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Francisco EC, Desnos-Ollivier M, Dieleman C, Boekhout T, Santos DWDCL, Medina-Pestana JO, Colombo AL, Hagen F. Unveiling Trichosporon austroamericanum sp. nov.: A Novel Emerging Opportunistic Basidiomycetous Yeast Species. Mycopathologia 2024; 189:43. [PMID: 38709328 PMCID: PMC11074034 DOI: 10.1007/s11046-024-00851-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/27/2024] [Indexed: 05/07/2024]
Abstract
During an epidemiological survey, a potential novel species within the basidiomycetous yeast genus Trichosporon was observed. The clinical strain was obtained from a urine sample taken from a Brazilian kidney transplant recipient. The strain was molecularly identified using the intergenic spacer (IGS1) ribosomal DNA locus and a subsequent phylogenetic analysis showed that multiple strains that were previously reported by other studies shared an identical IGS1-genotype most closely related to that of Trichosporon inkin. However, none of these studies provided an in-depth characterization of the involved strains to describe it as a new taxon. Here, we present the novel clinically relevant yeast for which we propose the name Trichosporon austroamericanum sp. nov. (holotype CBS H-24937). T. austroamericanum can be distinguished from other siblings in the genus Trichosporon using morphological, physiological, and phylogenetic characters.
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Affiliation(s)
- Elaine C Francisco
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute (WI-KNAW), Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
- Division of Infectious Diseases, Escola Paulista de Medicina-Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marie Desnos-Ollivier
- Département de Mycologie, Centre National de Référence des Mycoses invasives et Antifongiques, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Chendo Dieleman
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute (WI-KNAW), Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Teun Boekhout
- College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | | | - José O Medina-Pestana
- Serviço de Nefrologia, Hospital do Rim, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Arnaldo L Colombo
- Division of Infectious Diseases, Escola Paulista de Medicina-Universidade Federal de São Paulo, São Paulo, Brazil
- Antimicrobial Resistance Institute of São Paulo (ARIES), São Paulo, Brazil
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute (WI-KNAW), Uppsalalaan 8, 3584CT, Utrecht, The Netherlands.
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
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2
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Kaşaltı B, Gülmez D. Saprochaete/Magnusiomyces: identification, virulence factors, and antifungal susceptibility of a challenging rare yeast. Braz J Microbiol 2024; 55:41-49. [PMID: 38233642 PMCID: PMC10920568 DOI: 10.1007/s42770-024-01248-7] [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: 10/11/2023] [Accepted: 01/04/2024] [Indexed: 01/19/2024] Open
Abstract
Saprochaete/Magnusiomyces is among rare yeasts which might emerge as causes of breakthrough infections and nosocomial outbreaks. Identification to the species level might be a challenge in clinical laboratories. Data on virulence factors are scarce and antifungal susceptibility testing methodology is not definite. The aim of this study was to confirm species identification of clinical Saprochaete/Magnusiomyces isolates, find out their virulence factors, and obtain antifungal minimum inhibitory concentrations with two reference methods. Of the 57 isolates included, 54 were Saprochaete capitata and four were Saprochaete clavata as identified by ID32C, MALDI-TOF MS, and sequencing. When tested using phenotypic methods, all isolates were negative for coagulase, hemolysis, acid proteinase, and phospholipase, 56.1% were positive for esterase, and 19.3% had intermediate surface hydrophobicity. All isolates formed biofilms, with 40.4% of the isolates producing more biomass than biofilm-positive reference strain Candida albicans MYA-274. Antifungal susceptibility testing needed an adjusted spectrophotometric inoculum than recommended in reference methods for Candida/Cryptococcus. In conclusion, Saprochaete/Magnusiomyces species could be identified using methods available in the clinical laboratories. Despite the disadvantages of the phenotypic methods, esterase positivity was observed for the first time. A high biomass production was observed in biofilms. The need for standardization of antifungal susceptibility testing was brought to attention.
