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Opulente DA, LaBella AL, Harrison MC, Wolters JF, Liu C, Li Y, Kominek J, Steenwyk JL, Stoneman HR, VanDenAvond J, Miller CR, Langdon QK, Silva M, Gonçalves C, Ubbelohde EJ, Li Y, Buh KV, Jarzyna M, Haase MAB, Rosa CA, ČCadež N, Libkind D, DeVirgilio JH, Hulfachor AB, Kurtzman CP, Sampaio JP, Gonçalves P, Zhou X, Shen XX, Groenewald M, Rokas A, Hittinger CT. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science 2024; 384:eadj4503. [PMID: 38662846 DOI: 10.1126/science.adj4503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 03/22/2024] [Indexed: 05/03/2024]
Abstract
Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficiency and breadth and (ii) the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1154 yeast strains from 1051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but we found limited evidence for trade-offs. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.
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Affiliation(s)
- Dana A Opulente
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Biology Department, Villanova University, Villanova, PA 19085, USA
| | - Abigail Leavitt LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- North Carolina Research Center (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC 28081, USA
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - John F Wolters
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Chao Liu
- College of Agriculture and Biotechnology and Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | - Yonglin Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Jacek Kominek
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- LifeMine Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hayley R Stoneman
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jenna VanDenAvond
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Caroline R Miller
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Quinn K Langdon
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Margarida Silva
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Carla Gonçalves
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Emily J Ubbelohde
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Yuanning Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Kelly V Buh
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Martin Jarzyna
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Graduate Program in Neuroscience and Department of Biology, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Max A B Haase
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Vilcek Institute of Graduate Biomedical Sciences and Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Neža ČCadež
- Food Science and Technology Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Universidad Nacional del Comahue, CONICET, CRUB, Quintral 1250, San Carlos de Bariloche, 8400, Río Negro, Argentina
| | - Jeremy H DeVirgilio
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Cletus P Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA
| | - José Paulo Sampaio
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Paula Gonçalves
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- College of Agriculture and Biotechnology and Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | | | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
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2
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Akıncı B, Atay D, Yenigürbüz FD, Akçay A, Akar O, Öztürk G. Fatal disseminated Magnusiomyces clavatus infection with rash in pediatric acute lymphoblastic leukemia: A case report. Diagn Microbiol Infect Dis 2024; 108:116148. [PMID: 38128321 DOI: 10.1016/j.diagmicrobio.2023.116148] [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: 10/07/2023] [Revised: 11/12/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023]
Abstract
Magnusiomyces clavatus is a rare yeast-like fungus that can cause opportunistic infections in immunocompromised patients. Here, we present a 14-year-old patient who was followed up with the diagnosis of acute lymphoblastic leukemia, developed skin rashes, and Magnusiomyces clavatus infection detected. The patient died shortly after the infection was diagnosed.
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Affiliation(s)
- Burcu Akıncı
- Department of Pediatric Hematology-Oncology, Acıbadem University School of Medicine, Kayışdağı Street. No:32, Ataşehir, İstanbul 34752, Turkey.
| | - Didem Atay
- Department of Pediatric Hematology-Oncology, Acıbadem University School of Medicine, Kayışdağı Street. No:32, Ataşehir, İstanbul 34752, Turkey
| | - Fatma Demir Yenigürbüz
- Department of Pediatric Hematology-Oncology, Acıbadem University School of Medicine, Kayışdağı Street. No:32, Ataşehir, İstanbul 34752, Turkey
| | - Arzu Akçay
- Department of Pediatric Hematology-Oncology, Acıbadem University School of Medicine, Kayışdağı Street. No:32, Ataşehir, İstanbul 34752, Turkey
| | - Oğuz Akar
- Department of Microbiology, Acıbadem Altunizade Hospital, İstanbul, Turkey
| | - Gülyüz Öztürk
- Department of Pediatric Hematology-Oncology, Acıbadem University School of Medicine, Kayışdağı Street. No:32, Ataşehir, İstanbul 34752, Turkey
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3
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Styczynski T, Sadlok J, Richert-Przygonska M, Debski R, Zalas-Wiecek P, Czyzewski K, Styczynski J. Infection With Saprochaete Clavata in Children After Hematopoietic Cell Transplantation. J Pediatr Hematol Oncol 2023; 45:e976-e979. [PMID: 37278583 DOI: 10.1097/mph.0000000000002686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/16/2023] [Indexed: 06/07/2023]
Abstract
Septic shock is a very rare manifestation of invasive fungal disease (IFD) in children after allogeneic hematopoietic cell transplantation (allo-HCT). The objective of this paper is analysis of two cases of pediatric patients with IFD caused by Saprochaete clavata after allo-HCT. Literature data on this infection in children and its outcome were also summarized. Infection with Saprochaete clavate presenting with symptoms of septic shock was being reported in 4 children, and 2 of them survived the infection. In conclusion, with quick diagnosis and quick treatment, the outcome of therapy of infection with Saprochaete clavata was successful.
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Affiliation(s)
- Tomasz Styczynski
- Departments of Pediatric Hematology and Oncology
- Student Scientific Society, Collegium Medicum, Nicolaus Copernicus University, Poland
| | - Jagoda Sadlok
- Departments of Pediatric Hematology and Oncology
- Student Scientific Society, Collegium Medicum, Nicolaus Copernicus University, Poland
| | | | | | - Patrycja Zalas-Wiecek
- Microbiology, Collegium Medicum, Nicolaus Copernicus University, Jurasz University Hospital 1, Bydgoszcz
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Douglas AP, Stewart AG, Halliday CL, Chen SCA. Outbreaks of Fungal Infections in Hospitals: Epidemiology, Detection, and Management. J Fungi (Basel) 2023; 9:1059. [PMID: 37998865 PMCID: PMC10672668 DOI: 10.3390/jof9111059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
Nosocomial clusters of fungal infections, whilst uncommon, cannot be predicted and are associated with significant morbidity and mortality. Here, we review reports of nosocomial outbreaks of invasive fungal disease to glean insight into their epidemiology, risks for infection, methods employed in outbreak detection including genomic testing to confirm the outbreak, and approaches to clinical and infection control management. Both yeasts and filamentous fungi cause outbreaks, with each having general and specific risks. The early detection and confirmation of the outbreak are essential for diagnosis, treatment of affected patients, and termination of the outbreak. Environmental sampling, including the air in mould outbreaks, for the pathogen may be indicated. The genetic analysis of epidemiologically linked isolates is strongly recommended through a sufficiently discriminatory approach such as whole genome sequencing or a method that is acceptably discriminatory for that pathogen. An analysis of both linked isolates and epidemiologically unrelated strains is required to enable genetic similarity comparisons. The management of the outbreak encompasses input from a multi-disciplinary team with epidemiological investigation and infection control measures, including screening for additional cases, patient cohorting, and strict hygiene and cleaning procedures. Automated methods for fungal infection surveillance would greatly aid earlier outbreak detection and should be a focus of research.
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Affiliation(s)
- Abby P. Douglas
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia
| | - Adam G. Stewart
- Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women’s Hospital Campus, The University of Queensland, Herston, QLD 4006, Australia;
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
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Abdolrasouli A, Schelenz S. Answer to the Photo Quiz: Bloodstream infection in a neutropenic patient with severe aplastic anemia. J Clin Microbiol 2023; 61:e0057623. [PMID: 37732748 PMCID: PMC10575292 DOI: 10.1128/jcm.00576-23] [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] [Indexed: 09/22/2023] Open
Abstract
Read the full article for the answer.
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Affiliation(s)
- Alireza Abdolrasouli
- Department of Medical Microbiology, King’s College hospital, London, United Kingdom
| | - Silke Schelenz
- Department of Medical Microbiology, King’s College hospital, London, United Kingdom
- School of Immunology & Microbial Sciences, King’s College, London, United Kingdom
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6
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Abed AB, Hürkan K, Ünal A, Aydın B, Korcan SE. Phenotypic and molecular genetics study of Geotrichum candidumLink (1809) and Geotrichum silvicola Pimenta (2005) cultivated on mitis salivarius agar. Mol Biol Rep 2023:10.1007/s11033-023-08443-z. [PMID: 37294469 DOI: 10.1007/s11033-023-08443-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/11/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND Geotrichum is a genus of fungi found in different habitats throughout the world. Although Geotrichum and its related species have been extensively reclassified and taxonomically revised, it is still the target for many researches. METHODS AND RESULTS In this study, phenotypic and molecular genetics comparisons were performed between Geotrichum candidum and Geotrichum silvicola. Mitis Salivarius Agar was used as the growing medium for the phenotypic comparison study, which was carried out at two temperatures (20-25 and 37 °C). For genotypic comparison, we compared the 18 S, ITS, and 28 S sequences of universal DNA barcode regions of both species. Important findings on the new culture media for fungal isolation were revealed by the results. The phenotypic variation between the two species' colonies, including their shapes, sizes, textures and growth rates, were strikingly different. DNA sequences of both species showed that pairwise identities of the species were 99.9% for 18 S, 100% for ITS and 99.6% for 28 S regions. CONCLUSIONS Contrary to what is commonly seen, the results showed that 18 S, ITS and 28 S failed to discriminate the species. The first investigation into the performance of Mitis Salivarius Agar as a fungus culture medium is reported in this work, and proved its efficiency. Additionally, this is the first study to compare G. candidum with G. silvicola by means of both phenotypic and genotypic analysis.
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Affiliation(s)
- Ahmed Badri Abed
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Uşak University, Uşak, 64200, Turkey.
| | - Kaan Hürkan
- Faculty of Agriculture, Department of Agricultural Biotechnology, Iğdır University, Iğdır, Turkey
| | - Arzu Ünal
- Faculty of Agriculture, Department of Agricultural Biotechnology, Iğdır University, Iğdır, Turkey
| | - Büşra Aydın
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Uşak University, Uşak, 64200, Turkey
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Chen X, Jia X, Bing J, Zhang H, Hong N, Liu Y, Xi H, Wang W, Liu Z, Zhang Q, Li L, Kang M, Xiao Y, Yang B, Lin Y, Xu H, Fan X, Huang J, Gong J, Xu J, Xie X, Yang W, Zhang G, Zhang J, Kang W, Wang H, Hou X, Xiao M, Xu Y. Clonal Dissemination of Antifungal-Resistant Candida haemulonii, China. Emerg Infect Dis 2023; 29:576-584. [PMID: 36823029 PMCID: PMC9973686 DOI: 10.3201/eid2903.221082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Candida haemulonii, a relative of C. auris, frequently shows antifungal resistance and is transmissible. However, molecular tools for genotyping and investigating outbreaks are not yet established. We performed genome-based population analysis on 94 C. haemulonii strains, including 58 isolates from China and 36 other published strains. Phylogenetic analysis revealed that C. haemulonii can be divided into 4 clades. Clade 1 comprised strains from China and other global strains; clades 2-4 contained only isolates from China, were more recently evolved, and showed higher antifungal resistance. Four regional epidemic clusters (A, B, C, and D) were identified in China, each comprising ≥5 cases (largest intracluster pairwise single-nucleotide polymorphism differences <50 bp). Cluster A was identified in 2 hospitals located in the same city, suggesting potential intracity transmissions. Cluster D was resistant to 3 classes of antifungals. The emergence of more resistant phylogenetic clades and regional dissemination of antifungal-resistant C. haemulonii warrants further monitoring.
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Kraft L, Ribeiro VST, Petroski LP, Herai RH, Peronni KC, Figueiredo DLA, Motta FA, Tuon FF. Saprochaete clavata invasive infection: characterization, antifungal susceptibility, and biofilm evaluation of a rare yeast isolated in Brazil. Rev Inst Med Trop Sao Paulo 2023; 65:e12. [PMID: 36722674 PMCID: PMC9886229 DOI: 10.1590/s1678-9946202365012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 12/07/2022] [Indexed: 02/02/2023] Open
Abstract
Rare emerging pathogens such as Saprochaete clavata are associated with invasive fungal diseases, high morbidity, mortality, rapidly fatal infections, and outbreaks. However, little is known about S. clavata infections, epidemiology, risk factors, treatment, biofilms, and disease outcomes. The objective of this study was to describe a new case of severe S. clavata infection in a patient diagnosed at a referral children's hospital in Brazil, including antifungal minimal inhibitory concentration, S. clavata biofilm characterization, and molecular characterization. The S. clavata isolated from an immunocompromised 11-year-old male patient was characterized using MALDI-TOF, Gram staining, scanning electron microscopy (SEM), and next generation sequencing (NGS) of genomic DNA. Biofilm production was also evaluated in parallel with determining minimal inhibitory concentration (MIC) and biofilm sensitivity to antifungal treatment. We observed small to medium, whitish, farinose, dry, filamentous margin colonies, yeast-like cells with bacillary features, and biofilm formation. The MALDI-TOF system yielded a score of ≥ 2,000, while NGS confirmed S. clavata presence at the nucleotide level. The MIC values (in mg L-1) for tested drugs were as follows: fluconazole = 2, voriconazole ≤ 2, caspofungin ≥ 8, micafungin = 2, amphotericin B = 4, flucytosine ≤ 1, and anidulafungin = 1. Amphotericin B can be active against S. clavata biofilm and the fungus can be susceptible to new azoles. These findings were helpful for understanding the development of novel treatments for S. clavata-induced disease, including combined therapy for biofilm-associated infections.
