to develop effective management strategies, a more accurate and comprehensive understanding of the airways fungal microbiome is required. The study aimed to use DNA sequences from sputum to assess the load and diversity of fungi in adults with CF and non-CF bronchiectasis. Methods Next generation sequencing of the ITS2 region was used to examine fungal community composition (n = 176) by disease and underlying clinical subgroups including allergic bronchopulmonary aspergillosis, chronic necrotizing pulmonary aspergillosis, non-tuberculous mycobacteria, and fungal bronchitis. Patients with no known active fungal disease were included as disease controls. Results ITS2 sequencing greatly increased the detection of fungi from sputum. In patients with CF fungal diversity was lower, while burden was higher than those with non-CF bronchiectasis. The most common operational taxonomic unit (OTU) in patients with CF was Candida parapsilosis (20.4%), whereas in non-CF bronchiectasis sputum Candida albicans (21.8%) was most common. CF patients with overt fungal bronchitis were dominated by Aspergillus spp., Exophiala spp., Candida parapsilosis or Scedosporium spp. Conclusion This study provides a framework to more accurately characterize the extended spectrum of fungal airways diseases in adult suppurative lung diseases.
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Affiliation(s)
- Leah Cuthbertson
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK; National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
| | - Imogen Felton
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK; National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
| | - Phillip James
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK; National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
| | - Michael J Cox
- National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
| | - Diana Bilton
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK; National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
| | - Silke Schelenz
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK
| | - Michael R Loebinger
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK; National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
| | - William O C Cookson
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK; National Heart and Lung Institute, Imperial College, London SW3 6LY, UK.
| | - Nicholas J Simmonds
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK; National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
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20
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Evaluation of a New Culture Protocol for Enhancing Fungal Detection Rates in Respiratory Samples of Cystic Fibrosis Patients. J Fungi (Basel) 2020; 6:jof6020082. [PMID: 32526938 PMCID: PMC7345163 DOI: 10.3390/jof6020082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/07/2020] [Accepted: 06/08/2020] [Indexed: 01/11/2023] Open
Abstract
Cystic fibrosis (CF) can be complicated by fungal infection of the respiratory tract. Fungal detection rates in CF sputa are highly dependent on the culture protocol and incubation conditions and thus may lead to an underestimation of the true prevalence of fungal colonization. We conducted a prospective study to evaluate the additional value of mucolytic pre-treatment, increased inoculum (100 µL), additional fungal culture media (Sabouraud agar; SAB, Medium B+, Scedosporium selective agar; SceSel+ and Dichloran-Glycerol agar; DG18) and longer incubation time (3 weeks) compared with our current protocol. Using the new protocol, we prospectively analyzed 216 expectorated sputum samples from adult and pediatric CF patients (n = 77) and compared the culture yield to a three year retrospective cohort that used direct 10 µL loop inoculation on SAB with 5 days incubation (867 sputum samples/103 patients). Detection rates for molds increased from 42% to 76% (p < 0.0001). Twenty-six percent of cultures were polymicrobial in the prospective cohort as opposed to 4.7% in the retrospective cohort (p < 0.0001). Colonization rate with A. fumigatus increased from 36% to 57%. SAB and DG18 showed the highest detection rates for all molds (SAB 58.6%; DG18 56.9%) and DG18 had the best performance for molds other than A. fumigatus. The larger sample volume and longer incubation also contributed to the increased recovery of molds. The introduction of a modified fungal culture protocol leads to a major increase in detection rate and the diversity of molds, which influences fungal epidemiology and may have implications for treatment decisions.
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A 16-year retrospective study on fungal prevalence and diversity in patients with cystic fibrosis: Candida dubliniensis was associated with a decline in lung function. Int J Infect Dis 2020; 96:663-670. [PMID: 32450290 DOI: 10.1016/j.ijid.2020.05.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 01/13/2023] Open
Abstract
OBJECTIVES To study the prevalence of fungal species in cystic fibrosis (CF) patients over a 16 years period. To examine the impact of Candida albicans (C. albicans), Candida dubliniensis (C. dubliniensis) and Aspergillus fumigatus (A. fumigatus) on lung function. METHODS Observational single-center cohort study (2000-2015) including 133 CF patients (ages 6-66 years). Linear mixed models with autoregressive covariance matrix were used. RESULTS The most common fungus was C. albicans (prevalence 62%) followed by A. fumigatus (22%) and C. dubliniensis (11%). In the initial year of detection, there was no impact of C. albicans, C. dubliniensis or A. fumigatus on lung function. However, one and two years after detection of C. dubliniensis a reduction in percent predicted forced expiratory volume in the first second (ppFEV1) was observed of 3.8% (p = 0.022) and 4.1% (p = 0.017), respectively, compared with CF patients without these findings. Furthermore, patients with positive cultures for any of these fungal species for three consecutive years exhibited a decline in lung function: C. dubliniensis, 7.6% reduction in ppFEV1 (p = 0.001); A. fumigatus, 4.9% (p = 0.007); C. albicans, 2.6% (p = 0.014). The results were adjusted for age, CFTR genotype, chronic and intermittent P. aeruginosa colonization, and numbers of intravenous antibiotic treatments per year. Persistence of C. dubliniensis for three consecutive years was positively correlated to age and erythrocyte sedimentation rate (ESR) (both p = 0.001). CONCLUSIONS Cystic fibrosis patients who were cultured positive for C. dubliniensis, C. albicans or A. fumigatus in sputum exhibited a decline in ppFEV1 over time. The effect was most pronounced for C. dubliniensis.
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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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23
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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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Rammaert B, Puyade M, Cornely OA, Seidel D, Grossi P, Husain S, Picard C, Lass-Flörl C, Manuel O, Le Pavec J, Lortholary O. Perspectives on Scedosporium species and Lomentospora prolificans in lung transplantation: Results of an international practice survey from ESCMID fungal infection study group and study group for infections in compromised hosts, and European Confederation of Medical Mycology. Transpl Infect Dis 2019; 21:e13141. [PMID: 31283872 DOI: 10.1111/tid.13141] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Scedosporium species and Lomentospora prolificans (S/L) are the second most common causes of invasive mold infections following Aspergillus in lung transplant recipients. METHODS We assessed the current practices on management of S/L colonization/infection of the lower respiratory tract before and after lung transplantation in a large number of lung transplant centers through an international practice survey from October 2016 to March 2017. RESULTS A total of 51 respondents from 45 lung transplant centers (17 countries, 4 continents) answered the survey (response rate 58%). S/L colonization was estimated to be detected in candidates by 48% of centers. Only 18% of the centers used a specific medium to detect S/L colonization. Scedosporium spp. colonization was a contraindication to transplantation in 10% of centers whereas L prolificans was a contraindication in 31%; 22% of centers declared having had 1-5 recipients infected with S/L in the past 5 years. CONCLUSIONS This survey gives an overview of the current practices regarding S/L colonization and infection in lung transplant centers worldwide and underscores the need of S/L culture procedure standardization before implementing prospective studies.
