1
|
Kurbessoian T, Murante D, Crocker A, Hogan DA, Stajich JE. In host evolution of Exophiala dermatitidis in cystic fibrosis lung micro-environment. G3 (BETHESDA, MD.) 2023; 13:jkad126. [PMID: 37293838 PMCID: PMC10484061 DOI: 10.1093/g3journal/jkad126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/26/2022] [Accepted: 05/18/2023] [Indexed: 06/10/2023]
Abstract
Individuals with cystic fibrosis (CF) are susceptible to chronic lung infections that lead to inflammation and irreversible lung damage. While most respiratory infections that occur in CF are caused by bacteria, some are dominated by fungi such as the slow-growing black yeast Exophiala dermatitidis. Here, we analyze isolates of E. dermatitidis cultured from two samples, collected from a single subject 2 years apart. One isolate genome was sequenced using long-read Nanopore technology as an in-population reference to use in comparative single nucleotide polymorphism and insertion-deletion variant analyses of 23 isolates. We then used population genomics and phylo-genomics to compare the isolates to each other as well as the reference genome strain E. dermatitidis NIH/UT8656. Within the CF lung population, three E. dermatitidis clades were detected, each with varying mutation rates. Overall, the isolates were highly similar suggesting that they were recently diverged. All isolates were MAT 1-1, which was consistent with their high relatedness and the absence of evidence for mating or recombination between isolates. Phylogenetic analysis grouped sets of isolates into clades that contained isolates from both early and late time points indicating there are multiple persistent lineages. Functional assessment of variants unique to each clade identified alleles in genes that encode transporters, cytochrome P450 oxidoreductases, iron acquisition, and DNA repair processes. Consistent with the genomic heterogeneity, isolates showed some stable phenotype heterogeneity in melanin production, subtle differences in antifungal minimum inhibitory concentrations, and growth on different substrates. The persistent population heterogeneity identified in lung-derived isolates is an important factor to consider in the study of chronic fungal infections, and the analysis of changes in fungal pathogens over time may provide important insights into the physiology of black yeasts and other slow-growing fungi in vivo.
Collapse
Affiliation(s)
- Tania Kurbessoian
- Department of Microbiology and Plant Pathology and Institute of Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Daniel Murante
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Alex Crocker
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology and Institute of Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
| |
Collapse
|
2
|
Maraki S, Katzilakis N, Neonakis I, Stafylaki D, Meletiadis J, Hamilos G, Stiakaki E. Exophiala dermatitidis Central Line-Associated Bloodstream Infection in a Child with Ewing's Sarcoma: Case Report and Literature Review on Paediatric Infections. Mycopathologia 2022; 187:595-602. [PMID: 35994217 DOI: 10.1007/s11046-022-00658-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/04/2022] [Indexed: 10/15/2022]
Abstract
Exophiala dermatitidis is a dematiaceous, ubiquitous, dimorphic fungus, which can cause a wide range of invasive diseases in both immunocompromised and immunocompetent hosts. Bloodstream infections due to E. dermatitidis are rarely encountered in clinical practice, especially in pediatric patients. We describe a case of central line-associated bloodstream infection due to E. dermatitidis in a 4.5-year-old boy with Ewing's sarcoma. The fungus was isolated from blood specimens taken from the Hickman line. The isolate was identified by its phenotypic characteristics, by MALDI-TOF and by using molecular methods. The infection was successfully treated with voriconazole and catheter removal. The literature was also reviewed on pediatric infections caused by E. dermatitidis, focusing on clinical manifestations and challenges associated with diagnosis and management.