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Affiliation(s)
- Letícia Kraft
- Pontifícia Universidade Católica do Paraná, Escola de Medicina, Pós-Graduação em Ciências da Saúde, Laboratório de Doenças Infecciosas e Emergentes, Curitiba, Paraná, Brazil,Hospital Infantil Pequeno Príncipe, Curitiba, Paraná, Brazil
| | - Victoria Stadler Tasca Ribeiro
- Pontifícia Universidade Católica do Paraná, Escola de Medicina, Pós-Graduação em Ciências da Saúde, Laboratório de Doenças Infecciosas e Emergentes, Curitiba, Paraná, Brazil
| | - Luiz Pedro Petroski
- Pontifícia Universidade Católica do Paraná, Escola de Medicina, Pós-Graduação em Ciências da Saúde, Laboratório de Bioinformática e Neurogenética, Curitiba, Paraná, Brazil
| | - Roberto Hirochi Herai
- Pontifícia Universidade Católica do Paraná, Escola de Medicina, Pós-Graduação em Ciências da Saúde, Laboratório de Bioinformática e Neurogenética, Curitiba, Paraná, Brazil
| | | | | | | | - Felipe Francisco Tuon
- Pontifícia Universidade Católica do Paraná, Escola de Medicina, Pós-Graduação em Ciências da Saúde, Laboratório de Doenças Infecciosas e Emergentes, Curitiba, Paraná, Brazil
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Del Principe MI, Seidel D, Criscuolo M, Dargenio M, Rácil Z, Piedimonte M, Marchesi F, Nadali G, Koehler P, Fracchiolla N, Cattaneo C, Klimko N, Spolzino A, Yilmaz Karapinar D, Demiraslan H, Duarte RF, Demeter J, Stanzani M, Melillo LMA, Basilico CM, Cesaro S, Paterno G, Califano C, Delia M, Buzzatti E, Busca A, Cornely OA, Pagano L. Clincial features and prognostic factors of magnusiomyces (saprochaete) infections in hematology. a multicenter study of seifem/fungiscope. Mycoses 2022; 66:35-46. [PMID: 36064299 DOI: 10.1111/myc.13524] [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: 05/12/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Our multicenter study aims to identify baseline factors and provide guidance for therapeutic decisions regarding Magnusiomyces-associated infections, an emerging threat in patients with hematological malignancies. METHODS HM patients with proven M. capitatus or M. clavatus (formerly Saprochaete capitata and Saprochaete clavata) infection diagnosed between January 2010 and December 2020 were recorded from the SEIFEM (Sorveglianza Epidemiologica Infezioni nelle Emopatie) group and FungiScope (Global Emerging Fungal Infection Registry). Cases of Magnusiomyces fungemia were compared with candidemia. RESULTS Among 90 Magnusiomycescases (60 [66%] M. capitatus and 30 (34%) M. clavatus), median age was 50 years (range 2-78), 46 patients (51%) were female and 67 (74%) had acute leukemia. Thirty-six (40%) of Magnusiomyces-associated infections occurred during antifungal prophylaxis, mainly with posaconazole (n=13, 36%) and echinocandins (n=12, 34%). Instead, the candidemia rarely occurred during prophylaxis (p<0.0001). First-line antifungal therapy with azoles, alone or in combination, was associated with improved response compared to other antifungals (p=0.001). Overall day-30 mortality rate was 43%. Factors associated with higher mortality rates were septic shock (HR 2.696, 95%CI 1.396-5.204, p=.003), corticosteroid treatment longer than 14 days (HR 2.245, 95%CI 1.151-4.376, p=.018), and lack of neutrophil recovery (HR 3.997, 95%CI 2.102-7.601, p<.001). The latter was independently associated with poor outcome (HR 2.495, 95%CI 1.192-5.222, p=.015). CONCLUSIONS Magnusiomyces-associated infections are often breakthrough infections. Effective treatment regimens of these infections remain to be determined, but neutrophil recovery appears to play an important role in the favorable outcome.
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Affiliation(s)
- Maria Ilaria Del Principe
- Dipartimento di Biomedicina e Prevenzione, Università degli studi di Roma "Tor Vergata", Roma, Italy
| | - Danila Seidel
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Cologne, Germany.,University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Marianna Criscuolo
- Dipartimento di Diagnostica per immagini, Radioterapia Oncologica ed Ematologia Fondazione Policlinico Universitario A. Gemelli IRCCS Roma, Italy
| | - Michelina Dargenio
- Ematologia e Trapianto di Cellule Staminali, Ospedale Vito Fazzi, Lecce, Italy
| | - Zdenek Rácil
- Department of Physiology, Masaryk University, Brno Czech Republic. Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Monica Piedimonte
- Dipartimento di Medicina Clinica e Molecolare, Azienda Ospedaliera Universitaria Sant'Andrea di Roma Università Sapienza di Roma, Italy
| | - Francesco Marchesi
- Hematology and Stem Cell Transplant Unit, IRCCS Regina Elena National Cancer Institute, Roma, Italy
| | - Gianpaolo Nadali
- Unità Operativa Complessa di Ematologia, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Philipp Koehler
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Cologne, Germany.,University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Nicola Fracchiolla
- UOC di Ematologia, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milano, Italy
| | - Chiara Cattaneo
- Divisione di Ematologia, ASST-Spedali Civili di Brescia, Brescia, Italy
| | - Nikolai Klimko
- Department of Clinical Mycology, Allergy and Immunology, North Western State Medical University, St Petersburg, Russia
| | - Angelica Spolzino
- Department of Medicine and Surgery, University of Parma & Hematology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy ; Present address: Onco Hematology, Department of Oncology, Veneto Institute of Oncology IOV, IRCCS, Padua, Italy
| | - Deniz Yilmaz Karapinar
- Ege University, Faculty of Medicine, Children's Hospital, Department of Pediatric Hematology, Izmir, Turkey
| | - Hayati Demiraslan
- Department of Infectious Diseases, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Rafael F Duarte
- Department of Hematology, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain
| | - Judit Demeter
- Semmelweis University, Department of Internal Medicine and Oncology, Division of Hematology, Budapest, Hungary
| | - Marta Stanzani
- Istituto di Ematologia ed Oncologia Medica "L. e A. Seragnoli", Ospedale Sant'Orsola Malpighi - Bologna, Italy
| | | | - Claudia Maria Basilico
- Division of Hematology, ASST Sette Laghi, Ospedale di Circolo e Fondazione Macchi, Varese, Italy
| | - Simone Cesaro
- Pediatric Hematology Oncology, Department of Mother and Child, Azienda Ospedaliera Universitaria Integrata di Verona, Italy
| | - Giovangiacinto Paterno
- Dipartimento di Biomedicina e Prevenzione, Università degli studi di Roma "Tor Vergata", Roma, Italy
| | | | - Mario Delia
- Sezione di Ematologia, Dipartimento dell'Emergenza e dei Trapianti d'Organo, Università di Bari, Bari, Italy
| | - Elisa Buzzatti
- Dipartimento di Biomedicina e Prevenzione, Università degli studi di Roma "Tor Vergata", Roma, Italy
| | - Alessandro Busca
- Stem Cell Transplant Center, AOU Citta' della Salute e della Scienza, Torino, Italy
| | - Oliver A Cornely
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Cologne, Germany.,University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany.,University of Cologne, Faculty of Medicine and University Hospital Cologne, Clinical Trials Centre Cologne (ZKS Köln), Cologne, Germany.,German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Livio Pagano
- Istituto di Ematologia, Fondazione Policlinico Universitario A. Gemelli-IRCSS-Università Cattolica del Sacro Cuore, Roma, Italy
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10
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Goupillou P, Costa D, Gargala G, Favennec L, Rouzaud C, Muraine M, Schneider P, Gueudry J. Saprochaete clavata Chorioretinitis in a Post-chemotherapy Immunocompromised 9-Year-Old Child. Ocul Immunol Inflamm 2022:1-4. [PMID: 35587644 DOI: 10.1080/09273948.2022.2070502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
PURPOSE To describe the management of bilateral chorioretinitis with Saprochaete clavata in a post-chemotherapy immunocompromised young patient. METHOD A retrospective case report. RESULT A 9-year-old boy treated with chemotherapy for type 2 acute myeloid leukaemia was diagnosed with Saprochaete clavata (formerly called Geotrichum clavatum) fungaemia. Systematic ocular examination revealed chorioretinitis of the left eye becoming bilateral within the next 3 days. Therapy was based on systemic administration of voriconazole, amphotericin B and flucytosine associated with granulocytic stimulation without stabilizing the ophthalmological situation. Bilateral intravitreal injections of amphotericin B were administered. Voriconazole residual blood concentration was monitored to adjust daily dose. Final best corrected visual acuity in the right eye was 20/50 and 20/20 in the left eye. CONCLUSION This is the first report of chorioretinitis with Saprochaete clavata. Because of its unpredictable pharmacokinetics, especially in pediatric population, therapeutic drug monitoring of voriconazole is essential to control fungal infection.
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Affiliation(s)
- Paul Goupillou
- Department of Ophthalmology, Rouen University Hospital, Rouen, France
| | - Damien Costa
- Department of Parasitology and Mycology, Rouen University Hospital, Rouen, France.,EA 7510 Epidemio-surveillance and circulation of parasites in the environment, Faculty of Medicine and Pharmacy, Rouen University, Rouen, France
| | - Gilles Gargala
- Department of Parasitology and Mycology, Rouen University Hospital, Rouen, France.,EA 7510 Epidemio-surveillance and circulation of parasites in the environment, Faculty of Medicine and Pharmacy, Rouen University, Rouen, France
| | - Loic Favennec
- Department of Parasitology and Mycology, Rouen University Hospital, Rouen, France.,EA 7510 Epidemio-surveillance and circulation of parasites in the environment, Faculty of Medicine and Pharmacy, Rouen University, Rouen, France
| | - Claire Rouzaud
- Infectious Diseases Department, University Hospital Necker Enfants Malades, APHP, Paris, France
| | - Marc Muraine
- Department of Ophthalmology, Rouen University Hospital, Rouen, France
| | | | - Julie Gueudry
- Department of Ophthalmology, Rouen University Hospital, Rouen, France.,EA 7510 Epidemio-surveillance and circulation of parasites in the environment, Faculty of Medicine and Pharmacy, Rouen University, Rouen, France
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11
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Active Surveillance Program to Increase Awareness on Invasive Fungal Diseases: the French RESSIF Network (2012 to 2018). mBio 2022; 13:e0092022. [PMID: 35499498 PMCID: PMC9239099 DOI: 10.1128/mbio.00920-22] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The French National Reference Center for Invasive Mycoses and Antifungals leads an active and sustained nationwide surveillance program on probable and proven invasive fungal diseases (IFDs) to determine their epidemiology in France. Between 2012 and 2018, a total of 10,886 IFDs were recorded. The incidence increased slightly over time (2.16 to 2.36/10,000 hospitalization days, P = 0.0562) in relation with an increase of fungemia incidence (1.03 to 1.19/10,000, P = 0.0023), while that of other IFDs remained stable. The proportion of ≥65-year-old patients increased from 38.4% to 45.3% (P < 0.0001). Yeast fungemia (n = 5,444) was due mainly to Candida albicans (55.6%) with stable proportions of species over time. Echinocandins became the main drug prescribed (46.7% to 61.8%), but global mortality rate remained unchanged (36.3% at 1 month). Pneumocystis jirovecii pneumonia (n = 2,106) was diagnosed mostly in HIV-negative patients (80.7%) with a significantly higher mortality than in HIV-positive patients (21.9% versus 5.4% at 1 month, P < 0.0001). Invasive aspergillosis (n = 1,661) and mucormycosis (n = 314) were diagnosed mostly in hematology (>60% of the cases) with a global mortality rate of 42.5% and 59.3%, respectively, at 3 months and significant changes in diagnosis procedure over time. More concurrent infections were also diagnosed over time (from 5.4% to 9.4% for mold IFDs, P = 0.0115). In conclusion, we observed an aging of patients with IFD with a significant increase in incidence only for yeast fungemia, a trend toward more concurrent infections, which raises diagnostic and therapeutic issues. Overall, global survival associated with IFDs has not improved despite updated guidelines and new diagnostic tools.