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Affiliation(s)
- Blandine Rammaert
- Faculté de médecine et pharmacie, Univ Poitiers, Poitiers, France.,Service de maladies infectieuses et tropicales, CHU Poitiers, Poitiers, France.,INSERM U1070, Poitiers, France
| | - Mathieu Puyade
- Service de médecine interne, CHU Poitiers, Poitiers, France
| | - Oliver A Cornely
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Department I of Internal Medicine, Clinical Trials Centre Cologne (ZKS), German Centre for Infection Research (DZIF), Partner site Bonn-Cologne, University of Cologne, Cologne, Germany
| | - Danila Seidel
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Department I of Internal Medicine, Clinical Trials Centre Cologne (ZKS), German Centre for Infection Research (DZIF), Partner site Bonn-Cologne, University of Cologne, Cologne, Germany
| | - Paolo Grossi
- Department of Medicine & Surgery, Infectious and Tropical Diseases Unit, University of Insubria, Varese, Italy
| | - Shahid Husain
- Multi-Organ Transplant Program, Division of Infectious Diseases, University Health Network, University of Toronto, Toronto, Canada
| | | | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Oriol Manuel
- Transplantation Center and Infectious Diseases Service, University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Jérôme Le Pavec
- Université Paris-Sud, Faculté de Médecine, Université Paris Saclay, Le Kremlin Bicêtre, France.,Service de Chirurgie Thoracique, Vasculaire et Transplantation Cardio-pulmonaire, Hôpital Marie-Lannelongue, Le Plessis-Robinson, France.,UMR-S 999, Universite Paris-Sud, INSERM, Hôpital Marie Lannelongue, Le Plessis-Robinson, France
| | - Olivier Lortholary
- Université de Paris, APHP, Service des Maladies Infectieuses et Tropicales, Hôpital Necker-Enfants Malades, Centre d'Infectiologie Necker-Pasteur, Institut Imagine, Paris, France.,Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, CNRS UMR 2000, Paris, France
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25
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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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26
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Staerck C, Tabiasco J, Godon C, Delneste Y, Bouchara JP, Fleury MJJ. Transcriptional profiling of Scedosporium apiospermum enzymatic antioxidant gene battery unravels the involvement of thioredoxin reductases against chemical and phagocytic cells oxidative stress. Med Mycol 2019; 57:363-373. [PMID: 29889264 DOI: 10.1093/mmy/myy033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/22/2018] [Accepted: 05/01/2018] [Indexed: 12/15/2022] Open
Abstract
Scedosporium species rank the second, after Aspergillus fumigatus, among the filamentous fungi colonizing the airways of patients with cystic fibrosis (CF). Development of microorganisms in the respiratory tract depends on their capacity to evade killing by the host immune system, particularly through the oxidative response of macrophages and neutrophils, with the release of reactive oxygen species (ROS) and reactive nitrogen species (RNS). This is particularly true in the airways of CF patients which display an exacerbated inflammatory reaction. To protect themselves, pathogens have developed various enzymatic antioxidant systems implicated in ROS degradation, including superoxide dismutases, catalases, cytochrome C peroxidases, chloroperoxidases and enzymes of the glutathione and thioredoxin systems, or in RNS degradation, that is, flavohemoglobins, nitrate reductases, and nitrite reductases. Here we investigated the transcriptional regulation of the enzymatic antioxidant gene battery in 24-h-old hyphae of Scedosporium apiospermum in response to oxidative stress induced chemically or by exposure to activated phagocytic cells. We showed that 21 out of the 33 genes potentially implicated in the oxidative or nitrosative stress response were overexpressed upon exposure of the fungus to various chemical oxidants, while they were only 13 in co-cultures with macrophages or neutrophils. Among them, genes encoding two thioredoxin reductases and to a lesser extent, a peroxiredoxin and one catalase were found to be overexpressed after chemical oxidative stress as well as in co-cultures. These results suggest that thioredoxin reductases, which are known to be virulence factors in other pathogenic fungi, play a key role in pathogenesis of scedosporiosis, and may be new drug targets.
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Affiliation(s)
- Cindy Staerck
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Julie Tabiasco
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| | - Charlotte Godon
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Yves Delneste
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France.,Laboratoire d'Immunologie et Allergologie, Centre Hospitalier Universitaire d'Angers, France
| | - Jean-Philippe Bouchara
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France.,Laboratoire de Parasitologie-Mycologie, Centre Hospitalier Universitaire, Angers, France
| | - Maxime J J Fleury
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
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27
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Hong G, Lechtzin N. Cystic fibrosis: We see fungus among us, but should we care? J Cyst Fibros 2019; 18:163-164. [DOI: 10.1016/j.jcf.2019.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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28
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Mello TP, Bittencourt VCB, Liporagi-Lopes LC, Aor AC, Branquinha MH, Santos AL. Insights into the social life and obscure side of Scedosporium/Lomentospora species: ubiquitous, emerging and multidrug-resistant opportunistic pathogens. FUNGAL BIOL REV 2019. [DOI: 10.1016/j.fbr.2018.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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29
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Schwarz C, Vandeputte P, Rougeron A, Giraud S, Dugé de Bernonville T, Duvaux L, Gastebois A, Alastruey-Izquierdo A, Martín-Gomez MT, Mazuelos EM, Sole A, Cano J, Pemán J, Quindos G, Botterel F, Bougnoux ME, Chen S, Delhaès L, Favennec L, Ranque S, Sedlacek L, Steinmann J, Vazquez J, Williams C, Meyer W, Le Gal S, Nevez G, Fleury M, Papon N, Symoens F, Bouchara JP. Developing collaborative works for faster progress on fungal respiratory infections in cystic fibrosis. Med Mycol 2018. [PMID: 29538733 DOI: 10.1093/mmy/myx106] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cystic fibrosis (CF) is the major genetic inherited disease in Caucasian populations. The respiratory tract of CF patients displays a sticky viscous mucus, which allows for the entrapment of airborne bacteria and fungal spores and provides a suitable environment for growth of microorganisms, including numerous yeast and filamentous fungal species. As a consequence, respiratory infections are the major cause of morbidity and mortality in this clinical context. Although bacteria remain the most common agents of these infections, fungal respiratory infections have emerged as an important cause of disease. Therefore, the International Society for Human and Animal Mycology (ISHAM) has launched a working group on Fungal respiratory infections in Cystic Fibrosis (Fri-CF) in October 2006, which was subsequently approved by the European Confederation of Medical Mycology (ECMM). Meetings of this working group, comprising both clinicians and mycologists involved in the follow-up of CF patients, as well as basic scientists interested in the fungal species involved, provided the opportunity to initiate collaborative works aimed to improve our knowledge on these infections to assist clinicians in patient management. The current review highlights the outcomes of some of these collaborative works in clinical surveillance, pathogenesis and treatment, giving special emphasis to standardization of culture procedures, improvement of species identification methods including the development of nonculture-based diagnostic methods, microbiome studies and identification of new biological markers, and the description of genotyping studies aiming to differentiate transient carriage and chronic colonization of the airways. The review also reports on the breakthrough in sequencing the genomes of the main Scedosporium species as basis for a better understanding of the pathogenic mechanisms of these fungi, and discusses treatment options of infections caused by multidrug resistant microorganisms, such as Scedosporium and Lomentospora species and members of the Rasamsonia argillacea species complex.