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Affiliation(s)
- Beyzanur Kaşaltı
- Medical Microbiology Department, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Dolunay Gülmez
- Medical Microbiology Department, Hacettepe University Faculty of Medicine, Ankara, Turkey.
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3
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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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4
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Francisco EC, Ebbing M, Colombo AL, Hagen F. Identification of Clinical Trichosporon asteroides Strains by MALDI-TOF Mass Spectrometry: Evaluation of the Bruker Daltonics Commercial System and an In-House Developed Library. Mycopathologia 2023; 188:243-249. [PMID: 37067663 DOI: 10.1007/s11046-023-00723-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/27/2023] [Indexed: 04/18/2023]
Abstract
Trichosporon asteroides is an emerging yeast-like pathogen commonly misidentified by commercial biochemical identification systems. We evaluated the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of 21 clinical T. asteroides strains using the Bruker Daltonics database (BDAL) and an in-house developed library. Mass spectra were obtained by the FlexControl system v.3.4, and characterizations were performed in the Biotyper BDAL database v.4.1 and the developed in-house library. Species identification for T. asteroides failed as all 21 strains were misidentified as T. japonicum (log-scores 1.89-2.19). Extending the existing database was crucial to achieving 100% correct species-level identification and accurate distinction between species. Our results indicate that the commercial BDAL database has no discriminatory power to distinguish between T. japonicum and T. asteroides. Whereas improvement of the current BDAL database is pending, we strongly advise system users not to exclude the possibility of the failure to report T. asteroides.
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Affiliation(s)
- Elaine Cristina Francisco
- Division of Infectious Diseases, Escola Paulista de Medicina - Universidade Federal de São Paulo, São Paulo, 04024-002, Brazil.
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.
| | - Mexx Ebbing
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Arnaldo Lopes Colombo
- Division of Infectious Diseases, Escola Paulista de Medicina - Universidade Federal de São Paulo, São Paulo, 04024-002, Brazil
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
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5
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Sarvestani HK, Ramandi A, Getso MI, Razavyoon T, Javidnia J, Golrizi MB, Saboor-Yaraghi AA, Ansari S. Mass spectrometry in research laboratories and clinical diagnostic: a new era in medical mycology. Braz J Microbiol 2022; 53:689-707. [PMID: 35344203 PMCID: PMC9151960 DOI: 10.1007/s42770-022-00715-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
Diagnosis by clinical mycology laboratory plays a critical role in patient care by providing definitive knowledge of the cause of infection and antimicrobial susceptibility data to physicians. Rapid diagnostic methods are likely to improve patient. Aggressive resuscitation bundles, adequate source control, and appropriate antibiotic therapy are cornerstones for success in the treatment of patients. Routine methods for identifying clinical specimen fungal pathogen are based on the cultivation on different media with the subsequent examination of its phenotypic characteristics comprising a combination of microscopic and colony morphologies. As some fungi cannot be readily identified using these methods, molecular diagnostic methods may be required. These methods are fast, but it can cost a lot. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs. It can be considered an alternative for conventional biochemical and molecular identification systems in a microbiological laboratory. The reliability and accuracy of this method have been scrutinized in many surveys and have been compared with several methods including sequencing and molecular methods. According to these findings, the reliability and accuracy of this method are very high and can be trusted. With all the benefits of this technique, the libraries of MALDI-TOF MS need to be strengthened to enhance its performance. This review provides an overview of the most recent research literature that has investigated the applications and usage of MT-MS to the identification of microorganisms, mycotoxins, antifungal susceptibility examination, and mycobiome research.