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12
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Rokas A. Evolution of the human pathogenic lifestyle in fungi. Nat Microbiol 2022; 7:607-619. [PMID: 35508719 PMCID: PMC9097544 DOI: 10.1038/s41564-022-01112-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 03/25/2022] [Indexed: 02/07/2023]
Abstract
Fungal pathogens cause more than a billion human infections every year, resulting in more than 1.6 million deaths annually. Understanding the natural history and evolutionary ecology of fungi is helping us understand how disease-relevant traits have repeatedly evolved. Different types and mechanisms of genetic variation have contributed to the evolution of fungal pathogenicity and specific genetic differences distinguish pathogens from non-pathogens. Insights into the traits, genetic elements, and genetic and ecological mechanisms that contribute to the evolution of fungal pathogenicity are crucial for developing strategies to both predict emergence of fungal pathogens and develop drugs to combat them.
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Affiliation(s)
- Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA.
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13
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Duminuco A, Vetro C, Maugeri C, Mauro E, Palumbo GAM, Parisi MS, Esposito B, Giuliano G, Romano A, Di Raimondo F. Saprochete capitata: Emerging Infections from Uncommon Microorganisms in Hematological Diseases. Hematol Rep 2022; 14:67-72. [PMID: 35466175 PMCID: PMC9036236 DOI: 10.3390/hematolrep14020011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/04/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022] Open
Abstract
Infections occurring in immunocompromised patients after intensive chemotherapy are often difficult to eradicate and are capable of even being fatal. New emergent and dangerous drug-resistant micro-organisms are likely to appear in these specific scenarios. Clinical features mainly include progressive pneumonia, bacteriemia/fungemia, or extrapulmonary dissemination among infections. The treatment of these microorganisms is still an open challenge since there is a lack of clear treatment guidelines. Indeed, infections from these microorganisms can lead to a rapidly fatal clinical course in immunocompromised patients, especially those who have acute leukemia. We describe the case of a young patient with acute myeloid leukemia who contracted an infection from Saprochaete capitata during post-chemotherapy aplasia.
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Affiliation(s)
- Andrea Duminuco
- Post Graduation School of Hematology, University of Catania, A.O.U. “Policlinico-San Marco”, Via S. Sofia 78, 95123 Catania, Italy;
- Correspondence: ; Tel.: +39-095-378-2981; Fax: +39-095-378-2982
| | - Calogero Vetro
- Division of Hematology, A.O.U. “Policlinico-San Marco”, Via S. Sofia 78, 95123 Catania, Italy; (C.V.); (C.M.); (E.M.); (M.S.P.); (F.D.R.)
| | - Cinzia Maugeri
- Division of Hematology, A.O.U. “Policlinico-San Marco”, Via S. Sofia 78, 95123 Catania, Italy; (C.V.); (C.M.); (E.M.); (M.S.P.); (F.D.R.)
| | - Elisa Mauro
- Division of Hematology, A.O.U. “Policlinico-San Marco”, Via S. Sofia 78, 95123 Catania, Italy; (C.V.); (C.M.); (E.M.); (M.S.P.); (F.D.R.)
| | - Giuseppe A. M. Palumbo
- Department of Scienze Mediche Chirurgiche e Tecnologie Avanzate “G.F. Ingrassia”, University of Catania, 95123 Catania, Italy; (G.A.M.P.); (A.R.)
| | - Marina S. Parisi
- Division of Hematology, A.O.U. “Policlinico-San Marco”, Via S. Sofia 78, 95123 Catania, Italy; (C.V.); (C.M.); (E.M.); (M.S.P.); (F.D.R.)
| | - Benedetta Esposito
- Post Graduation School of Hematology, University of Catania, A.O.U. “Policlinico-San Marco”, Via S. Sofia 78, 95123 Catania, Italy;
| | - Giuseppe Giuliano
- Division of Anesthesiology and Intensive Care, A.O.U. “Policlinico-San Marco”, Via S. Sofia 78, 95123 Catania, Italy;
| | - Alessandra Romano
- Department of Scienze Mediche Chirurgiche e Tecnologie Avanzate “G.F. Ingrassia”, University of Catania, 95123 Catania, Italy; (G.A.M.P.); (A.R.)
| | - Francesco Di Raimondo
- Division of Hematology, A.O.U. “Policlinico-San Marco”, Via S. Sofia 78, 95123 Catania, Italy; (C.V.); (C.M.); (E.M.); (M.S.P.); (F.D.R.)
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14
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Chang CC, Hall V, Cooper C, Grigoriadis G, Beardsley J, Sorrell TC, Heath CH. Consensus guidelines for the diagnosis and management of cryptococcosis and rare yeast infections in the haematology/oncology setting, 2021. Intern Med J 2021; 51 Suppl 7:118-142. [PMID: 34937137 DOI: 10.1111/imj.15590] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cryptococcosis caused by the Cryptococcus neoformans-Cryptococcus gattii complex is an important opportunistic infection in people with immunodeficiency, including in the haematology/oncology setting. This may manifest clinically as cryptococcal meningitis or pulmonary cryptococcosis, or be detected incidentally by cryptococcal antigenemia, a positive sputum culture or radiological imaging. Non-Candida, non-Cryptococcus spp. rare yeast fungaemia are increasingly common in this population. These consensus guidelines aim to provide clinicians working in the Australian and New Zealand haematology/oncology setting with clear guiding principles and practical recommendations for the management of cryptococcosis, while also highlighting important and emerging rare yeast infections and their recommended management.
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Affiliation(s)
- Christina C Chang
- Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Therapeutic and Vaccine Research Programme, Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, KwaZulu Natal, South Africa
| | - Victoria Hall
- Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Transplant Infectious Diseases and Multi-Organ Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Celia Cooper
- Department of Microbiology and Infectious Diseases, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - George Grigoriadis
- Monash Haematology, Monash Health, Melbourne, Victoria, Australia.,School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia.,Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Haematology, Alfred Hospital, Prahran, Victoria, Australia
| | - Justin Beardsley
- Marie Bashir Institute for Infectious Diseases & Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Department of Infectious Diseases, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Tania C Sorrell
- Marie Bashir Institute for Infectious Diseases & Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Infectious Diseases and Sexual Health, Western Sydney Local Health District, Parramatta, New South Wales, Australia
| | - Christopher H Heath
- Department of Microbiology, Fiona Stanley Hospital Network, PathWest Laboratory Medicine, Murdoch, Western Australia, Australia.,Department of Infectious Diseases, Fiona Stanley Hospital, Murdoch, Western Australia, Australia.,Department of Infectious Diseases, Royal Perth Hospital, Perth, Western Australia, Australia.,Faculty of Health and Medical Sciences, University of Western Australia, Murdoch, Western Australia, Australia
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15
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Bloodstream infections caused by Magnusiomyces capitatus and Magnusiomyces clavatus: epidemiological, clinical and microbiological features of two emerging yeast species. Antimicrob Agents Chemother 2021; 66:e0183421. [PMID: 34930027 PMCID: PMC8846490 DOI: 10.1128/aac.01834-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Magnusiomyces clavatus and Magnusiomyces capitatus are emerging yeasts with intrinsic resistance to many commonly used antifungal agents. Identification is difficult, and determination of susceptibility patterns with commercial and reference methods is equally challenging. For this reason, few data on invasive infections by Magnusiomyces spp. are available. OBJECTIVES To determine the epidemiology and susceptibility of Magnusiomyces isolates from bloodstream infections (BSI) isolated in Germany and Austria from 2001-2020. METHODS In seven institutions a total of 34 Magnusiomyces BSI were identified. Identification was done by ITS sequencing and MALDI-TOF MS. Antifungal susceptibility was determined by EUCAST broth microdilution and gradient tests. RESULTS Of the 34 isolates, M. clavatus was more common (N=24) compared to M. capitatus (N=10). BSI by Magnusiomyces spp. were more common in men (62%) and mostly occurred in patients with haemato-oncological malignancies (79%). The highest in vitro antifungal activity against M. clavatus/M. capitatus was observed for voriconazole (MIC50 0.03/0.125 mg/L), followed by posaconazole (MIC50 0.125/0.25 mg/L). M. clavatus isolates showed overall lower MICs compared to M. capitatus. With the exception of amphotericin B, low essential agreement between gradient test and microdilution was recorded for all antifungals (0-70%). Both species showed distinct morphologic traits on ChromAgar Orientation and Columbia blood agar, which can be used for differentiation if no MALDI-TOF or molecular identification is available. CONCLUSION Most BSI were caused by M. clavatus. The lowest MICs were recorded for voriconazole. Gradient tests demonstrated unacceptably low agreement and should preferably not be used for susceptibility testing of Magnusiomyces spp.
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16
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Valade S, Picard M, Mokart D, Calvet L, Bruneel F, de Montmollin E, Aissaoui N, Champigneulle B, Bigé N, Boissier F, Pène F, Mayaux J, Argaud L, Moreau AS, Murgier M, Azoulay E, Darmon M. Critically ill patients with severe infections related to Geotrichum species: A French retrospective multicentre study. Mycoses 2021; 65:226-232. [PMID: 34856032 DOI: 10.1111/myc.13407] [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: 10/27/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Geotrichum spp can be responsible for severe infections in immunocompromised patients. We aim to describe Geotrichum-related infections in the ICU and to assess risk factors of mortality. METHODS Retrospective multicentre study, conducted in 14 French ICUs between 2002 and 2018, including critically ill adult patients with proven or probable infection related to Geotrichum species. Data were obtained from the medical charts. RESULTS Thirty-six patients, median age 60 years IQR [53; 66] were included. Most of the patients had haematological malignancies (78%). The reason for ICU admission was shock in half of the patients (n = 19, 53%) and respiratory failure in thirteen patients (36%). Median SOFA score was 8.5 IQR [7; 15]. Time between ICU admission and fungal diagnosis was 2.5 days [-1; 4]. Infection was disseminated in 27 (75%) patients with positive blood cultures in 25 patients (69%). Thirty patients (83%) received curative antifungal treatment in the ICU, in a median time of 1 day [0;1] after ICU admission. Twenty-four patients (67%) died in the ICU and hospital mortality rate was 69%. The number and extent of organ failures, as represented by SOFA score, were associated with mortality. CONCLUSIONS This study demonstrates poor outcome in critically ill patients with Geotrichum-related infections, which encourages a high level of suspicion.
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Affiliation(s)
- Sandrine Valade
- AP-HP, Hôpital Saint-Louis, Medical ICU, Université de Paris, Paris, France
| | - Muriel Picard
- Service de Réanimation Polyvalente, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Djamel Mokart
- Critical Care Department, Institut Paoli Calmettes, Marseille, France
| | - Laure Calvet
- Service de Reanimation Medicale, Hopital Gabriel Monpied, CHU, Clermont-Ferrand, France
| | - Fabrice Bruneel
- Intensive Care Unit, André Mignot Hospital, Le Chesnay, France
| | - Etienne de Montmollin
- Medical and infectious diseases ICU, AP-HP, Bichat-Claude Bernard Hospital, Paris Cedex, France
| | - Nadia Aissaoui
- Medical Intensive Care Unit, European Hospital Georges-Pompidou, Sorbonne Paris Cité, Paris Descartes University, Paris, France
| | - Benoit Champigneulle
- Anaesthesiology and Intensive Care Department, European Hospital Georges-Pompidou, Paris, France
| | - Naike Bigé
- Service de Médecine Intensive-Réanimation, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Florence Boissier
- CHU de Poitiers, Service de Médecine Intensive Réanimation, INSERM CIC 1402 (ALIVE group), Université de Poitiers, Poitiers, France
| | - Frédéric Pène
- AP-HP, Hôpital Cochin, Service de Médecine Intensive et Réanimation, CNRS UMR8104, INSERM U1016AP-HP, Université de Paris, Paris, France
| | - Julien Mayaux
- Intensive Care Unit, AP-HP, Pitié-Salpétrière Hospital, Paris University, Paris, France
| | - Laurent Argaud
- Medical ICU, Edouard Herriot University Hospital, Lyon, France
| | | | - Martin Murgier
- Medical-surgical Intensive care unit, Saint-Etienne University Hospital, Saint Etienne, France
| | - Elie Azoulay
- AP-HP, Hôpital Saint-Louis, Medical ICU, Université de Paris, Paris, France
| | - Michael Darmon
- AP-HP, Hôpital Saint-Louis, Medical ICU, Université de Paris, Paris, France
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17
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Gurrieri F, Corbellini S, Piccinelli G, Turra A, Morello E, Malagola M, Russo D, Caruso A, De Francesco MA. Management of Invasive Infections due to a Rare Arthroconidial Yeast, Saprochaete capitata, in Two Patients with Acute Hematological Malignancies. Vaccines (Basel) 2021; 9:vaccines9111289. [PMID: 34835220 PMCID: PMC8619284 DOI: 10.3390/vaccines9111289] [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: 09/25/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 11/17/2022] Open
Abstract
Saprochaete capitata is an arthroconidial yeast, found principally in the environment, even if it belongs also to the normal microbial flora that colonize human subjects. This yeast is increasingly associated with invasive infections in hematological patients, in particular in those affected by acute leukemia. An important risk factor that predisposes to this infection is the profound neutropenia present in such immunocompromised patients. Saprochaete spp. were found resistant to both echinocandins and fluconazole so the treatment is often difficult. Here, we report two cases of sepsis in two patients with acute leukemia. All of them had fatal events, due to the worsening of their clinical condition. An early diagnosis and appropriate management of these pathogens is important in consideration of the poor prognosis associated to these fungal invasive infections.