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Affiliation(s)
- Carsten Schwarz
- Department of Pediatric Pneumology and Immunology, Cystic Fibrosis Center Berlin/Charité -Universitätsmedizin Berlin, Berlin, Germany
| | - Patrick Vandeputte
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France.,Laboratoire de Parasitologie-Mycologie, CHU, Angers, France
| | - Amandine Rougeron
- Université de Bordeaux, Microbiologie Fondamentale et Pathogénicité UMR 5234, Bordeaux, France; CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France; Laboratoire de Parasitologie-Mycologie, CHU, Bordeaux, France
| | - Sandrine Giraud
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Thomas Dugé de Bernonville
- Biomolécules et Biotechnologies Végétales (EA 2106), Département de Biologie et Physiologie Végétales, UFR Sciences et Techniques, Université François Rabelais, Tours
| | - Ludovic Duvaux
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France.,Institut de Recherche en Horticulture et Semences (IRHS), UMR INRA 1345, Beaucouzé, France
| | - Amandine Gastebois
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Ana Alastruey-Izquierdo
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Maria Teresa Martín-Gomez
- Respiratory Bacteriology Unit & Clinical Mycology Unit, Department of Microbiology, Vall D'Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Amparo Sole
- Unidad de Trasplante Pulmonar y Fibrosis Quística, Hospital Universitari la Fe, Valencia, Spain
| | - Josep Cano
- Mycology Unit, Medical School/Oenology School, Universitat Rovira i Virgili, Reus, Spain
| | - Javier Pemán
- Unidad de Micología, Servicio de Microbiología, Universitari la Fe, Valencia, Spain
| | - Guillermo Quindos
- Laboratorio de Micología Médica, Departamento de Inmunología, Microbiología y Parasitología, Facultad de Medicina y Enfermería, Universidad del País Vasco, Bilbao, Spain
| | - Françoise Botterel
- Laboratoire de Parasitologie-Mycologie, CHU Henri Mondor, Créteil, France
| | | | - Sharon Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, Westmead Hospital, Westmead, New South Wales, Australia
| | - Laurence Delhaès
- Center for Cardiothoracic Research of Bordeaux, Inserm U1045, Bordeaux, France
| | - Loïc Favennec
- Laboratoire de Parasitologie-Mycologie, EA 3800, CHU Charles Nicolle and Université de Rouen, Rouen, France
| | - Stéphane Ranque
- Laboratoire de Parasitologie-Mycologie, AP-HM Timone, Marseille, France
| | - Ludwig Sedlacek
- Institute of Medical Microbiology and Hospital Epidemiology, Medical School Hannover, Hannover, Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jose Vazquez
- Division of Infectious Diseases, Department of Medicine, Georgia Regents University, Augusta, GA, USA
| | - Craig Williams
- University of the West of Scotland, Institute of Healthcare Associated Infection, University Hospital Crosshouse, Kilmarnock, United Kingdom
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Solène Le Gal
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Brest, France.,Laboratoire de Parasitologie-Mycologie, CHU, Brest, France
| | - Gilles Nevez
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Brest, France.,Laboratoire de Parasitologie-Mycologie, CHU, Brest, France
| | - Maxime Fleury
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Nicolas Papon
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Françoise Symoens
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Jean-Philippe Bouchara
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France.,Laboratoire de Parasitologie-Mycologie, CHU, Angers, France
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30
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Chen M, Kondori N, Deng S, Gerrits van den Ende AHG, Lackner M, Liao W, de Hoog GS. Direct detection of Exophiala and Scedosporium species in sputa of patients with cystic fibrosis. Med Mycol 2018; 56:695-702. [PMID: 29228273 DOI: 10.1093/mmy/myx108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/05/2017] [Indexed: 01/09/2023] Open
Abstract
Detection of species of Exophiala and Scedosporium in the respiratory tracts of cystic fibrosis (CF) patients remains controversial because of highly variable results. The results of our study suggested a significantly higher prevalence and more complex colonization than previously estimated. Approximately 17% (27/162) of clinical sputum samples were found to be positive for Exophiala dermatitidis and 30% (49/162) were positive for Scedosporium apiospermum / S. boydii species complex determined by reverse line blot (RLB) hybridization. In contrast, only 14.2% (23/162) and 1.2% (2/162) of clinical sputa were positive for E. dermatitidis and S. apiospermum / S. boydii species complex when tested by culture, respectively. Molecular detection methods, such as loop-mediated isothermal amplification (LAMP) or reverse line blot (RLB) hybridization, have the potential to become powerful alternatives to selective culture, providing a more realistic understanding on the prevalence of E. dermatitidis and S. apiospermum / S. boydii species complex in the respiratory tract of CF patients.