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Affiliation(s)
- Hasti Kamali Sarvestani
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Ramandi
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Muhammad Ibrahim Getso
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Bayero University, PMB, Kano, 3011, Nigeria
| | - Taraneh Razavyoon
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Javidnia
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Miaad Banay Golrizi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ali-Akbar Saboor-Yaraghi
- Department of Nutrition and Biochemistry, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Saham Ansari
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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6
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Salah H, Kolecka A, Rozaliyani A, Wahyuningsih R, Taj-Aldeen SJ, Boekhout T, Houbraken J. A New Filter Based Cultivation Approach for Improving Aspergillus Identification using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Mycopathologia 2022; 187:39-52. [PMID: 35006478 PMCID: PMC8807449 DOI: 10.1007/s11046-021-00603-8] [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: 05/12/2021] [Accepted: 10/27/2021] [Indexed: 11/30/2022]
Abstract
Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) is widely used in clinical laboratories for routine identification of bacteria and yeasts. However, methodological difficulties are still apparent when applied to filamentous fungi. The liquid cultivation method recommended by Bruker Daltonics GmbH for identification of filamentous fungi by MALDI-TOF MS is labour intensive and time-consuming. In this study, growth of Aspergillus species on different (porous) surfaces was investigated with the aim to develop a more reliable, quicker and less laborious identification method using MALDI-TOF MS. Mycelial growth without sporulation mimicking liquid cultivation and reliable MALDI-TOF MS spectra were obtained when A. fumigatus strains were grown on and in between a polycarbonate membrane filter on Sabouraud dextrose agar. A database of in-house reference spectra was created by growing Aspergillus reference strains (mainly focusing on sections Fumigati and Flavi) under these selected conditions. A test set of 50 molecularly identified strains grown under different conditions was used to select the best growth condition for identification and to perform an initial validation of the in-house database. Based on these results, the cultivation method on top of a polycarbonate filter proved to be most successful for species identification. This method was therefore selected for the identification of two sets of clinical isolates that mainly consisted of Aspergilli (100 strains originating from Indonesia, 70 isolates from Qatar). The results showed that this cultivation method is reliable for identification of clinically relevant Aspergillus species, with 67% and 76% correct identification of strains from Indonesia and Qatar, respectively. In conclusion, cultivation of Aspergilli on top of a polycarbonate filter showed improved results compared to the liquid cultivation protocol recommended by Bruker in terms of percentage of correct identification, ease of MSP creation, time consumption, cost and labour intensity. This method can be reliably applied for identification of clinically important Aspergilli and has potential for identification of other filamentous fungi.
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Affiliation(s)
- Husam Salah
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Anna Kolecka
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Anna Rozaliyani
- Department of Parasitology Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Retno Wahyuningsih
- Department of Parasitology Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.,Department of Parasitology Faculty of Medicine, Universitas Kristen Indonesia, Jakarta, Indonesia
| | - Saad J Taj-Aldeen
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar.,University of Babylon, Hilla, Iraq
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.
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7
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Lara BR, de Camargo BB, Paula CR, Junior DPL, Garces HG, Arnoni MV, Silveira M, Gimenes VMF, Siqueira LPM, Takahashi JPF, Melhem MDSC, Richini-Pereira VB, Anversa L, Ruiz LDS. Comparing the phenotypic, genotypic, and proteomic identification of Trichosporon species: A globally emerging yeast of medical importance. Med Mycol 2021; 59:1181-1190. [PMID: 34424343 DOI: 10.1093/mmy/myab050] [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: 05/05/2021] [Revised: 08/03/2021] [Accepted: 08/19/2021] [Indexed: 12/27/2022] Open
Abstract
Trichosporon spp. are widely distributed in the nature, comprising species that inhabit different ecological niches and can be found in the water, soil, and body surface of animals and humans. Such microorganisms have been classically associated with superficial infections; however, in the last decades, they have also been related to disseminated infections in immunocompromised patients, behaving as opportunistic agents, which demands rapid and accurate species identification for efficient therapy. Concordance level between the traditional phenotypic method and the molecular technique (gold standard) in the identification of all 59 Trichosporon samples was 59.3%. Identification concordance between MALDI-TOF spectrometry and the molecular technique was 71.2%. No isolate of environmental origin was identifiable by MALDI-TOF mass spectrometry (MS), and 100% of such environmental isolates were discordant for IGS region sequencing and phenotypic characterization. Both comparisons evidenced greatest concordance in the identification of T. asahii. The species T. debeurmannianum, T. dermatis, T. venhuisii and T. insectorum were not properly identified by both MALDI-TOF MS and the phenotypic technique. MALDI-TOF MS, in particular, seems to be appropriate to investigate yeasts of the genus Trichosporon; however, database updates are still necessary, especially for species that are not common in the clinical routine. With the aim of helping understand the aspects involved in early and accurate diagnosis of infections caused by this opportunistic agent, the present study compared the phenotypic, molecular (IGS region) and mass-spectrometry (MALDI-TOF) identification of 59 yeasts of the genus Trichosporon which had clinical and environmental origin and were kept in a mycology collection.