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Affiliation(s)
- Francesca Gurrieri
- Department of Molecular and Translational Medicine, Institute of Microbiology, University of Brescia-ASST Spedali Civili, 25123 Brescia, Italy; (F.G.); (S.C.); (G.P.); (A.C.)
| | - Silvia Corbellini
- Department of Molecular and Translational Medicine, Institute of Microbiology, University of Brescia-ASST Spedali Civili, 25123 Brescia, Italy; (F.G.); (S.C.); (G.P.); (A.C.)
| | - Giorgio Piccinelli
- Department of Molecular and Translational Medicine, Institute of Microbiology, University of Brescia-ASST Spedali Civili, 25123 Brescia, Italy; (F.G.); (S.C.); (G.P.); (A.C.)
| | - Alessandro Turra
- Chair of Hematology, Unit of Blood Diseases and Stem Cells Transplantation, University of Brescia-ASST Spedali Civili, 25123 Brescia, Italy; (A.T.); (E.M.); (M.M.); (D.R.)
| | - Enrico Morello
- Chair of Hematology, Unit of Blood Diseases and Stem Cells Transplantation, University of Brescia-ASST Spedali Civili, 25123 Brescia, Italy; (A.T.); (E.M.); (M.M.); (D.R.)
| | - Michele Malagola
- Chair of Hematology, Unit of Blood Diseases and Stem Cells Transplantation, University of Brescia-ASST Spedali Civili, 25123 Brescia, Italy; (A.T.); (E.M.); (M.M.); (D.R.)
| | - Domenico Russo
- Chair of Hematology, Unit of Blood Diseases and Stem Cells Transplantation, University of Brescia-ASST Spedali Civili, 25123 Brescia, Italy; (A.T.); (E.M.); (M.M.); (D.R.)
| | - Arnaldo Caruso
- Department of Molecular and Translational Medicine, Institute of Microbiology, University of Brescia-ASST Spedali Civili, 25123 Brescia, Italy; (F.G.); (S.C.); (G.P.); (A.C.)
| | - Maria Antonia De Francesco
- Department of Molecular and Translational Medicine, Institute of Microbiology, University of Brescia-ASST Spedali Civili, 25123 Brescia, Italy; (F.G.); (S.C.); (G.P.); (A.C.)
- Correspondence:
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18
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β-1,3-D-glucan and galactomannan as biomarkers for the detection of invasive Geotrichum and Magnusiomyces infections: a retrospective evaluation. J Clin Microbiol 2021; 60:e0160721. [PMID: 34669454 DOI: 10.1128/jcm.01607-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVES Magnusiomyces and Geotrichum species are ascomycetous yeasts that can cause potentially life-threatening invasive fungal infections commonly referred to as geotrichosis. In this study, we aimed to estimate the incidence and mortality of these infections in a German tertiary care centre. Furthermore, we evaluated the suitability of the fungal biomarkers galactomannan (GM) and β-1,3-D-glucan (BDG), which are both recommended as surrogate markers for M. capitatus infection by the ESCMID and ECMM joint clinical guidelines for the diagnosis and management of rare invasive yeast infections, for detection of invasive geotrichosis. METHODS Cases meeting the inclusion criteria for invasive Magnusiomyces/Geotrichum infection were retrospectively identified. Serum samples and culture supernatants were analysed with two commercially available fungal antigen tests (Platelia Aspergillus Ag EIA and Wako β-Glucan Test). For a control cohort, outpatient samples sent for lues testing were included. RESULTS Thirty-eight cases of Magnusiomyces/Geotrichum infection were identified over an eleven-year observation period. In the majority of cases, the fungus was isolated from intraabdominal specimens of patients with a history of abdominal surgery/procedures (n=32). All cases of fungemia occurred exclusively in haemato-oncologic patients (n=14). 30 day-survival was 42% in the fungemia and 43% in the intraabdominal geotrichosis group. Serum samples were available for 23 patients (14 bloodstream and nine intraabdominal infections). While BDG sensitivity was 65%, none of the sera was GM positive. This finding was supported by in vitro experiments analysing fungal culture supernatants: M. capitatus secretes significant amounts of BDG but not GM. Specificity was 96% for BDG and 100% for GM. CONCLUSIONS Magnusiomyces and Geotrichum infections are not limited to haemato-oncologic patients. Contrasting the current ESCMID/ECMM recommendation, our results indicate that GM is no suitable biomarker for the diagnosis of Magnusiomyces infection. Contrarily, BDG sensitivity is comparable to that of candidemia.
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Bowers JR, Monroy-Nieto J, Gade L, Travis J, Refojo N, Abrantes R, Santander J, French C, Dignani MC, Hevia AI, Roe CC, Lemmer D, Lockhart SR, Chiller T, Litvintseva AP, Clara L, Engelthaler DM. Rhizopus microsporus Infections Associated with Surgical Procedures, Argentina, 2006-2014. Emerg Infect Dis 2021; 26:937-944. [PMID: 32310081 PMCID: PMC7181922 DOI: 10.3201/eid2605.191045] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Rhizopus spp. fungi are ubiquitous in the environment and a rare but substantial cause of infection in immunosuppressed persons and surgery patients. During 2005–2017, an abnormally high number of Rhizopus infections in surgery patients, with no apparent epidemiologic links, were reported in Argentina. To determine the likelihood of a common source of the cluster, we performed whole-genome sequencing on samples collected during 2006–2014. Most isolates were separated by >60 single-nucleotide polymorphisms, and we found no evidence for recombination or nonneutral mutation accumulation; these findings do not support common source or patient-to-patient transmission. Assembled genomes of most isolates were ≈25 Mbp, and multiple isolates had substantially larger assembled genomes (43–51 Mbp), indicative of infections with strain types that underwent genome expansion. Whole-genome sequencing has become an essential tool for studying epidemiology of fungal infections. Less discriminatory techniques may miss true relationships, possibly resulting in inappropriate attribution of point source.
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Chowdhary A, Sharada K, Singh PK, Bhagwani DK, Kumar N, de Groot T, Meis JF. Outbreak of Dirkmeia churashimaensis Fungemia in a Neonatal Intensive Care Unit, India. Emerg Infect Dis 2021; 26:764-768. [PMID: 32186501 PMCID: PMC7101094 DOI: 10.3201/eid2604.190847] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Bloodstream infections caused by uncommon or novel fungal species are challenging to identify and treat. We report a series of cases of fungemia due to a rare basidiomycete yeast, Dirkmeia churashimaensis, in neonatal patients in India. Whole-genome sequence typing demonstrated that the patient isolates were genetically indistinguishable, indicating a single-source infection.
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21
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Menu E, Criscuolo A, Desnos-Ollivier M, Cassagne C, D'Incan E, Furst S, Ranque S, Berger P, Dromer F. Saprochaete clavata Outbreak Infecting Cancer Center through Dishwasher. Emerg Infect Dis 2021; 26:2031-2038. [PMID: 32818391 PMCID: PMC7454083 DOI: 10.3201/eid2609.200341] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Saprochaete clavata is a pathogenic yeast responsible for rare outbreaks involving immunocompromised patients, especially those with hematologic malignancies. During February 2016–December 2017, we diagnosed S. clavata infections in 9 patients (8 with fungemia), including 3 within 1 month, at a cancer center in Marseille, France. The patients (median age 58 years), 4 of 9 of whom had acute myeloid leukemia, were hospitalized in 3 different wards. Ten environmental samples, including from 2 dishwashers and 4 pitchers, grew S. clavata, but no contaminated food was discovered. The outbreak ended after contaminated utensils and appliances were discarded. Whole-genome sequencing analysis demonstrated that all clinical and environmental isolates belonged to the same phylogenetic clade, which was unrelated to clades from previous S. clavata outbreaks in France. We identified a dishwasher with a deficient heating system as the vector of contamination.
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Larcher R, Platon L, Amalric M, Brunot V, Besnard N, Benomar R, Daubin D, Ceballos P, Rispail P, Lachaud L, Bourgeois N, Klouche K. Emerging Invasive Fungal Infections in Critically Ill Patients: Incidence, Outcomes and Prognosis Factors, a Case-Control Study. J Fungi (Basel) 2021; 7:jof7050330. [PMID: 33923333 PMCID: PMC8146331 DOI: 10.3390/jof7050330] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/12/2021] [Accepted: 04/23/2021] [Indexed: 12/29/2022] Open
Abstract
Comprehensive data on emerging invasive fungal infections (EIFIs) in the critically ill are scarce. We conducted a case-control study to characterize EIFIs in patients admitted to a French medical ICU teaching hospital from 2006 to 2019. Among 6900 patients, 26 (4 per 1000) had an EIFI: Mucorales accounted for half, and other isolates were mainly Saprochaete, Fusarium and Scedosporium. EIFIs occurred mostly in patients with immunosuppression and severe critical illness. Antifungal treatments (mainly amphotericin B) were administered to almost all patients, whereas only 19% had surgery. In-ICU, mortality was high (77%) and associated with previous conditions such as hematological malignancy or cancer, malnutrition, chronic kidney disease and occurrence of acute respiratory distress syndrome and/or hepatic dysfunction. Day-90 survival rates, calculated by the Kaplan–Meier method, were similar between patients with EIFIs and a control group of patients with aspergillosis: 20%, 95% CI (9- 45) versus 18%, 95% CI (8- 45) (log-rank: p > 0.99). ICU management of such patients should be assessed on the basis of underlying conditions, reversibility and acute event severity rather than the mold species.
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Affiliation(s)
- Romaric Larcher
- Intensive Care Medicine Department, Lapeyronie Hospital, Montpellier University Hospital, 371, Avenue du Doyen Gaston Giraud, 34090 Montpellier, France; (L.P.); (M.A.); (V.B.); (N.B.); (R.B.); (D.D.); (K.K.)
- PhyMedExp, INSERM (French Institute of Health and Medical Research), CNRS (French National Centre for Scientific Research), University of Montpellier, 34090 Montpellier, France
- Correspondence:
| | - Laura Platon
- Intensive Care Medicine Department, Lapeyronie Hospital, Montpellier University Hospital, 371, Avenue du Doyen Gaston Giraud, 34090 Montpellier, France; (L.P.); (M.A.); (V.B.); (N.B.); (R.B.); (D.D.); (K.K.)
| | - Matthieu Amalric
- Intensive Care Medicine Department, Lapeyronie Hospital, Montpellier University Hospital, 371, Avenue du Doyen Gaston Giraud, 34090 Montpellier, France; (L.P.); (M.A.); (V.B.); (N.B.); (R.B.); (D.D.); (K.K.)
| | - Vincent Brunot
- Intensive Care Medicine Department, Lapeyronie Hospital, Montpellier University Hospital, 371, Avenue du Doyen Gaston Giraud, 34090 Montpellier, France; (L.P.); (M.A.); (V.B.); (N.B.); (R.B.); (D.D.); (K.K.)
| | - Noemie Besnard
- Intensive Care Medicine Department, Lapeyronie Hospital, Montpellier University Hospital, 371, Avenue du Doyen Gaston Giraud, 34090 Montpellier, France; (L.P.); (M.A.); (V.B.); (N.B.); (R.B.); (D.D.); (K.K.)
| | - Racim Benomar
- Intensive Care Medicine Department, Lapeyronie Hospital, Montpellier University Hospital, 371, Avenue du Doyen Gaston Giraud, 34090 Montpellier, France; (L.P.); (M.A.); (V.B.); (N.B.); (R.B.); (D.D.); (K.K.)
| | - Delphine Daubin
- Intensive Care Medicine Department, Lapeyronie Hospital, Montpellier University Hospital, 371, Avenue du Doyen Gaston Giraud, 34090 Montpellier, France; (L.P.); (M.A.); (V.B.); (N.B.); (R.B.); (D.D.); (K.K.)
| | - Patrice Ceballos
- Hematology Department, Saint Eloi Hospital, Montpellier University Hospital, 34090 Montpellier, France;
| | - Philippe Rispail
- Mycology and Parasitology Laboratory, Lapeyronie Hospital, Montpellier University Hospital, 34090 Montpellier, France; (P.R.); (L.L.); (N.B.)
| | - Laurence Lachaud
- Mycology and Parasitology Laboratory, Lapeyronie Hospital, Montpellier University Hospital, 34090 Montpellier, France; (P.R.); (L.L.); (N.B.)