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Affiliation(s)
- Min Chen
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Nahid Kondori
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Shuwen Deng
- Department of Medical Microbiology, People's Hospital of Suzhou National New & Hi-Tech Industrial Development Zone, Jiangsu, China
| | | | - M Lackner
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - G S de Hoog
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.,Peking University First Hospital, Research Center for Medical Mycology, Beijing, China; Department of Basic Biology, University of Paraná, Curitiba, Brazil
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31
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Tracy MC, Moss RB. The myriad challenges of respiratory fungal infection in cystic fibrosis. Pediatr Pulmonol 2018; 53:S75-S85. [PMID: 29992775 DOI: 10.1002/ppul.24126] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/21/2018] [Indexed: 12/27/2022]
Abstract
Fungal infection in cystic fibrosis (CF) is a recognized challenge, with many areas requiring further investigation. Consensus definitions exist for allergic bronchopulmonary aspergillus in CF, but the full scope of clinically relevant non-allergic fungal disease in CF-asymptomatic colonization, transient or chronic infection localized to endobronchial mucus plugs or airway tissue, and invasive disease-is yet to be clearly defined. Recent advances in mycological culture and non-culture identification have expanded the list of both potential pathogens and community commensals in the lower respiratory tract. Here we aim to outline the current understanding of fungal presence in the CF respiratory tract, risk factors for acquiring fungi, host-pathogen interactions that influence the role of fungi from bystander to pathogen, advances in the diagnostic approaches to isolating and identifying fungi in CF respiratory samples, challenges of classifying clinical phenotypes of CF patients with fungi, and current treatment approaches. Development and validation of biomarkers characteristic of different fungal clinical phenotypes, and controlled trials of antifungal agents in well-characterized target populations, remain central challenges to surmount and goals to be achieved.
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Affiliation(s)
- Michael C Tracy
- Center for Excellence in Pulmonary Biology, Division of Pulmonary, Asthma and Sleep Medicine, Department of Pediatrics, Stanford University Medical School, Palo Alto, California
| | - Richard B Moss
- Center for Excellence in Pulmonary Biology, Division of Pulmonary, Asthma and Sleep Medicine, Department of Pediatrics, Stanford University Medical School, Palo Alto, California
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32
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Delhaes L, Touati K, Faure-Cognet O, Cornet M, Botterel F, Dannaoui E, Morio F, Le Pape P, Grenouillet F, Favennec L, Le Gal S, Nevez G, Duhamel A, Borman A, Saegeman V, Lagrou K, Gomez E, Carro ML, Canton R, Campana S, Buzina W, Chen S, Meyer W, Roilides E, Simitsopoulou M, Manso E, Cariani L, Biffi A, Fiscarelli E, Ricciotti G, Pihet M, Bouchara JP. Prevalence, geographic risk factor, and development of a standardized protocol for fungal isolation in cystic fibrosis: Results from the international prospective study "MFIP". J Cyst Fibros 2018; 18:212-220. [PMID: 30348610 DOI: 10.1016/j.jcf.2018.10.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 08/07/2018] [Accepted: 10/01/2018] [Indexed: 01/18/2023]
Affiliation(s)
| | - Kada Touati
- University & CHU of Lille, F-59000 Lille, France
| | - Odile Faure-Cognet
- Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France
| | - Muriel Cornet
- Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France
| | | | | | | | | | | | | | | | | | | | | | - Veroniek Saegeman
- University of Leuven, National Reference center for Mycosis, Belgium
| | - Katrien Lagrou
- University of Leuven, National Reference center for Mycosis, Belgium
| | - Elia Gomez
- Hosital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Madrid, Spain
| | - Maiz-Luis Carro
- Hosital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Madrid, Spain
| | - Rafael Canton
- Hosital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Madrid, Spain
| | | | | | - Sharon Chen
- Molecular Mycology Research Laboratory, Marie Bashir Institute for Biosecurity and Emerging Infections, University of Sydney, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Marie Bashir Institute for Biosecurity and Emerging Infections, University of Sydney, Australia
| | | | | | | | - Lisa Cariani
- Microbiology and Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Milano, Italy
| | - Arianna Biffi
- Microbiology and Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Milano, Italy
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33
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Abdolrasouli A, Bercusson AC, Rhodes JL, Hagen F, Buil JB, Tang AYY, de Boer LL, Shah A, Milburn AJ, Elborn JS, Jones AL, Meis JF, Fisher MC, Schelenz S, Simmonds NJ, Armstrong-James D. Airway persistence by the emerging multi-azole-resistant Rasamsonia argillacea complex in cystic fibrosis. Mycoses 2018; 61:665-673. [PMID: 29702751 DOI: 10.1111/myc.12789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 11/26/2022]
Abstract
Infections caused by Rasamsonia argillacea complex have been reported in various clinical settings. Cystic fibrosis (CF) is one of the main underlying conditions. An observational cohort study of CF patients with Rasamsonia in respiratory samples was conducted. Eight isolates from 6 patients were identified as R. argillacea complex and tested for antifungal susceptibility. All isolates had high MICs to voriconazole and posaconazole and low MECs to echinocandins. Four patients experienced lung function decline in the year preceding first Rasamsonia isolation. This continued in the year following first isolation in 3 out of 4 cases. Antifungal therapy was initiated in 2 patients, to which only one exhibited a clinical response. Three out of 6 patients died within 3 years of isolating Rasamsonia. Genotyping suggests that similar genotypes of Rasamsonia can persist in CF airways. Consistent with other fungi in CF, the clinical impact of airway colonisation by Rasamsonia is variable. In certain patients, Rasamsonia may be able to drive clinical decline. In others, though a clear impact on lung function may be difficult to determine, the appearance of Rasamsonia acts as a marker of disease severity. In others it does not appear to have an obvious clinical impact on disease progression.