Collapse
Affiliation(s)
- Sofia Maraki
- Department of Clinical Microbiology and Microbial Pathogenesis, University Hospital of Heraklion, Crete, Greece.
| | - Nikolaos Katzilakis
- Department of Pediatric Hematology-Oncology, University Hospital of Heraklion and Laboratory of Blood Diseases and Childhood Cancer Biology, Medical School, University of Crete, Heraklion, Greece
| | - Ioannis Neonakis
- Department of Clinical Microbiology and Microbial Pathogenesis, University Hospital of Heraklion, Crete, Greece
| | - Dimitra Stafylaki
- Department of Clinical Microbiology and Microbial Pathogenesis, University Hospital of Heraklion, Crete, Greece
| | - Joseph Meletiadis
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - George Hamilos
- Department of Clinical Microbiology and Microbial Pathogenesis, University Hospital of Heraklion, Crete, Greece
| | - Eftichia Stiakaki
- Department of Pediatric Hematology-Oncology, University Hospital of Heraklion and Laboratory of Blood Diseases and Childhood Cancer Biology, Medical School, University of Crete, Heraklion, Greece
| |
Collapse
|
3
|
Brackin AP, Hemmings SJ, Fisher MC, Rhodes J. Fungal Genomics in Respiratory Medicine: What, How and When? Mycopathologia 2021; 186:589-608. [PMID: 34490551 PMCID: PMC8421194 DOI: 10.1007/s11046-021-00573-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/14/2021] [Indexed: 12/20/2022]
Abstract
Respiratory infections caused by fungal pathogens present a growing global health concern and are a major cause of death in immunocompromised patients. Worryingly, coronavirus disease-19 (COVID-19) resulting in acute respiratory distress syndrome has been shown to predispose some patients to airborne fungal co-infections. These include secondary pulmonary aspergillosis and mucormycosis. Aspergillosis is most commonly caused by the fungal pathogen Aspergillus fumigatus and primarily treated using the triazole drug group, however in recent years, this fungus has been rapidly gaining resistance against these antifungals. This is of serious clinical concern as multi-azole resistant forms of aspergillosis have a higher risk of mortality when compared against azole-susceptible infections. With the increasing numbers of COVID-19 and other classes of immunocompromised patients, early diagnosis of fungal infections is critical to ensuring patient survival. However, time-limited diagnosis is difficult to achieve with current culture-based methods. Advances within fungal genomics have enabled molecular diagnostic methods to become a fast, reproducible, and cost-effective alternative for diagnosis of respiratory fungal pathogens and detection of antifungal resistance. Here, we describe what techniques are currently available within molecular diagnostics, how they work and when they have been used.
Collapse
Affiliation(s)
- Amelie P Brackin
- MRC Centre for Global Disease Analysis, Imperial College London, London, UK
| | - Sam J Hemmings
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Matthew C Fisher
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Johanna Rhodes
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| |
Collapse
|
4
|
Abstract
Although survival of individuals with cystic fibrosis (CF) has been continuously improving for the past 40 years, respiratory failure secondary to recurrent pulmonary infections remains the leading cause of mortality in this patient population. Certain pathogens such as Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus, and species of the Burkholderia cepacia complex continue to be associated with poorer clinical outcomes including accelerated lung function decline and increased mortality. In addition, other organisms such as anaerobes, viruses, and fungi are increasingly recognized as potential contributors to disease progression. Culture-independent molecular methods are also being used for diagnostic purposes and to examine the interaction of microorganisms in the CF airway. Given the importance of CF airway infections, ongoing initiatives to promote understanding of the epidemiology, clinical course, and treatment options for these infections are needed.