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Affiliation(s)
- Bruna Rossini Lara
- São Paulo State University (Unesp), Institute of Biosciences, 18618-689, Botucatu, São Paulo (SP), Brazil.,Adolfo Lutz Institute (IAL) CLR II, Biomedical Sciences Center, 17015-110, Bauru, SP, Brazil
| | | | | | - Diniz Pereira Leite Junior
- Faculty of Medicine, Federal University of Mato Grosso (UFMT), Av. Fernando Corrêa da Costa, 2.367, Cuiabá, MT, Brazil
| | - Hans Garcia Garces
- São Paulo State University (Unesp), Institute of Biosciences, 18618-689, Botucatu, São Paulo (SP), Brazil
| | - Mariana Volpe Arnoni
- "Irmandade da Santa Casa de Misericórdia de São Paulo", Hospital, 01221-010, São Paulo, SP, Brazil.,Darcy Vargas Children's Hospital, 05614-040, São Paulo, SP, Brazil
| | | | | | | | | | | | | | - Laís Anversa
- Adolfo Lutz Institute (IAL) CLR II, Biomedical Sciences Center, 17015-110, Bauru, SP, Brazil
| | - Luciana da Silva Ruiz
- Adolfo Lutz Institute (IAL) CLR II, Biomedical Sciences Center, 17015-110, Bauru, SP, Brazil
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8
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Chen SCA, Perfect J, Colombo AL, Cornely OA, Groll AH, Seidel D, Albus K, de Almedia JN, Garcia-Effron G, Gilroy N, Lass-Flörl C, Ostrosky-Zeichner L, Pagano L, Papp T, Rautemaa-Richardson R, Salmanton-García J, Spec A, Steinmann J, Arikan-Akdagli S, Arenz DE, Sprute R, Duran-Graeff L, Freiberger T, Girmenia C, Harris M, Kanj SS, Roudbary M, Lortholary O, Meletiadis J, Segal E, Tuon FF, Wiederhold N, Bicanic T, Chander J, Chen YC, Hsueh PR, Ip M, Munoz P, Spriet I, Temfack E, Thompson L, Tortorano AM, Velegraki A, Govender NP. Global guideline for the diagnosis and management of rare yeast infections: an initiative of the ECMM in cooperation with ISHAM and ASM. THE LANCET. INFECTIOUS DISEASES 2021; 21:e375-e386. [PMID: 34419208 DOI: 10.1016/s1473-3099(21)00203-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 01/10/2023]
Abstract
Uncommon, or rare, yeast infections are on the rise given increasing numbers of patients who are immunocompromised or seriously ill. The major pathogens include those of the genera Geotrichum, Saprochaete, Magnusiomyces, and Trichosporon (ie, basidiomycetes) and Kodamaea, Malassezia, Pseudozyma (ie, now Moesziomyces or Dirkmeia), Rhodotorula, Saccharomyces, and Sporobolomyces (ie, ascomycetes). A considered approach to the complex, multidisciplinary management of infections that are caused by these pathogens is essential to optimising patient outcomes; however, management guidelines are either region-specific or require updating. In alignment with the One World-One Guideline initiative to incorporate regional differences, experts from diverse geographical regions analysed publications describing the epidemiology and management of the previously mentioned rare yeasts. This guideline summarises the consensus recommendations with regards to the diagnostic and therapeutic options for patients with these rare yeast infections, with the intent of providing practical assistance in clinical decision making. Because there is less clinical experience of patients with rare yeast infections and studies on these patients were not randomised, nor were groups compared, most recommendations are not robust in their validation but represent insights by use of expert opinions and in-vitro susceptibility results. In this Review, we report the key features of the epidemiology, diagnosis, antifungal susceptibility, and treatment outcomes of patients with Geotrichum, Saprochaete, Magnusiomyces, and Trichosporon spp infections.