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Affiliation(s)
- Alireza Abdolrasouli
- Fungal Pathogens Laboratory, National Heart and Lung Institute, Imperial College London, London, UK
| | - Amelia C Bercusson
- Fungal Pathogens Laboratory, National Heart and Lung Institute, Imperial College London, London, UK
| | - Johanna L Rhodes
- Department of Infectious Diseases Epidemiology, Imperial College School of Public Health, London, UK
| | - Ferry Hagen
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital (CWZ), Nijmegen, The Netherlands.,Centre of Expertise in Mycology Radboud UMC/CWZ and ECMM Excellence Center for Medical Mycology, Nijmegen, The Netherlands.,Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Jochem B Buil
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital (CWZ), Nijmegen, The Netherlands.,Centre of Expertise in Mycology Radboud UMC/CWZ and ECMM Excellence Center for Medical Mycology, Nijmegen, The Netherlands
| | - Alison Y Y Tang
- Fungal Pathogens Laboratory, National Heart and Lung Institute, Imperial College London, London, UK
| | - Leonard L de Boer
- Fungal Pathogens Laboratory, National Heart and Lung Institute, Imperial College London, London, UK
| | - Anand Shah
- Adult Cystic Fibrosis Centre, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Andrew J Milburn
- Adult Cystic Fibrosis Centre, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - J Stuart Elborn
- Adult Cystic Fibrosis Centre, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Andrew L Jones
- Adult Cystic Fibrosis Centre, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital (CWZ), Nijmegen, The Netherlands.,Centre of Expertise in Mycology Radboud UMC/CWZ and ECMM Excellence Center for Medical Mycology, Nijmegen, The Netherlands
| | - Matthew C Fisher
- Department of Infectious Diseases Epidemiology, Imperial College School of Public Health, London, UK
| | - Silke Schelenz
- Department of Microbiology, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Nicholas J Simmonds
- Adult Cystic Fibrosis Centre, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Darius Armstrong-James
- Fungal Pathogens Laboratory, National Heart and Lung Institute, Imperial College London, London, UK.,Department of Microbiology, Royal Brompton and Harefield NHS Foundation Trust, London, UK
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Guegan H, Chevrier S, Belleguic C, Deneuville E, Robert-Gangneux F, Gangneux JP. Performance of Molecular Approaches for Aspergillus Detection and Azole Resistance Surveillance in Cystic Fibrosis. Front Microbiol 2018; 9:531. [PMID: 29636731 PMCID: PMC5880881 DOI: 10.3389/fmicb.2018.00531] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/08/2018] [Indexed: 11/13/2022] Open
Abstract
Aspergillus fumigatus triazole resistance is an emerging concern for treating chronically infected/colonized patients. This study sought to evaluate the performance of PCR assays to detect Aspergillus fungi together with azole resistance in sputum samples from cystic fibrosis (CF) patients. In total, 119 sputum samples from 87 CF patients were prospectively processed for Aspergillus detection by means of mycological culture and four qPCR assays, 2 in-house methods and two commercial multiplex real-time PCR assays simultaneously detecting Aspergillus and the most relevant cyp51A gene mutations (MycoGENIE® and AsperGenius®). Azole susceptibility of A. fumigatus isolates was assessed using Etest® method and cyp51A gene mutation were characterized by sequencing. The overall rate of Aspergillus detection with the four qPCR assays ranged from 47.9 to 57.1%, contrasting with 42/119 (35.3%) positive cultures with A. fumigatus. The high sensitivity of PCR on sputum could then contribute to more effective grading of Aspergillus disease in CF patients. Five out of 41 isolated strains (12.2%) exhibited azole-resistant MIC patterns, three of which harbored cyp51A mutations and only 1/3 with the sequence TR34/L98H. Combined with culture, PCR assay achieved high sensitivity Aspergillus screening in CF samples. However, cyp51A targeting was only moderately effective for azole resistance monitoring, while Aspergillus resistance remains of great concern.
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Affiliation(s)
- Hélène Guegan
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Sylviane Chevrier
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Chantal Belleguic
- Centre de Ressources et de Compétences de la Mucoviscidose Adulte, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Eric Deneuville
- Centre de Ressources et de Compétences de la Mucoviscidose Pédiatrique, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Florence Robert-Gangneux
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalier Universitaire de Rennes, Rennes, France.,Université de Rennes 1, INSERM, Institut de Recherche en Santé, Environnement et Travail - UMR_S 1085, Rennes, France
| | - Jean-Pierre Gangneux
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalier Universitaire de Rennes, Rennes, France.,Université de Rennes 1, INSERM, Institut de Recherche en Santé, Environnement et Travail - UMR_S 1085, Rennes, France
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35
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Luplertlop N. Pseudallescheria/Scedosporium complex species: From saprobic to pathogenic fungus. J Mycol Med 2018; 28:249-256. [PMID: 29567285 DOI: 10.1016/j.mycmed.2018.02.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 12/16/2022]
Abstract
Scedosporiosis is an emerging fungal infection caused by Pseudallescheria/Scedosporium complex species (PSC). This pathogen has been drawn significant interest in recent years due to its worldwide prevalence, the seriousness of its infection, associated with high mortality in both immunocompromised and immunocompetent hosts and its cryptic ecology, distribution and epidemiology across the globe. These species complexes can be found in environments impacted by human. The purpose of this review is to describe the characteristics, mode of transmission, ecology, prevalence, global epidemiology of this fungal group in order to increase the awareness of among clinicians and microbiologists, especially in regions with high endemic, as well as to promote further research on all of its aspects.
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Affiliation(s)
- N Luplertlop
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 10400 Bangkok, Thailand.
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36
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Laboratory Diagnosis and Characterization of Fungal Disease in Patients with Cystic Fibrosis (CF): A Survey of Current UK Practice in a Cohort of Clinical Microbiology Laboratories. Mycopathologia 2018; 183:723-729. [PMID: 29500636 DOI: 10.1007/s11046-018-0251-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 02/13/2018] [Indexed: 10/17/2022]
Abstract
There is much uncertainty as to how fungal disease is diagnosed and characterized in patients with cystic fibrosis (CF). A 19-question anonymous electronic questionnaire was developed and distributed to ascertain current practice in clinical microbiology laboratories providing a fungal laboratory service to CF centres in the UK. Analyses of responses identified the following: (1) current UK laboratory practice, in general, follows the current guidelines, but the scope and diversity of what is currently being delivered by laboratories far exceeds what is detailed in the guidelines; (2) there is a lack of standardization of fungal tests amongst laboratories, outside of the current guidelines; (3) both the UK CF Trust Laboratory Standards for Processing Microbiological Samples from People with Cystic Fibrosis and the US Cumulative Techniques and Procedures in Clinical Microbiology (Cumitech) Guidelines 43 Cystic Fibrosis Microbiology need to be updated to reflect both new methodological innovations, as well as better knowledge of fungal disease pathophysiology in CF; (4) there is a need for clinical medicine to decide upon a stratification strategy for the provision of new fungal assays that will add value to the physician in the optimal management of CF patients; (5) there is also a need to rationale what assays should be performed at local laboratory level and those which are best served at National Mycology Reference Laboratory level; and (6) further research is required in developing laboratory assays, which will help ascertain the clinical importance of 'old' fungal pathogens, as well as 'emerging' fungal pathogens.