- MiVEGEC (Infectious Diseases and Vectors: Ecology, Genetic, Evolution and Control), IRD (Research and Development Institute), CNRS, University of Montpellier, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Nathalie Bourgeois
- Mycology and Parasitology Laboratory, Lapeyronie Hospital, Montpellier University Hospital, 34090 Montpellier, France; (P.R.); (L.L.); (N.B.)
- MiVEGEC (Infectious Diseases and Vectors: Ecology, Genetic, Evolution and Control), IRD (Research and Development Institute), CNRS, University of Montpellier, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Kada Klouche
- Intensive Care Medicine Department, Lapeyronie Hospital, Montpellier University Hospital, 371, Avenue du Doyen Gaston Giraud, 34090 Montpellier, France; (L.P.); (M.A.); (V.B.); (N.B.); (R.B.); (D.D.); (K.K.)
- PhyMedExp, INSERM (French Institute of Health and Medical Research), CNRS (French National Centre for Scientific Research), University of Montpellier, 34090 Montpellier, France
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Saprochaete clavata Infection in Immunosuppressed Patients: Systematic Review of Cases and Report of the First Oral Manifestation, Focusing on Differential Diagnosis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18052385. [PMID: 33804487 PMCID: PMC7957747 DOI: 10.3390/ijerph18052385] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/22/2022]
Abstract
Background: Saprochaete clavata infection is an emerging issue in immunosuppressed patients, causing fulminant fungaemia. The purpose of this systematic review of cases is to retrieve all cases of S. clavata infection and describe oral lesions as the first manifestation of S. clavata infection. Methods: We report the first case of intraoral S. clavata infection in Acute Myeloid Leukemia (AML) affected subject, presenting as multiple grayish rapidly growing ulcerated swellings, and provide a review of all published cases of infection caused by S. clavata, according to PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, conducted by searching SCOPUS, Medline, and CENTRAL databases. Only articles in English were considered. Individual patient data were analyzed to identify risk factors for S. clavata infection. Results: Seventeen of 68 retrieved articles were included in the review reporting data on 96 patients (mean age 51.8 years, 57 males and 38 females). Most cases were disseminated (86) with a 60.2% mortality rate. Ninety-five were hematological patients, with AML being the most common (57 cases). Conclusions:S. clavata infection in immunosuppressed patients has a poor prognosis: middle-age patients, male gender and Acute Myeloid Leukemia should be considered risk factors. In immunosuppressed patients, the clinical presentation can be particularly unusual, imposing difficult differential diagnosis, as in the reported case.
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Development and Analysis of qPCR for the Identification of Arthroconidial Yeasts of the Genus Magnusiomyces. Mycopathologia 2021; 186:41-51. [PMID: 33392857 DOI: 10.1007/s11046-020-00510-4] [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: 10/04/2019] [Accepted: 11/19/2020] [Indexed: 10/20/2022]
Abstract
The arthroconidial yeasts Magnusiomyces capitatus and M. clavatus are emerging opportunistic pulmonary pathogens. They are closely related and difficult to distinguish based on morphological and physiological traits. We applied an SYBR® green-based quantitative PCR (qPCR) assay to identify the species. We analyzed 30 reference strains originating from clinical and environmental sources by targeting the Rpb2 gene encoding the second largest subunit of RNA polymerase II. The qPCR assays were tested by direct identification of M. capitatus and M. clavatus in spiked sputum and household dishwasher swabs, respectively, as models for clinical and environmental samples. The assays were proved to be reliable for species-level identification of both species, with 100% sensitivity and 100% specificity, lowest inter-assay deviations (RSDr ≤ 1.65%, R2 values >0.99), detection limit of 10 theoretical copy number of target DNA, and detection cell limit of ≥5000 yeast cells from spiked sputum samples. The developed qPCR assay is a practical molecular approach for the detection of M. capitatus and M. clavatus that can be used as a stand-alone assay or in conjunction with culture-dependent approaches.
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25
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Abdolrasouli A, Gibani MM, de Groot T, Borman AM, Hoffman P, Azadian BS, Mughal N, Moore LSP, Johnson EM, Meis JF. A pseudo-outbreak of Rhinocladiella similis in a bronchoscopy unit of a tertiary care teaching hospital in London, United Kingdom. Mycoses 2020; 64:394-404. [PMID: 33314345 DOI: 10.1111/myc.13227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 01/15/2023]
Abstract
Outbreaks of fungal infections due to emerging and rare species are increasingly reported in healthcare settings. We investigated a pseudo-outbreak of Rhinocladiella similis in a bronchoscopy unit of a tertiary care teaching hospital in London, UK. We aimed to determine route of healthcare-associated transmission and prevent additional infections. From July 2018 through February 2019, we detected a pseudo-outbreak of R. similis isolated from bronchoalveolar lavage (BAL) fluid samples collected from nine patients who had undergone bronchoscopy in a multispecialty teaching hospital, during a period of 8 months. Isolates were identified by MALDI-TOF mass spectrometry. Antifungal susceptibility testing was performed by EUCAST broth microdilution. To determine genetic relatedness among R. similis isolates, we undertook amplified fragment length polymorphism analysis. To determine the potential source of contamination, an epidemiological investigation was carried out. We reviewed patient records retrospectively and audited steps taken during bronchoscopy as well as the subsequent cleaning and decontamination procedures. Fungal cultures were performed on samples collected from bronchoscopes and automated endoscope washer-disinfector systems. No patient was found to have an infection due to R. similis either before or after bronchoscopy. One bronchoscope was identified to be used among all affected patients with positive fungal cultures. Physical damage was found in the index bronchoscope; however, no fungus was recovered after sampling of the affected scope or the rinse water of automated endoscope washer-disinfectors. Use of the scope was halted, and, during the following 12-month period, Rhinocladiella species were not isolated from any BAL specimen. All pseudo-outbreak isolates were identified as R. similis with high genetic relatedness (>90% similarity) on ALFP analysis. The study emphasises the emergence of a rare and uncommon black yeast R. similis, with reduced susceptibility to echinocandins, in a bronchoscope-related pseudo-outbreak with a potential water-related reservoir. Our findings highlight the importance of prolonged fungal culture and species-level identification of melanised yeasts isolated from bronchoscopy samples. Possibility of healthcare-associated transmission should be considered when R. similis is involved in clinical microbiology samples.
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Affiliation(s)
- Alireza Abdolrasouli
- Department of Medical Microbiology, King's College Hospital NHS Foundation Trust, London, UK.,Department of Infectious Diseases, Imperial College London, London, UK
| | - Malick M Gibani
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital (CWZ), Nijmegen, The Netherlands
| | - Andrew M Borman
- National Mycology Reference Laboratory, Public Health England, Bristol, UK.,Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Peter Hoffman
- HCAI & AMR Division, National Infection Service, Public Health England, London, UK
| | - Berge S Azadian
- Chelsea and Westminster National Health Service (NHS) Foundation Trust, London, UK
| | - Nabeela Mughal
- Department of Infectious Diseases, Imperial College London, London, UK.,Chelsea and Westminster National Health Service (NHS) Foundation Trust, London, UK.,North West London Pathology, Imperial College Healthcare NHS Trust, London, UK
| | - Luke S P Moore
- Department of Infectious Diseases, Imperial College London, London, UK.,Chelsea and Westminster National Health Service (NHS) Foundation Trust, London, UK.,North West London Pathology, Imperial College Healthcare NHS Trust, London, UK
| | - Elizabeth M Johnson
- National Mycology Reference Laboratory, Public Health England, Bristol, UK.,Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital (CWZ), Nijmegen, The Netherlands.,Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná, Curitiba, Brazil.,Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
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Özkaya E, Tosun İ, Tüfekçİ EF, Buruk CK, Kaklıkkaya N, Aydın F. Identification and antifungal susceptibility of Saprochaete clavata from invasive infections in Turkey. Acta Microbiol Immunol Hung 2020; 67:252-257. [PMID: 33258797 DOI: 10.1556/030.2020.01301] [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: 09/20/2020] [Accepted: 10/28/2020] [Indexed: 11/19/2022]
Abstract
Saprochaete clavata is an emerging opportunistic pathogen, that causes life-threatening infections, but there are limited evidence and information about the evaluation of in vitro antifungal susceptibility test results. The aim of this study was to determine S. clavata isolates from clinical specimens and to investigate their in vitro antifungal susceptibility. S. clavata was identified by API ID20C AUX (BioMérieux, Brussels, Belgium), MALDI TOF (Bruker Daltonik, Germany), and ITS gene region sequencing. In vitro susceptibility tests were performed using Sensititre YeastOne (TREK Diagnostic System, East Grinstead, UK). During the study period, 4,736 fungi were isolated from various clinical samples and, S. clavata was identified in eight patients with underlying diseases namely, pancreatic neoplasma, acute myeloid leukaemie, follicular lymphoma, cholelithiasis. Anidulafungin and micafungin minimum inhibitory concentration values were 1-2 and 1-4 mg/L, respectively, while those of the azole group antifungals were much lower. This is the first study in Turkey reporting isolation, identification and antifungal susceptibilities of S. clavata from clinical specimens. Higher MIC values seen in some isolates suggest that continuous monitoring of sensitivity rates and observation of regional differences will thus be useful guides in determining infection control and antifungal use policies.
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Affiliation(s)
- Esra Özkaya
- 1Department of Clinical Microbiology, Karadeniz Technical University School of Medicine, Trabzon, Turkey
| | - İlknur Tosun
- 1Department of Clinical Microbiology, Karadeniz Technical University School of Medicine, Trabzon, Turkey
| | - Enİs Fuat Tüfekçİ
- 2Department of Clinical Microbiology, Kastamonu University School of Medicine, Kastamonu, Turkey
| | - Celal Kurtuluş Buruk
- 1Department of Clinical Microbiology, Karadeniz Technical University School of Medicine, Trabzon, Turkey
| | - Neşe Kaklıkkaya
- 1Department of Clinical Microbiology, Karadeniz Technical University School of Medicine, Trabzon, Turkey
| | - Faruk Aydın
- 1Department of Clinical Microbiology, Karadeniz Technical University School of Medicine, Trabzon, Turkey
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El Zein S, Hindy JR, Kanj SS. Invasive Saprochaete Infections: An Emerging Threat to Immunocompromised Patients. Pathogens 2020; 9:pathogens9110922. [PMID: 33171713 PMCID: PMC7694990 DOI: 10.3390/pathogens9110922] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 12/16/2022] Open
Abstract
Saprochaete clavata and Saprochaete capitata are emerging fungal pathogens that are responsible for life threatening infections in immunocompromised patients, particularly in the setting of profound neutropenia. They have been associated with multiple hospital outbreaks mainly in Europe. In this article, we present a comprehensive review of the epidemiology, clinical presentation, diagnosis, antifungal susceptibility and treatment of these organisms. The diagnosis of invasive Saprochaete disease is challenging and relies primarily on the isolation of the fungi from blood or tissue samples. Both species are frequently misidentified as they are identical macroscopically and microscopically. Internal transcribed spacer sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry are useful tools for the differentiation of these fungi to a species level. Saprochaete spp. are intrinsically resistant to echinocandins and highly resistant to fluconazole. Current literature suggests the use of an amphotericin B formulation with or without flucytosine for the initial treatment of these infections. Treatment with extended spectrum azoles might be promising based on in vitro minimum inhibitory concentration values and results from case reports and case series. Source control and recovery of the immune system are crucial for successful therapy.