Collapse
Affiliation(s)
- Ana C Blanchard
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Valerie J Waters
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
5
|
Exophiala dermatitidis Revealing Cystic Fibrosis in Adult Patients with Chronic Pulmonary Disease. Mycopathologia 2017; 183:71-79. [PMID: 29094263 DOI: 10.1007/s11046-017-0218-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/20/2017] [Indexed: 12/20/2022]
Abstract
Cystic fibrosis (CF) is a genetic inherited disease due to mutations in the gene cystic fibrosis transmembrane conductance regulator (CFTR). Because of the huge diversity of CFTR mutations, the CF phenotypes are highly heterogeneous, varying from typical to mild form of CF, also called atypical CF. These atypical features are more frequently diagnosed at adolescence or adulthood, and among clinical signs and symptoms leading to suspect a mild form of CF, colonization or infection of the respiratory tract due to well-known CF pathogens should be a warning signal. Exophiala dermatitidis is a melanized dimorphic fungus commonly detected in respiratory specimens from CF patients, but only very rarely from respiratory specimens from non-CF patients. We described here two cases of chronic colonization of the airways by E. dermatitidis, with recurrent pneumonia and hemoptysis in one patient, which led clinicians to diagnose mild forms of CF in these elderly patients who were 68- and 87-year-old. These cases of late CF diagnosis suggest that airway colonization or respiratory infections due to E. dermatitidis in patients with bronchiectasis should led to search for a mild form of CF, regardless of the age and associated symptoms. On a broader level, in patients with chronic respiratory disease and recurrent pulmonary infections, an allergic bronchopulmonary mycosis or an airway colonization by CF-related fungi like E. dermatitidis or some Aspergillus, Scedosporium or Rasamsonia species, should be considered as potential markers of atypical CF and should led clinicians to conduct investigations for CF diagnosis.
Collapse
|
6
|
Tanuskova D, Horakova J, Buzassyova D, Poczova M, Bodova I, Svec P, Chocholova A, Adamcakova J, Sykora T, Pozdechova M, Geczova L, Kolenova A. A case of Exophiala dermatitidis infection in a child after allogeneic stem cell transplantation: case report and literature review of paediatric cases. JMM Case Rep 2017; 4:e005102. [PMID: 29026629 PMCID: PMC5630971 DOI: 10.1099/jmmcr.0.005102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 05/31/2017] [Indexed: 01/20/2023] Open
Abstract
Introduction.Exophiala dermatitidisis a relatively common environmental black yeast with worldwide distribution and is a rare cause of fungal infection, mostly in patients with certain predisposing factors. Due to the rarity of the infection, little is known about the specific predisposing factors, way of infection or treatment. Case presentation. Here, we report what is to our knowledge the first case of E. dermatitidis infection in a child after allogeneic stem cell transplantation. We also review all paediatric cases reported in the literature since 1993. Conclusion. This is, to our knowledge, the first reported case of E. dermatitidis infection in a child after allogeneic stem cell transplantation. This report should increase the awareness of E. dermatitidis in immunocompromised paediatric patients, particularly after stem cell transplantation.
Collapse
Affiliation(s)
- Dominika Tanuskova
- Department of Paediatric Haematology and Oncology, Haematopoietic Stem Cell Transplantation Unit, Comenius University Children's Hospital, Bratislava, Slovakia
| | - Julia Horakova
- Department of Paediatric Haematology and Oncology, Haematopoietic Stem Cell Transplantation Unit, Comenius University Children's Hospital, Bratislava, Slovakia
| | - Darina Buzassyova
- Department of Paediatric Anaesthesiology and Intensive Medicine, Comenius University Children's Hospital, Bratislava, Slovakia
| | - Miroslava Poczova
- Department of Mycology, HPL Ltd, The Medirex Group, Bratislava, Slovakia
| | - Ivana Bodova
- Department of Paediatric Haematology and Oncology, Haematopoietic Stem Cell Transplantation Unit, Comenius University Children's Hospital, Bratislava, Slovakia
| | - Peter Svec
- Department of Paediatric Haematology and Oncology, Haematopoietic Stem Cell Transplantation Unit, Comenius University Children's Hospital, Bratislava, Slovakia
| | - Alica Chocholova
- Department of Paediatric Haematology and Oncology, Haematopoietic Stem Cell Transplantation Unit, Comenius University Children's Hospital, Bratislava, Slovakia
| | - Jaroslava Adamcakova
- Department of Paediatric Haematology and Oncology, Haematopoietic Stem Cell Transplantation Unit, Comenius University Children's Hospital, Bratislava, Slovakia
| | - Tomas Sykora
- Department of Paediatric Haematology and Oncology, Haematopoietic Stem Cell Transplantation Unit, Comenius University Children's Hospital, Bratislava, Slovakia
| | - Miroslava Pozdechova
- Department of Paediatric Haematology and Oncology, Haematopoietic Stem Cell Transplantation Unit, Comenius University Children's Hospital, Bratislava, Slovakia
| | - Lucia Geczova
- Department of Paediatric Haematology and Oncology, Haematopoietic Stem Cell Transplantation Unit, Comenius University Children's Hospital, Bratislava, Slovakia
| | - Alexandra Kolenova
- Department of Paediatric Haematology and Oncology, Haematopoietic Stem Cell Transplantation Unit, Comenius University Children's Hospital, Bratislava, Slovakia
| |
Collapse
|
7
|
Abstract
Black-pigmented sputum, also called “melanoptysis,” is a symptom that may be observed in certain pathologies such us coal workers’ pneumoconiosis (anthracosis). The cavitation and liquefaction of a fibrosed mass by an infectious process (tuberculosis, infections by anaerobes, etc.) or by ischemic necrosis may cause expectoration of a blackish secretion. We report the case of a patient with labor precedents as a coal worker, from whom abundant black sputum was obtained in the course of an incidental expectoration. Cyto-histological findings are shown and a differential diagnosis is established.