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Abstract
In the expanding population of immunocompromised patients and those treated in intensive care units, rare fungal infectious agents have emerged as important pathogens, causing invasive infections associated with high morbidity and mortality. These infections may present either as de novo or as breakthrough invasive infections in high-risk patients with hematologic malignancies receiving prophylactic or empirical antifungal therapy or in patients with central venous catheters. Diagnosis and treatment are challenging. Physicians should have a high index of suspicion because early diagnosis is of paramount importance. Conventional diagnostic methods such as cultures and histopathology are still essential, but rapid and more specific molecular techniques for both detection and identification of the infecting pathogens are being developed and hopefully will lead to early targeted treatment. The management of invasive fungal infections is multimodal. Reversal of risk factors, if feasible, should be attempted. Surgical debridement is recommended in localized mold infections. The efficacy of various antifungal drugs is not uniform. Amphotericin B is active against most yeasts, except Trichosporon, as well as against Mucorales, Fusarium, and some species of Paecilomyces and dimorphic fungi. The use of voriconazole is suggested for the treatment of trichosporonosis and scedosporiosis. Combination treatment, though recommended as salvage therapy in some infections, is controversial in most cases. Despite the use of available antifungals, mortality remains high. The optimization of molecular-based techniques, with expansion of reference libraries and the possibility for direct detection of resistance mechanisms, is awaited with great interest in the near future. Further research is necessary, however, in order to find the best ways to confront and destroy these lurking enemies.
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Affiliation(s)
- Anna Skiada
- 1st Department of Medicine, Laiko Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Maria Drogari-Apiranthitou
- Infectious Diseases Research Laboratory, 4th Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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Mina S, Staerck C, Marot A, Godon C, Calenda A, Bouchara JP, Fleury MJJ. Scedosporium boydii CatA1 and SODC recombinant proteins, new tools for serodiagnosis of Scedosporium infection of patients with cystic fibrosis. Diagn Microbiol Infect Dis 2017; 89:282-287. [PMID: 28974395 DOI: 10.1016/j.diagmicrobio.2017.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 01/24/2023]
Abstract
Scedosporium species rank the second among the filamentous fungi colonizing the airways of patients with cystic fibrosis (CF), after Aspergillus fumigatus. In CF, these fungi may cause various respiratory infections similar to those caused by A. fumigatus, including bronchitis and allergic broncho-pulmonary mycoses. Diagnosis of these infections relies on the detection of serum antibodies using crude antigenic extracts. However, many components of these extracts are common to Scedosporium and Aspergillus species, leading to cross-reactions. Here, 5 recombinant proteins from S. apiospermum or S. boydii were produced, and their value in serodiagnosis of Scedosporium infections was investigated by enzyme-linked immunosorbent assay. Two of them, corresponding to the Scedosporium catalase A1 or cytosolic Cu,Zn-superoxyde dismutase, allowed the detection of Scedosporium infection, and the differentiation with an Aspergillus infection. These recombinant proteins therefore may serve as a basis for the development of a standardized serological test.
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Affiliation(s)
- Sara Mina
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France; Beirut Arab University, Faculty of Health Sciences, Beirut, Lebanon
| | - Cindy Staerck
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Agnès Marot
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Charlotte Godon
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Alphonse Calenda
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Jean-Philippe Bouchara
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France; Laboratoire de Parasitologie-Mycologie, Centre Hospitalier Universitaire, Angers, France
| | - Maxime J J Fleury
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France.
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39
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Fungal Pathogens in CF Airways: Leave or Treat? Mycopathologia 2017; 183:119-137. [PMID: 28770417 DOI: 10.1007/s11046-017-0184-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/22/2017] [Indexed: 02/07/2023]
Abstract
Chronic airway infection plays an essential role in the progress of cystic fibrosis (CF) lung disease. In the past decades, mainly bacterial pathogens, such as Pseudomonas aeruginosa, have been the focus of researchers and clinicians. However, fungi are frequently detected in CF airways and there is an increasing body of evidence that fungal pathogens might play a role in CF lung disease. Several studies have shown an association of fungi, particularly Aspergillus fumigatus and Candida albicans, with the course of lung disease in CF patients. Mechanistically, in vitro and in vivo studies suggest that an impaired immune response to fungal pathogens in CF airways renders them more susceptible to fungi. However, it remains elusive whether fungi are actively involved in CF lung disease pathologies or whether they rather reflect a dysregulated airway colonization and act as microbial bystanders. A key issue for dissecting the role of fungi in CF lung disease is the distinction of dynamic fungal-host interaction entities, namely colonization, sensitization or infection. This review summarizes key findings on pathophysiological mechanisms and the clinical impact of fungi in CF lung disease.
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40
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Botterel F, Angebault C, Cabaret O, Stressmann FA, Costa JM, Wallet F, Wallaert B, Bruce K, Delhaes L. Fungal and Bacterial Diversity of Airway Microbiota in Adults with Cystic Fibrosis: Concordance Between Conventional Methods and Ultra-Deep Sequencing, and Their Practical use in the Clinical Laboratory. Mycopathologia 2017; 183:171-183. [DOI: 10.1007/s11046-017-0185-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/22/2017] [Indexed: 11/29/2022]
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41
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Toward the Standardization of Mycological Examination of Sputum Samples in Cystic Fibrosis: Results from a French Multicenter Prospective Study. Mycopathologia 2017; 183:101-117. [DOI: 10.1007/s11046-017-0173-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 06/27/2017] [Indexed: 02/03/2023]
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42
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AbdulWahab A, Salah H, Chandra P, Taj-Aldeen SJ. Persistence of Candida dubliniensis and lung function in patients with cystic fibrosis. BMC Res Notes 2017; 10:326. [PMID: 28747217 PMCID: PMC5530559 DOI: 10.1186/s13104-017-2656-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/21/2017] [Indexed: 01/03/2023] Open
Abstract
Objectives Candida dubliniensis is an emerging yeast and demonstrated a high adherence property to cystic fibrosis respiratory tract. Therefore, it is important to determine the persistence of C. dubliniensis and to assess the possible relationship to the body mass index (BMI) and forced expiratory volume in 1st second (FEV1). Results Candida isolates were identified by MALDI-TOF MS to species level from 40/52 (76.9%) cystic fibrosis patients. C. dubliniensis was the most common organism isolated from 50/77 (65%) lower respiratory specimens of 29 patients. Patients with persistent C. dubliniensis isolates have higher mean BMI in comparison to intermittent C. dubliniensis group. However, this difference did not reach statistical significance (P = 0.539). In contrast, patients with persistent C. dubliniensis isolates have significantly lower FEV1% mean in comparison to intermittent C. dubliniensis group particularly at initial two visits (P < 0.05); however, at subsequent visit the difference observed was not statistically significant (P = 0.456). The persistence of C. dubliniensis is more frequent in adults having more advanced disease, co-infections with chronic P. aeruginosa, cystic fibrosis related diabetes, long-term nebulized tobramycin and oral Zithromax therapy than patients with intermittent C. dubliniensis. Patients with persistent C. dubliniensis have lower FEV1 percentage and higher BMI than the intermittent C. dubliniensis.