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Affiliation(s)
- Said El Zein
- Internal Medicine Department, Wayne State University/Detroit Medical Center, Detroit, MI 48201, USA;
| | - Joya-Rita Hindy
- Division of Infectious Diseases, Internal Medicine Department, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon;
| | - Souha S. Kanj
- Division of Infectious Diseases, Internal Medicine Department, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon;
- Correspondence:
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Vitzilaiou E, Aunsbjerg SD, Mahyudin NA, Knøchel S. Stress Tolerance of Yeasts Dominating Reverse Osmosis Membranes for Whey Water Treatment. Front Microbiol 2020; 11:816. [PMID: 32431679 PMCID: PMC7214788 DOI: 10.3389/fmicb.2020.00816] [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: 12/20/2019] [Accepted: 04/06/2020] [Indexed: 11/13/2022] Open
Abstract
Filamentous yeast species belonging to the closely related Saprochaete clavata and Magnusiomyces spicifer were recently found to dominate biofilm communities on the retentate and permeate surface of Reverse Osmosis (RO) membranes used in a whey water treatment system after CIP (Cleaning-In-Place). Microscopy revealed that the two filamentous yeast species can cover extensive areas due to their large cell size and long hyphae formation. Representative strains from these species were here further characterized and displayed similar physiological and biochemical characteristics. Both strains tested were able to grow in twice RO-filtrated permeate water and metabolize the urea present. Little is known about the survival characteristics of these strains. Here, their tolerance toward heat (60, 70, and 80°C) and Ultraviolet light (UV-C) treatment at 255 nm using UV-LED was assessed as well as their ability to form biofilm and withstand cleaning associated stress. According to the heat tolerance experiments, the D60°C of S. clavata and M. spicifer is 16.37 min and 7.24 min, respectively, while a reduction of 3.5 to >4.5 log (CFU/mL) was ensured within 5 min at 70°C. UV-C light at a dose level 10 mJ/cm2 had little effect, while doses of 40 mJ/cm2 and upward ensured a ≥4log reduction in a static laboratory scale set-up. The biofilm forming potential of one filamentous yeast and one budding yeast, Sporopachydermia lactativora, both isolated from the same biofilm, was compared in assays employing flat-bottomed polystyrene microwells and peg lids, respectively. In these systems, employing both nutrient rich as well as nutrient poor media, only the filamentous yeast was able to create biofilm. However, on RO membrane coupons in static systems, both the budding yeast and a filamentous yeast were capable of forming single strain biofilms and when these coupons were exposed to different simulations of CIP treatments both the filamentous and budding yeast survived these. The dominance of these yeasts in some filter systems tested, their capacity to adhere and their tolerance toward relevant stresses as demonstrated here, suggest that these slow growing yeasts are well suited to initiate microbial biofouling on surfaces in low nutrient environments.
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Affiliation(s)
- Eirini Vitzilaiou
- Laboratory of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Stina D. Aunsbjerg
- Laboratory of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - N. A. Mahyudin
- Department of Food Service and Management, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Malaysia
| | - Susanne Knøchel
- Laboratory of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Copenhagen, Denmark
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Alp S, Gulmez D, Ayaz CM, Arikan-Akdagli S, Akova M. Fungaemia due to rare yeasts in a tertiary care university centre within 18 years. Mycoses 2020; 63:488-493. [PMID: 32145101 DOI: 10.1111/myc.13072] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/19/2020] [Accepted: 02/26/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Fungaemia due to rare yeasts has been recognised as an emerging, clinically relevant, but less investigated condition. Intrinsic resistance or reduced susceptibility of these species to echinocandins or fluconazole remains as a challenge in empirical treatment. OBJECTIVES To describe the clinical characteristics, administered antifungal agents, outcomes of patients with rare yeasts other than Candida (RY-OTC) fungaemia and determine the antifungal susceptibility profiles of the isolates. PATIENTS AND METHODS RY-OTC fungaemia between January-2001 and December-2018 were retrospectively evaluated. Antifungal susceptibility tests were performed according to CLSI M27-A3. RESULTS We identified 19 patients with fungaemia due to 20 RY-OTC (8 Trichosporon asahii, 4 Cryptococcus neoformans, 4 Saprochaete capitata, 3 Rhodotorula mucilaginosa, 1 Trichosporon mucoides) with an incidence of 2.2% among 859 fungaemia episodes. Haematological malignancy was the most common (42%) underlying disorder. In 6 patients, RY-OTC fungaemia developed as breakthrough infection while receiving echinocandins, amphotericin B or fluconazole. Amphotericin B, fluconazole or voriconazole were the drugs of choice for the initial treatment of breakthrough fungaemia. Among patients without previous exposure to antifungals, the most common empirical treatment was an echinocandin (50%), followed by fluconazole (42%) and amphotericin B (8%). Overall mortality was 47%. Worse outcome was most common among patients receiving echinocandins (83% vs 25%, P < .05). Voriconazole and posaconazole showed the highest in vitro activity against all the isolates tested. Amphotericin B MICs were relatively higher and the degree of activity of fluconazole and itraconazole was variable. CONCLUSIONS Early recognition of RY-OTC and knowledge about their susceptibility patterns remain crucial in initial treatment pending susceptibility data of isolates.
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Affiliation(s)
- Sehnaz Alp
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Dolunay Gulmez
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Caglayan Merve Ayaz
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Sevtap Arikan-Akdagli
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Murat Akova
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
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Lo Cascio G, Vincenzi M, Soldani F, De Carolis E, Maccacaro L, Sorrentino A, Nadali G, Cesaro S, Sommavilla M, Niero V, Naso L, Grancini A, Azzini AM, Sanguinetti M, Tacconelli E, Cornaglia G. Outbreak of Saprochaete clavata Sepsis in Hematology Patients: Combined Use of MALDI-TOF and Sequencing Strategy to Identify and Correlate the Episodes. Front Microbiol 2020; 11:84. [PMID: 32082293 PMCID: PMC7004961 DOI: 10.3389/fmicb.2020.00084] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
Introduction New fungal species are increasingly reported in immunocompromised patients. Saprochaete clavata (S. clavata), an ascomycetous fungus formerly called Geotrichum clavatum, is intrinsically resistant to echinocandins and is often misidentified. Objective We describe a cluster of seven S. clavata infections in hospitalized hematology patients who developed this rare fungemia within a span of 11 months. Three of the seven patients died. Identification of the isolates was determined only with the Saramis database of VitekMS system and sequencing of the internal transcribed spacer (ITS) region. Clonal relatedness of the isolates was determined by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF) analysis; clonal correlation between the strains was investigated by means of phylogenetic analysis, based on single-nucleotide variants (SNPs). Clinical presentation, 1–3 β-D-glucan (BG) and galactomannan (GM) antigen results and analysis of possible sources of contamination are also described with a prospective case–control study of the outbreak. Results MALDI-TOF MS-Vitek (bioMerieux, Marcy l’Etoile, France) failed to identify the six isolates, while SARAMIS (bioMerieux, Marcy l’Etoile, France) identified the isolates as S. clavata. Initially, Vitek 2 identified the strains as Geotrichum capitatum in two of the seven cases. Molecular identification gave 99% homology with S. clavata. BG was positive in three out of six patients (range 159 to >523 pg/ml), GM results were always negative. All the isolates were resistant to echinocandins (anidulafungin, micafungin, and caspofungin) and Fluconazole, but susceptible to Flucytosine and Voriconazole. One isolate showed acquired resistance to Flucytosine and Amphotericin B during treatment. Both the correlation-based dendrograms obtained by MALDI-TOF MS (Bruker Daltonics) and MS-Vitek not only clustered six of the seven bloodstream infection (BSI) isolates in the same group, but also showed their strong relatedness. Phylogenetic analysis using SNPrelate showed that the seven samples recorded during the investigation period clustered together. We observed a split between one case and the remainder with a node supported by a z-score of 2.3 (p-value = 0.021) and 16 mutations unique to each branch. Conclusion The use of proteomics for identification and evaluation of strain clonality in outbreaks of rare pathogens is a promising alternative to laborious and time-consuming molecular methods, even if molecular whole-genome sequencing (WGS) typing will still remain the reference method for rare emergent pathogens.
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Affiliation(s)
- Giuliana Lo Cascio
- Microbiology and Virology Unit, Department of Pathology, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Marcello Vincenzi
- Infectious Disease Unit, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Fabio Soldani
- Infectious Disease Unit, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Elena De Carolis
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Laura Maccacaro
- Microbiology and Virology Unit, Department of Pathology, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Annarita Sorrentino
- Microbiology and Virology Unit, Department of Pathology, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Gianpaolo Nadali
- Haematology Unit, Department of Medicine, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Simone Cesaro
- Division of Pediatric Oncohaematology, Department of Pediatrics, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Michele Sommavilla
- Direzione Medica Ospedaliera, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Valentina Niero
- Sezione di Igiene e Medicina Preventiva, Ambientale e Occupazionale, Dipartimento Diagnostica e Sanità Pubblica, Università di Verona, Verona, Italy
| | - Laura Naso
- Microbiology and Virology Unit, Department of Pathology, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Anna Grancini
- Laboratorio di Analisi Chimico - Cliniche e Microbiologia, Fondazione IRCCS Cà Granda O. Maggiore Policlinico, Milan, Italy
| | - Anna Maria Azzini
- Infectious Disease Unit, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - E Tacconelli
- Infectious Disease Unit, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Giuseppe Cornaglia
- Microbiology and Virology Unit, Department of Pathology, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
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Esposto MC, Prigitano A, Lo Cascio G, Ossi C, Grancini A, Cavanna C, Lallitto F, Tejada M, Bandettini R, Mularoni A, Tortorano AM. Yeast-like filamentous fungi: Molecular identification and in vitro susceptibility study. Med Mycol 2020; 57:909-913. [PMID: 30521007 DOI: 10.1093/mmy/myy133] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/20/2018] [Accepted: 11/07/2018] [Indexed: 11/14/2022] Open
Abstract
Yeast-like filamentous fungi, collected in Italy from 1985 to 2018, were submitted to molecular identification and antifungal susceptibility testings. Clinical isolates were identified as Magnusiomyces capitatus (28), M. clavatus (18), and Geotrichum candidum (2). M. clavatus was prevalent among blood isolates (18/24), M. capitatus among isolates from other biological materials. The intrinsic echinocandin resistance was confirmed. Both species had low minimum inhibitory concentrations (MICs) of itraconazole, posaconazole, and voriconazole, while M. clavatus had lower MIC of flucytosine and higher MIC of isavuconazole than M. capitatus. The intrinsic resistance of these species to echinocandins could be the reason of the recent increase of M. clavatus bloodstream infections.
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Affiliation(s)
| | - Anna Prigitano
- Department of Biomedical Sciences for Health, Università degli Studi di Milano
| | | | - Cristina Ossi
- Laboratory Medicine Service, Ospedale San Raffaele, Milano
| | - Anna Grancini
- IRCCS Foundation, Cà Granda Ospedale Maggiore Policlinico, Milano
| | - Caterina Cavanna
- Microbiology and Virology Unit, IRCCS San Matteo Hospital Foundation, Pavia
| | - Fabiola Lallitto
- Microbiology and Virology Unit, IRCCS San Matteo Hospital Foundation, Pavia
| | | | - Roberto Bandettini
- Clinical Pathology and Microbiology Laboratory Unit, Istituto Giannina Gaslini, Genova
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32
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Wee LWY, Ling HY, Chong CY, Soe MN, Koh MJA. A rare case of purpuric rash caused by Saprochaete clavata in a pediatric patient with acute leukemia. Pediatr Dermatol 2019; 36:990-991. [PMID: 31423625 DOI: 10.1111/pde.13963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a 13-year-old boy who developed invasive infection with Saprochaete clavata after induction chemotherapy for B-cell acute lymphoblastic leukemia, complicated by fungemia, septic shock and acute renal, and liver failure. He developed purpuric papulonodules over bilateral upper and lower limbs, which also grew S clavata on fungal culture.
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Affiliation(s)
- Lynette Wei Yi Wee
- Dermatology Service, KK Women's and Children's Hospital, Singapore City, Singapore
| | - Hua Yen Ling
- Dermatology Service, KK Women's and Children's Hospital, Singapore City, Singapore
| | - Chia Yin Chong
- Infectious Disease Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore City, Singapore
| | - Mya Nwe Soe
- Haematology and Oncology Service, Department of Paediatric Subspecialties, KK Women's and Children's Hospital, Singapore City, Singapore
| | - Mark Jean Aan Koh
- Dermatology Service, KK Women's and Children's Hospital, Singapore City, Singapore
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Buchta V, Bolehovská R, Hovorková E, Cornely OA, Seidel D, Žák P. Saprochaete clavata Invasive Infections - A New Threat to Hematological-Oncological Patients. Front Microbiol 2019; 10:2196. [PMID: 31736883 PMCID: PMC6830389 DOI: 10.3389/fmicb.2019.02196] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/09/2019] [Indexed: 12/17/2022] Open
Abstract
Background Saprochaete clavata (formerly Geotrichum clavatum, now proposed as Magnusiomyces clavatus) is a filamentous yeast-like fungus that has recently been described as an emerging pathogen mostly in patients with acute leukemia. Methods This is a retrospective study of patients diagnosed with proven and probable S. clavata infection at the University Hospital, Hradec Králové, Czechia between March 2005 and December 2017. Previous cases were identified from the literature and FungiScope® database. Results Six new cases (5 females, 1 male) of blood-stream S. clavata infections at the hemato-oncological department were described including epidemiological data of additional 48 patients colonized with the species. Overall, 116 strains of S. clavata were isolated from different clinical specimens of 54 patients; most of them belonged to the respiratory tract (60.3%). S. clavata was the most frequent species among arthroconidial yeasts (Trichosporon, Galactomyces, Magnusiomyces) recovered from the blood. All our patients with S. clavata infection had profound neutropenia, a central venous catheter, broad-spectrum antibiotics and antifungal prophylaxis; four had a history of a biliary tract system disease. The diagnosis was based on a positive blood culture in all patients. Four patients died of multiorgan failure and sepsis despite treatment with lipid-based amphotericin B and/or voriconazole. From the literature and FungiScope database, 67 previous cases of S. clavata infections were evaluated in context of our cases. Conclusion Saprochaete clavata infection represents a life-threatening mycosis in severely immunocompromised patients. The successful outcome of treatment seems to be critically dependent on the early diagnosis and the recovery of underlying conditions associated with immune dysfunction or deficiency.