Collapse
|
8
|
Suzuki K, Nakamura A, Fujieda A, Nakase K, Katayama N. Pulmonary infection caused by Exophiala dermatitidis in a patient with multiple myeloma: A case report and a review of the literature. Med Mycol Case Rep 2012; 1:95-8. [PMID: 24371750 DOI: 10.1016/j.mmcr.2012.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 10/09/2012] [Accepted: 10/09/2012] [Indexed: 10/27/2022] Open
Abstract
Exophiala dermatitidis is a dematiaceous fungus that is increasingly being identified as a cause of fungal infection especially in patients with immunodeficiency. To date, however, the factors predisposing E. dermatitidis and its optimal treatments have not been fully addressed. Here, we report the first patient with untreated multiple myeloma who developed E. dermatitidis pulmonary infection. We also review recent clinical reports describing the features of E. dermatitidis infection.
Collapse
Affiliation(s)
- Kei Suzuki
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie 514-8507, Japan
| | - Akiko Nakamura
- Central Clinical Laboratories, Mie University Hospital, 2-174 Edobashi, Tsu, Mie 514-8507, Japan
| | - Atsushi Fujieda
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie 514-8507, Japan
| | - Kazunori Nakase
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie 514-8507, Japan
| | - Naoyuki Katayama
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie 514-8507, Japan
| |
Collapse
|
9
|
Rogers GB, Hoffman LR, Johnson MW, Mayer-Hamblett N, Schwarze J, Carroll MP, Bruce KD. Using bacterial biomarkers to identify early indicators of cystic fibrosis pulmonary exacerbation onset. Expert Rev Mol Diagn 2011; 11:197-206. [PMID: 21405970 DOI: 10.1586/erm.10.117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Acute periods of pulmonary exacerbation are the single most important cause of morbidity in cystic fibrosis patients, and may be associated with a loss of lung function. Intervening prior to the onset of a substantially increased inflammatory response may limit the associated damage to the airways. While a number of biomarker assays based on inflammatory markers have been developed, providing useful and important measures of disease during these periods, such factors are typically only elevated once the process of exacerbation has been initiated. Identifying biomarkers that can predict the onset of pulmonary exacerbation at an early stage would provide an opportunity to intervene before the establishment of a substantial immune response, with major implications for the advancement of cystic fibrosis care. The precise triggers of pulmonary exacerbation remain to be determined; however, the majority of models relate to the activity of microbes present in the patient's lower airways of cystic fibrosis. Advances in diagnostic microbiology now allow for the examination of these complex systems at a level likely to identify factors on which biomarker assays can be based. In this article, we discuss key considerations in the design and testing of assays that could predict pulmonary exacerbations.
Collapse
Affiliation(s)
- Geraint B Rogers
- Molecular Microbiology Research Laboratory, Pharmaceutical Science Division, 150 Stamford Street, Franklin-Wilkins Building, King's College London, London, SE1 9NH, UK
| | | | | | | | | | | | | |
Collapse
|