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Affiliation(s)
- Atqah AbdulWahab
- Departments of Pediatrics, Hamad Medical Corporation, Doha, Qatar. .,Weill Cornell Medicine, Doha, Qatar.
| | - Husam Salah
- Microbiology Division, Laboratory of Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar.,CBS Fungal Biodiversity Center, Utrecht, The Netherlands
| | - Prem Chandra
- Department of Medical Research, Hamad Medical Corporation, Doha, Qatar
| | - Saad J Taj-Aldeen
- Weill Cornell Medicine, Doha, Qatar.,Microbiology Division, Laboratory of Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
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43
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Chen SCA, Meyer W, Pashley CH. Challenges in Laboratory Detection of Fungal Pathogens in the Airways of Cystic Fibrosis Patients. Mycopathologia 2017; 183:89-100. [PMID: 28589247 DOI: 10.1007/s11046-017-0150-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 05/20/2017] [Indexed: 12/11/2022]
Abstract
Study of the clinical significance of fungal colonization/infection in the airways of cystic fibrosis (CF) patients, especially by filamentous fungi, is challenged by the absence of standardized methodology for the detection and identification of an ever-broadening range of fungal pathogens. Culture-based methods remain the cornerstone diagnostic approaches, but current methods used in many clinical laboratories are insensitive and unstandardized, rendering comparative studies unfeasible. Guidelines for standardized processing of respiratory specimens and for their culture are urgently needed and should include recommendations for specific processing procedures, inoculum density, culture media, incubation temperature and duration of culture. Molecular techniques to detect fungi directly from clinical specimens include panfungal PCR assays, multiplex or pathogen-directed assays, real-time PCR, isothermal methods and probe-based assays. In general, these are used to complement culture. Fungal identification by DNA sequencing methods is often required to identify cultured isolates, but matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is increasingly used as an alternative to DNA sequencing. Genotyping of isolates is undertaken to investigate relatedness between isolates, to pinpoint the infection source and to study the population structure. Methods range from PCR fingerprinting and amplified fragment length polymorphism analysis, to short tandem repeat typing, multilocus sequencing typing (MLST) and whole genome sequencing (WGS). MLST is the current preferred method, whilst WGS offers best case resolution but currently is understudied.
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Affiliation(s)
- Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, Westmead Hospital, 3rd Level ICPMR Building, Westmead, NSW, 2145, Australia.
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia.
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Catherine H Pashley
- Department of Infection, Immunity and Inflammation, Institute for Lung Health, University of Leicester, Leicester, LE1 9HN, UK
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44
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Aspergillus Species in Bronchiectasis: Challenges in the Cystic Fibrosis and Non-cystic Fibrosis Airways. Mycopathologia 2017; 183:45-59. [DOI: 10.1007/s11046-017-0143-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 05/08/2017] [Indexed: 12/26/2022]
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45
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Proteomics as a Tool to Identify New Targets Against Aspergillus and Scedosporium in the Context of Cystic Fibrosis. Mycopathologia 2017; 183:273-289. [PMID: 28484941 DOI: 10.1007/s11046-017-0139-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/25/2017] [Indexed: 12/26/2022]
Abstract
Cystic fibrosis (CF) is a genetic disorder that increases the risk of suffering microbial, including fungal, infections. In this paper, proteomics-based information was collated relating to secreted and cell wall proteins with potential medical applications from the most common filamentous fungi in CF, i.e., Aspergillus and Scedosporium/Lomentospora species. Among the Aspergillus fumigatus secreted allergens, β-1,3-endoglucanase, the alkaline protease 1 (Alp1/oryzin), Asp f 2, Asp f 13/15, chitinase, chitosanase, dipeptidyl-peptidase V (DppV), the metalloprotease Asp f 5, mitogillin/Asp f 1, and thioredoxin reductase receive a special mention. In addition, the antigens β-glucosidase 1, catalase, glucan endo-1,3-β-glucosidase EglC, β-1,3-glucanosyltransferases Gel1 and Gel2, and glutaminase A were also identified in secretomes of other Aspergillus species associated with CF: Aspergillus flavus, Aspergillus niger, Aspergillus nidulans, and Aspergillus terreus. Regarding cell wall proteins, cytochrome P450 and eEF-3 were proposed as diagnostic targets, and alkaline protease 2 (Alp2), Asp f 3 (putative peroxiredoxin pmp20), probable glycosidases Asp f 9/Crf1 and Crf2, GPI-anchored protein Ecm33, β-1,3-glucanosyltransferase Gel4, conidial hydrophobin Hyp1/RodA, and secreted aspartyl protease Pep2 as protective vaccines in A. fumigatus. On the other hand, for Scedosporium/Lomentospora species, the heat shock protein Hsp70 stands out as a relevant secreted and cell wall antigen. Additionally, the secreted aspartyl proteinase and an ortholog of Asp f 13, as well as the cell wall endo-1,3-β-D-glucosidase and 1,3-β-glucanosyl transferase, were also found to be significant proteins. In conclusion, proteins mentioned in this review may be promising candidates for developing innovative diagnostic and therapeutic tools for fungal infections in CF patients.