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Affiliation(s)
- Vladimir Buchta
- Department of Clinical Microbiology, Faculty of Medicine in Hradec Králové, Faculty Hospital in Hradec Králové, Charles University in Prague, Hradec Králové, Czechia
| | - Radka Bolehovská
- Department of Clinical Biochemistry and Diagnostics, Faculty of Medicine in Hradec Králové, Faculty Hospital in Hradec Králové, Charles University in Prague, Hradec Králové, Czechia
| | - Eva Hovorková
- The Fingerland Department of Pathology, Faculty of Medicine in Hradec Králové, Faculty Hospital in Hradec Králové, Charles University in Prague, Hradec Králové, Czechia
| | - Oliver A Cornely
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Department I of Internal Medicine, ECMM Diamond Center of Excellence in Medical Mycology, German Centre for Infection Research (DZIF), University of Cologne, Cologne, Germany.,Clinical Trials Centre Cologne (ZKS Köln), University of Cologne, Cologne, Germany
| | - Danila Seidel
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Department of Internal Medicine, ECMM Diamond Center of Excellence in Medical Mycology, University of Cologne, Cologne, Germany
| | - Pavel Žák
- 4th Department of Internal Medicine - Division of Hematology, Faculty of Medicine in Hradec Králové, Faculty Hospital in Hradec Králové, Charles University in Prague, Hradec Králové, Czechia
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Chang CC, Levitz SM. Fungal immunology in clinical practice: Magical realism or practical reality? Med Mycol 2019; 57:S294-S306. [PMID: 31292656 DOI: 10.1093/mmy/myy165] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/21/2018] [Accepted: 01/28/2019] [Indexed: 12/15/2022] Open
Abstract
Invasive fungal infections (IFIs) occur predominantly in immunocompromised individuals but can also be seen in previously well persons. The human innate immune system recognizes key components of the fungal cell wall as foreign resulting in a myriad of signaling cascades. This triggers release of antifungal molecules as well as adaptive immune responses, which kill or at least contain the invading fungi. However, these defences may fail in hosts with primary or secondary immunodeficiencies resulting in IFIs. Knowledge of a patient's immune status enables the clinician to predict the fungal infections most likely to occur. Moreover, the occurrence of an opportunistic mycosis in a patient without known immunocompromise usually should prompt a search for an occult immune defect. A rapidly expanding number of primary and secondary immunodeficiencies associated with mycoses has been identified. An investigative approach to determining the nature of these immunodeficiencies is suggested to help guide clinicians encountering patients with IFI. Finally, promising adjunctive immunotherapy measures are currently being investigated in IFI.
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Affiliation(s)
- Christina C Chang
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Stuart M Levitz
- Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, Massachusetts, United States
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Stanzani M, Cricca M, Sassi C, Sutto E, De Cicco G, Bonifazi F, Bertuzzi C, Bacci F, Paolini S, Cavo M, Lewis RE. Saprochaete clavata infections in patients undergoing treatment for haematological malignancies: A report of a monocentric outbreak and review of the literature. Mycoses 2019; 62:1100-1107. [PMID: 31365161 DOI: 10.1111/myc.12978] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 11/29/2022]
Abstract
Saprochaete clavata is a rare cause of fungaemia with deep organ involvement in patients with haematological malignancies with reported mortality rates of 60%-80%. We describe four cases of S clavata infection in a haematology unit over several months that were treated with voriconazole-based regimens. We also review the literature on factors that could contribute to earlier recognition and effective treatment of S clavata. We included all cases of culture-positive S clavata from sterile sites with associated signs of infection in patients undergoing treatment for a haematological malignancy. Isolates were identified by MALDI-TOF MS, and spectrum profiles were used to prepare clustering analysis of isolates. Susceptibility testing was performed using a commercial microtitre methods. Saprochaete clavata was isolated from the bloodstream in three cases and bronchial alveolar lavage (BAL) fluid in one case. Clustering analysis suggested strains of S clavata were clonal without evidence of divergence although a common source was not identified. Susceptibility testing yielded elevated MICs to fluconazole (8 mg/L) and echinocandins (>1-8 mg/L). All patients were treated with voriconazole-based regimens resulting in survival of 3/4 patients, who continued chemotherapy for their underlying malignancy without evidence of relapse. Saprochaete clavata is a rare but aggressive cause of breakthrough yeast infection in patients undergoing treatment for haematological malignancies, particularly patients with a prior history of echinocandin treatment. Timely initiation of appropriate treatment, aided by more rapid identification in microbiology laboratory, can reduce the risk of deep organ dissemination and patient death.
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Affiliation(s)
- Marta Stanzani
- Department of Hematology and Oncology, Seràgnoli Institute of Hematology and Clinical Oncology, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Monica Cricca
- Unit of Microbiology, Department of Experimental, Diagnostic and Specialty Medicine, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Claudia Sassi
- Unit of Radiology, Department of Experimental, Scientific and Specialty Medicine, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Emanuele Sutto
- Department of Hematology and Oncology, Seràgnoli Institute of Hematology and Clinical Oncology, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Gabriella De Cicco
- Department of Hematology and Oncology, Seràgnoli Institute of Hematology and Clinical Oncology, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Francesca Bonifazi
- Department of Hematology and Oncology, Seràgnoli Institute of Hematology and Clinical Oncology, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Clara Bertuzzi
- Unit of Hemolymph-Pathology, Department of Hematology and Oncology, Seràgnoli Institute of Hematology and Clinical Oncology, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Francesco Bacci
- Unit of Hemolymph-Pathology, Department of Hematology and Oncology, Seràgnoli Institute of Hematology and Clinical Oncology, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Stefania Paolini
- Department of Hematology and Oncology, Seràgnoli Institute of Hematology and Clinical Oncology, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Michele Cavo
- Department of Hematology and Oncology, Seràgnoli Institute of Hematology and Clinical Oncology, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Russell E Lewis
- Unit of Infectious Diseases, Department of Medical and Surgical Sciences, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
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36
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Microbial biofilm communities on Reverse Osmosis membranes in whey water processing before and after cleaning. J Memb Sci 2019. [DOI: 10.1016/j.memsci.2019.117174] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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37
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Marek C, Croxen MA, Dingle TC, Bharat A, Schwartz IS, Wiens R, Smith S. The use of genome sequencing to investigate an outbreak of hospital‐acquired mucormycosis in transplant patients. Transpl Infect Dis 2019; 21:e13163. [DOI: 10.1111/tid.13163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/29/2019] [Accepted: 08/23/2019] [Indexed: 11/27/2022]
Affiliation(s)
| | - Matthew A. Croxen
- University of Alberta Edmonton AB Canada
- Public Health Laboratory Edmonton AB Canada
| | - Tanis C. Dingle
- University of Alberta Edmonton AB Canada
- Public Health Laboratory Edmonton AB Canada
| | - Amrita Bharat
- National Microbiology Laboratory Public Health Agency of Canada Winnipeg MB Canada
| | | | - Rhoda Wiens
- Alberta Health Services University of Alberta Edmonton AB Canada
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Studying fungal pathogens of humans and fungal infections: fungal diversity and diversity of approaches. Microbes Infect 2019; 21:237-245. [PMID: 31255676 DOI: 10.1016/j.micinf.2019.06.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 04/15/2019] [Indexed: 12/26/2022]
Abstract
Seminal work by Louis Pasteur revealed the contribution of fungi - yeasts and microsporidia to agroindustry and disease in animals, respectively. More than 150 years later, the impact of fungi on human health and beyond is an ever-increasing issue, although often underestimated. Recent studies estimate that fungal infections, especially those caused by Candida, Cryptococcus and Aspergillus species, kill more than one million people annually. Indeed, these neglected infections are in general very difficult to cure and the associated mortality remains very high even when antifungal treatments exist. The development of new antifungals and diagnostic tools that are both necessary to fight fungal diseases efficiently, requires greater insights in the biology of the fungal pathogens of humans in the context of the infection, on their epidemiology, and on their role in the human mycobiota. We also need a better understanding of the host immune responses to fungal pathogens as well as the genetic basis for the increased sensitivity of some individuals to fungal infections. Here, we highlight some recent progress made in these different areas of research, in particular based on work conducted in our own laboratories. These progresses should lay the ground for better management of fungal infections, as they provide opportunities for better diagnostic, vaccination, the development of classical antifungals but also strategies for targeting virulence factors or the host.
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39
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Pavone P, Oliva A, Raponi G, Pugliese F, Martelli S, Celli P, Sacco F, Vullo V, Mastroianni CM, Russo G. Disseminated fungal infection due to Saprochaete clavata in a kidney transplant recipient. J Mycol Med 2019; 29:278-281. [PMID: 31202517 DOI: 10.1016/j.mycmed.2019.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/24/2019] [Accepted: 06/04/2019] [Indexed: 10/26/2022]
Abstract
Saprochaete clavata and Saprochaete capitata are closely related fungal species (family Dipodascaceae, order Saccharomycetales) that are rarely involved in the etiology of systemic infections in humans. In recent years, these yeasts are emerging as cause of life-threatening infections in patients with severe neutropenia and haematological malignancies. Infections by these fungi have been reported mostly from Mediterranean countries. To the best of our knowledge, only 2 cases of infection due to S. capitata have been reported in solid organ transplant recipients and none due to S. clavata. Herein we report a fatal case of S. clavata disseminated infection occurring in a patient with recent kidney transplantation and severe neutropenia. Patient was receiving antifungal echinocandin prophylaxis and the yeast was isolated from the blood and multiple non contiguous sites. Saprochaete spp. should be considered in the differential diagnosis of invasive mycoses in transplant recipients, especially if they are neutropenic and living or travelling in Mediterranean countries.
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Affiliation(s)
- P Pavone
- Public Health and Infectious Diseases Department, Sapienza University of Rome, Rome, Italy.
| | - A Oliva
- Public Health and Infectious Diseases Department, Sapienza University of Rome, Rome, Italy
| | - G Raponi
- Public Health and Infectious Diseases Department, Sapienza University of Rome, Rome, Italy
| | - F Pugliese
- Department of Anaesthesiology, Critical Care Medicine and Pain Therapy, Sapienza University of Rome, Rome, Italy
| | - S Martelli
- Department of Anaesthesiology, Critical Care Medicine and Pain Therapy, Sapienza University of Rome, Rome, Italy
| | - P Celli
- Department of Anaesthesiology, Critical Care Medicine and Pain Therapy, Sapienza University of Rome, Rome, Italy
| | - F Sacco
- Public Health and Infectious Diseases Department, Sapienza University of Rome, Rome, Italy
| | - V Vullo
- Public Health and Infectious Diseases Department, Sapienza University of Rome, Rome, Italy
| | - C M Mastroianni
- Public Health and Infectious Diseases Department, Sapienza University of Rome, Rome, Italy
| | - G Russo
- Public Health and Infectious Diseases Department, Sapienza University of Rome, Rome, Italy
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40
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Studying fungal pathogens of humans and fungal infections: fungal diversity and diversity of approaches. Genes Immun 2019; 20:403-414. [PMID: 31019254 DOI: 10.1038/s41435-019-0071-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 04/15/2019] [Indexed: 12/24/2022]
Abstract
Seminal work by Louis Pasteur revealed the contribution of fungi-yeasts and microsporidia to agroindustry and disease in animals, respectively. More than 150 years later, the impact of fungi on human health and beyond is an ever-increasing issue, although often underestimated. Recent studies estimate that fungal infections, especially those caused by Candida, Cryptococcus and Aspergillus species, kill more than one million people annually. Indeed, these neglected infections are in general very difficult to cure and the associated mortality remains very high even when antifungal treatments exist. The development of new antifungals and diagnostic tools that are both necessary to fight fungal diseases efficiently, requires greater insights in the biology of the fungal pathogens of humans in the context of the infection, on their epidemiology, and on their role in the human mycobiota. We also need a better understanding of the host immune responses to fungal pathogens as well as the genetic basis for the increased sensitivity of some individuals to fungal infections. Here, we highlight some recent progress made in these different areas of research, in particular based on work conducted in our own laboratories. These progress should lay the ground for better management of fungal infections, as they provide opportunities for better diagnostic, vaccination, the development of classical antifungals but also strategies for targeting virulence factors or the host.