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Rapid Identification of Clinically Relevant Members of the Genus Exophiala by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry and Description of Two Novel Species, Exophiala campbellii and Exophiala lavatrina. J Clin Microbiol 2017; 55:1162-1176. [PMID: 28122875 DOI: 10.1128/jcm.02459-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 01/22/2017] [Indexed: 11/20/2022] Open
Abstract
Exophiala is a ubiquitous pleomorphic genus comprising at least 40 species, many of which have been associated with superficial, visceral, or systemic infections in humans, other mammals, or cold-blooded animals. In this study, we investigated the potential of matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS) for the identification of Exophiala species. A total of 89 isolates (including 50 human and 4 animal clinical isolates) stored in the National Collection of Pathogenic Fungi were identified by PCR amplification and sequencing of internal transcribed spacer region 1. Eighty-three of the isolates corresponded to 16 known species within Exophiala/Rhinocladiella The remaining six isolates are shown by phylogenetic analyses based on four loci to represent two novel Exophiala species. Four isolates from domestic bathrooms which form a sister species with Exophiala lecanii-corni are described here as Exophiala lavatrina sp. nov. The remaining two isolates, both from subcutaneous infections, are distantly related to Exophiala oligosperma and are described here as Exophiala campbellii sp. nov. The triazoles and terbinafine exhibited low MICs against all Exophiala isolates in vitro MALDI-TOF MS successfully distinguished all 18 species and identified all isolates after appropriate reference spectra were created and added to commercial databases. Intraspecific mean log scores ranged from 1.786 to 2.584 and were consistently significantly higher than interspecific scores (1.193 to 1.624), with the exception of E. lecanii-corni and E. lavatrina, for which there was considerable log score overlap. In summary, MALDI-TOF MS allows the rapid and accurate identification of a wide range of clinically relevant Exophiala species.
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47
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Use of Selective Fungal Culture Media Increases Rates of Detection of Fungi in the Respiratory Tract of Cystic Fibrosis Patients. J Clin Microbiol 2017; 55:1122-1130. [PMID: 28100601 DOI: 10.1128/jcm.02182-16] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/13/2017] [Indexed: 01/26/2023] Open
Abstract
The prevalence of fungi in the respiratory tracts of cystic fibrosis (CF) patients has risen. However, fungal surveillance is not routinely performed in most clinical centers in the United States, which may lead to an underestimation of the true prevalence of the problem. We conducted a prospective study comparing the rates of detection for clinically important fungi (CIF), defined as Aspergillus, Scedosporium, and Trichosporon species and Exophiala dermatitidis, in CF sputa using standard bacterial and selective fungal culture media, including Sabouraud dextrose agar with gentamicin (SDA), inhibitory mold agar (IMA), and brain heart infusion (BHI) agar with chloramphenicol and gentamicin. We described the prevalence of these fungi in an adult CF population. A total of 487 CF respiratory samples were collected from 211 unique participants. CIF were detected in 184 (37.8%) samples. Only 26.1% of CIF-positive samples were detected in bacterial culture medium, whereas greater rates of detection for fungi were found in IMA (65.8%; P < 0.001), in SDA (at 30°C, 64.7%; P = 0.005), and in BHI agar (63.0%; P = 0.001). The prevalences of Aspergillus and Scedosporium species were 40.8% and 5.2%, respectively, which are greater than the nationally reported prevalence numbers of 20.4% and 1.9%. Selective fungal culture media and longer incubation periods yielded higher rates of detection for CIF in CF sputum samples compared with that detected in bacterial culture medium, resulting in an underdetection of fungi by bacterial culture alone. The prevalence of fungi in CF may be better estimated by using selective fungal culture media, and this may translate to important clinical decisions.
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48
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Abstract
For a long time, the microbiology of cystic fibrosis has been focussed on Pseudomonas aeruginosa and associated Gram-negative pathogens. An increasing body of evidence has been compiled demonstrating an important role for moulds and yeasts within this complex patient group. Whether or not fungi are active participants, spectators or transient passersby remain to be elucidated. However, functionally, they do appear to play a contributory role in pathogenesis, albeit we do not know if this is a direct or indirect effect. The following review examines some of the key evidence for the role of fungi in CF pathogenesis.
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49
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Burgel PR, Paugam A, Hubert D, Martin C. Aspergillus fumigatus in the cystic fibrosis lung: pros and cons of azole therapy. Infect Drug Resist 2016; 9:229-238. [PMID: 27703383 PMCID: PMC5036609 DOI: 10.2147/idr.s63621] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Aspergillus fumigatus is the main fungus cultured in the airways of patients with cystic fibrosis (CF). Allergic bronchopulmonary aspergillosis occurs in ~10% of CF patients and is clearly associated with airway damage and lung function decline. The effects of A. fumigatus colonization in the absence of allergic bronchopulmonary aspergillosis are less well established. Retrospective clinical studies found associations of A. fumigatus-positive cultures with computed tomography scan abnormalities, greater risk of CF exacerbations and hospitalizations, and/or lung function decline. These findings were somewhat variable among studies and provided only circumstantial evidence for a role of A. fumigatus colonization in CF lung disease progression. The availability of a growing number of oral antifungal triazole drugs, together with the results of nonrandomized case series suggesting positive effects of azole therapies, makes it tempting to treat CF patients with these antifungal drugs. However, the only randomized controlled trial that has used itraconazole in CF patients showed no significant benefit. Because triazoles may have significant adverse effects and drug interactions, and because their prolonged use has been associated with the emergence of azole-resistant A. fumigatus isolates, it remains unclear whether or not CF patients benefit from azole therapy.
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Affiliation(s)
- Pierre-Régis Burgel
- Department of Respiratory Medicine, Cochin Hospital, Assistance Publique - Hôpitaux de Paris; Université Paris Descartes, Sorbonne Paris Cité
| | - André Paugam
- Université Paris Descartes, Sorbonne Paris Cité; Parasitology-Mycology Laboratory, Cochin Hospital, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Dominique Hubert
- Department of Respiratory Medicine, Cochin Hospital, Assistance Publique - Hôpitaux de Paris; Université Paris Descartes, Sorbonne Paris Cité
| | - Clémence Martin
- Department of Respiratory Medicine, Cochin Hospital, Assistance Publique - Hôpitaux de Paris; Université Paris Descartes, Sorbonne Paris Cité
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50
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Wardlaw AJ, Woolnough K, Pashley CH. Lassoing a chimera: the semantics of allergic fungal airway disease. Clin Exp Allergy 2016; 45:1746-9. [PMID: 26581852 DOI: 10.1111/cea.12659] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- A J Wardlaw
- Department of Infection Immunity and Inflammation, Institute for Lung Health, University of Leicester, Leicester, UK.,Department of Respiratory Medicine, University Hospitals of Leicester NHS Trust, Glenfield Hospital, Leicester, UK
| | - K Woolnough
- Department of Infection Immunity and Inflammation, Institute for Lung Health, University of Leicester, Leicester, UK.,Department of Respiratory Medicine, University Hospitals of Leicester NHS Trust, Glenfield Hospital, Leicester, UK
| | - C H Pashley
- Department of Infection Immunity and Inflammation, Institute for Lung Health, University of Leicester, Leicester, UK.,Department of Respiratory Medicine, University Hospitals of Leicester NHS Trust, Glenfield Hospital, Leicester, UK
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