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Leoni M, Riccardi N, Rotulo GA, Godano E, Faraci M, Bandettini R, Esposto MC, Castagnola E. Magnusiomyces clavatus infection in a child after allogeneic hematotopoetic stem cell transplantation: Diagnostic and therapeutic implications. Med Mycol Case Rep 2018; 23:65-67. [PMID: 30656133 PMCID: PMC6329693 DOI: 10.1016/j.mmcr.2018.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/15/2018] [Accepted: 12/20/2018] [Indexed: 01/06/2023] Open
Abstract
Magnusiomyces clavatus is an ascomycetous fungus causing invasive disease in immuno-compromised patients. Neutropenia, contaminated venous catheters, previous antifungal treatment are risk factors for this infection. We report a case of Magnusiomyces clavatus fungemia with pulmonary, renal and skin localizations in a 6-year-old boy with prolonged neutropenia because of three allogeneic hematopoietic stem cell transplantations. The infection was controlled by aggressive and strictly monitored combination therapy with voriconazole and liposomial-ampthotericine-B along with durable recover from neutropenia.
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Affiliation(s)
- Massimiliano Leoni
- Hematopoietic Stem Cell Transplantation Unit, IRCCS G Gaslini, via Gaslini 5, 16147 Genova, Italy
| | - Niccolò Riccardi
- Clinic of Infectious Diseases, Policlinico San Martino Hospital, University of Genoa, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | | | - Elisabetta Godano
- Pediatric Department, IRCCS Istituto Giannina Gaslini, Via Gaslini 5, 16147 Genova, Italy
| | - Maura Faraci
- Hematopoietic Stem Cell Transplantation Unit, IRCCS G Gaslini, via Gaslini 5, 16147 Genova, Italy
| | - Roberto Bandettini
- Laboratory of Microbiology, IRCCS Istituto Giannina Gaslini, Via Gaslini 5, 16147 Genova, Italy
| | - Maria Carmela Esposto
- Biomedical Sciences for Health Unit, University of Milan, Via Pascal 36, 20133 Milano, Italy
| | - Elio Castagnola
- Infectious Disease Unit, IRCCS Istituto Giannina Gaslini, Via Gaslini 5, 16147 Genova, Italy
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Salgüero Fernández I, Nájera Botello L, Orden Martinez B, Roustan Gullón G. Disseminated fungemia by Saprochaete clavata. Enferm Infecc Microbiol Clin 2018; 37:283-284. [PMID: 29908750 DOI: 10.1016/j.eimc.2018.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 12/01/2022]
Affiliation(s)
| | - Laura Nájera Botello
- Servicio de Anatomía Patológica, Hospital Puerta de Hierro, Majadahonda, Madrid, España
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Outbreak of Invasive Wound Mucormycosis in a Burn Unit Due to Multiple Strains of Mucor circinelloides f. circinelloides Resolved by Whole-Genome Sequencing. mBio 2018; 9:mBio.00573-18. [PMID: 29691339 PMCID: PMC5915733 DOI: 10.1128/mbio.00573-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Mucorales are ubiquitous environmental molds responsible for mucormycosis in diabetic, immunocompromised, and severely burned patients. Small outbreaks of invasive wound mucormycosis (IWM) have already been reported in burn units without extensive microbiological investigations. We faced an outbreak of IWM in our center and investigated the clinical isolates with whole-genome sequencing (WGS) analysis. We analyzed M. circinelloides isolates from patients in our burn unit (BU1, Hôpital Saint-Louis, Paris, France) together with nonoutbreak isolates from Burn Unit 2 (BU2, Paris area) and from France over a 2-year period (2013 to 2015). A total of 21 isolates, including 14 isolates from six BU1 patients, were analyzed by whole-genome sequencing (WGS). Phylogenetic classification based on de novo assembly and assembly free approaches showed that the clinical isolates clustered in four highly divergent clades. Clade 1 contained at least one of the strains from the six epidemiologically linked BU1 patients. The clinical isolates were specific to each patient. Two patients were infected with more than two strains from different clades, suggesting that an environmental reservoir of clonally unrelated isolates was the source of contamination. Only two patients from BU1 shared one strain, which could correspond to direct transmission or contamination with the same environmental source. In conclusion, WGS of several isolates per patients coupled with precise epidemiological data revealed a complex situation combining potential cross-transmission between patients and multiple contaminations with a heterogeneous pool of strains from a cryptic environmental reservoir. Invasive wound mucormycosis (IWM) is a severe infection due to environmental molds belonging to the order Mucorales. Severely burned patients are particularly at risk for IWM. Here, we used whole-genome sequencing (WGS) analysis to resolve an outbreak of IWM due to Mucor circinelloides that occurred in our hospital (BU1). We sequenced 21 clinical isolates, including 14 from BU1 and 7 unrelated isolates, and compared them to the reference genome (1006PhL). This analysis revealed that the outbreak was mainly due to multiple strains that seemed patient specific, suggesting that the patients were more likely infected from a pool of diverse strains from the environment rather than from direct transmission among them. This study revealed the complexity of a Mucorales outbreak in the settings of IWM in burn patients, which has been highlighted based on WGS combined with careful sampling.
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Bougnoux ME, Brun S, Zahar JR. Healthcare-associated fungal outbreaks: New and uncommon species, New molecular tools for investigation and prevention. Antimicrob Resist Infect Control 2018; 7:45. [PMID: 29599969 PMCID: PMC5870726 DOI: 10.1186/s13756-018-0338-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/21/2018] [Indexed: 11/10/2022] Open
Abstract
Outbreaks of healthcare-associated fungal infections have repeatedly been described over recent years, often caused by new or uncommon species. Candida auris, a recently described multidrug-resistant yeast species, is certainly the most worrisome species having caused several severe healthcare outbreaks of invasive infections, on four continents. Also, large nosocomial outbreaks due to uncommon fungal species such as Exserohilum rostratum and Sarocladium kiliense, were both linked to contamination of medical products, however the source of another outbreak, caused by Saprochaete clavata, remains unresolved. Furthermore, these outbreaks identified new populations under threat in addition to those commonly at risk for invasive fungal infections, such as immunosuppressed and intensive care unit patients. All of these outbreaks have highlighted the usefulness of a high level of awareness, rapid diagnostic methods, and new molecular typing tools such as Whole Genome Sequencing (WGS), prompt investigation and aggressive interventions, including notification of public health agencies. This review summarizes the epidemiological and clinical data of the majority of healthcare-associated outbreaks reported over the last 6 years caused by uncommon or new fungal pathogens, as well as the contribution of WGS as support to investigate the source of infection and the most frequent control measures used.
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Affiliation(s)
- Marie-Elisabeth Bougnoux
- 1Unité de Parasitologie-Mycologie, Service de Microbiologie clinique, Hôpital Necker Enfants-Malades, Assistance Publique - Hôpitaux de Paris (APHP), Paris, France.,2Université Paris Descartes, Sorbonne Paris-Cité, Paris, France.,3Département Mycologie, Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Sophie Brun
- 4Service de Parasitologie-Mycologie, Hôpital Avicenne, Groupe Hospitalier Paris-Seine-Saint-Denis, Assistance Publique - Hôpitaux de Paris (APHP), Bobigny, France.,5Université Paris 13, Bobigny, France
| | - Jean-Ralph Zahar
- 6Département de microbiologie clinique, unité de contrôle et de prévention du risque infectieux, Hôpital Avicenne, Groupe Hospitalier Paris-Seine-Saint-Denis, Assistance Publique - Hôpitaux de Paris (APHP), Bobigny, France.,7IAME, UMR 1137, Université Paris 13, Sorbonne Paris Cité, Paris, France
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Molecular Diagnostics of Arthroconidial Yeasts, Frequent Pulmonary Opportunists. J Clin Microbiol 2017; 56:JCM.01427-17. [PMID: 29070656 DOI: 10.1128/jcm.01427-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 10/18/2017] [Indexed: 02/02/2023] Open
Abstract
Magnusiomyces capitatus and Saprochaete clavata are members of the clade of arthroconidial yeasts that represent emerging opportunistic pulmonary pathogens in immunocompromised patients. Given that standard ribosomal DNA (rDNA) identification often provides confusing results, in this study, we analyzed 34 isolates with the goal of finding new genetic markers for classification using multilocus sequencing and amplified fragment length polymorphism (AFLP). The interspecific similarity obtained using rDNA markers (the internal transcribed spacer [ITS] and large subunit regions) was in the range of 96 to 99%, whereas that obtained using protein-coding loci (Rbp2, Act, and Tef1α) was lower at 89.4 to 95.2%. Ultimately, Rbp2 was selected as the best marker for species distinction. On the basis of cloned ITS data, some strains proved to be misidentified in comparison with the identities obtained with phenotypic characters, protein sequences, and AFLP profiles, indicating that different copies of the ribosomal operon were present in a single species. Antifungal susceptibility testing revealed that voriconazole had the lowest MIC against M. capitatus, while amphotericin B had the lowest MIC against S. clavata Both species exhibited in vitro resistance to fluconazole and micafungin.
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Investigating Clinical Issues by Genotyping of Medically Important Fungi: Why and How? Clin Microbiol Rev 2017; 30:671-707. [PMID: 28490578 DOI: 10.1128/cmr.00043-16] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genotyping studies of medically important fungi have addressed elucidation of outbreaks, nosocomial transmissions, infection routes, and genotype-phenotype correlations, of which secondary resistance has been most intensively investigated. Two methods have emerged because of their high discriminatory power and reproducibility: multilocus sequence typing (MLST) and microsatellite length polymorphism (MLP) using short tandem repeat (STR) markers. MLST relies on single-nucleotide polymorphisms within the coding regions of housekeeping genes. STR polymorphisms are based on the number of repeats of short DNA fragments, mostly outside coding regions, and thus are expected to be more polymorphic and more rapidly evolving than MLST markers. There is no consensus on a universal typing system. Either one or both of these approaches are now available for Candida spp., Aspergillus spp., Fusarium spp., Scedosporium spp., Cryptococcus neoformans, Pneumocystis jirovecii, and endemic mycoses. The choice of the method and the number of loci to be tested depend on the clinical question being addressed. Next-generation sequencing is becoming the most appropriate method for fungi with no MLP or MLST typing available. Whatever the molecular tool used, collection of clinical data (e.g., time of hospitalization and sharing of similar rooms) is mandatory for investigating outbreaks and nosocomial transmission.
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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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Sekse C, Holst-Jensen A, Dobrindt U, Johannessen GS, Li W, Spilsberg B, Shi J. High Throughput Sequencing for Detection of Foodborne Pathogens. Front Microbiol 2017; 8:2029. [PMID: 29104564 PMCID: PMC5655695 DOI: 10.3389/fmicb.2017.02029] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/04/2017] [Indexed: 12/23/2022] Open
Abstract
High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data. The influence of sample processing, nucleic acid extraction and purification, harmonized protocols for generation and interpretation of data, and properly annotated and curated reference databases including non-pathogenic "natural" strains are other major obstacles to the realization of the full potential of HTS in analytical food surveillance, epidemiological and outbreak investigations, and in complementing preventive approaches for the control and management of foodborne pathogens. Despite significant obstacles, the achieved progress in capacity and broadening of the application range over the last decade is impressive and unprecedented, as illustrated with the chosen examples from the literature. Large consortia, often with broad international participation, are making coordinated efforts to cope with many of the mentioned obstacles. Further rapid progress can therefore be prospected for the next decade.
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Affiliation(s)
- Camilla Sekse
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Arne Holst-Jensen
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Gro S. Johannessen
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Weihua Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Bjørn Spilsberg
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Oslo, Norway
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Byrne DD, Reboli AC. Rare Yeast Infections: Risk Factors, Clinical Manifestations, Treatment, and Special Considerations. CURRENT CLINICAL MICROBIOLOGY REPORTS 2017. [DOI: 10.1007/s40588-017-0073-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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50
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Yeasts. Microbiol Spectr 2017; 4. [PMID: 27726781 DOI: 10.1128/microbiolspec.dmih2-0030-2016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yeasts are unicellular organisms that reproduce mostly by budding and less often by fission. Most medically important yeasts originate from Ascomycota or Basidiomycota. Here, we review taxonomy, epidemiology, disease spectrum, antifungal drug susceptibility patterns of medically important yeast, laboratory diagnosis, and diagnostic strategies.
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