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Affiliation(s)
- Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, NSW, Australia; Centre for Infectious Diseases and Microbiology, Westmead Hospital, The University of Sydney, Sydney, NSW, Australia.
| | | | - Arnaldo L Colombo
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Oliver A Cornely
- Department I of Internal Medicine, Excellence Center for Medical Mycology, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany; Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany; Clinical Trials Centre Cologne (ZKS Köln), Cologne, Germany
| | - Andreas H Groll
- Infectious Disease Research Program, Centre for Bone Marrow Transplantation and Department of Paediatric Hematology and Oncology, University Children's Hospital Münster, Münster, Germany
| | - Danila Seidel
- Department I of Internal Medicine, Excellence Center for Medical Mycology, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany; Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Kerstin Albus
- Department I of Internal Medicine, Excellence Center for Medical Mycology, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany; Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Joao N de Almedia
- Central Laboratory Division, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Guillermo Garcia-Effron
- Laboratorio de Micología y Diagnóstico Molecular, Cátedra de Parasitología y Micología, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas, CCT Santa Fe, Santa Fe, Argentina
| | - Nicole Gilroy
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, The University of Sydney, Sydney, NSW, Australia
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, ECMM Excellence Centre, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Livio Pagano
- Fondazione Policlinico Universitario A Gemelli-IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Tamas Papp
- Fungal Pathogenicity Mechanisms Research Group, Department of Microbiology, University of Szeged, Szeged, Hungary
| | - Riina Rautemaa-Richardson
- Wythenshawe Hospital, ECMM Excellence Centre, Manchester University NHS Foundation Trust, Manchester, UK; Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jon Salmanton-García
- Department I of Internal Medicine, Excellence Center for Medical Mycology, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany; Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Andrej Spec
- Division of Infectious Disease, School of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Joerg Steinmann
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Nuremberg, Germany; Institute of Medical Microbiology, University Hospital Essen, Essen, Germany
| | - Sevtap Arikan-Akdagli
- Department of Medical Microbiology, Hacettepe University Medical School, Ankara, Turkey
| | - Dorothee E Arenz
- Department I of Internal Medicine, Excellence Center for Medical Mycology, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany; German Centre for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Rosanne Sprute
- Department I of Internal Medicine, Excellence Center for Medical Mycology, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany; German Centre for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Luisa Duran-Graeff
- Clínica Las Condes, Departamento de Medicina Interna, Unidad de Infectología, Santiago, Chile
| | - Tomas Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic; Medical Faculty, Masaryk University, Brno, Czech Republic
| | - Corrado Girmenia
- Department of Hematology, Umberto I Policlinico di Roma, Rome, Italy
| | | | - Souha S Kanj
- Department of Internal Medicine, Division of Infectious Diseases, American University of Beirut Medical Centre, Beirut, Lebanon
| | - Maryam Roudbary
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Olivier Lortholary
- Service des Maladies Infectieuses et Tropicales, Hôpital Necker-Enfants malades, Université Paris V, Paris, France
| | - Joseph Meletiadis
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Esther Segal
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Felipe Francisco Tuon
- Laboratory of Emerging Infectious Diseases, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Nathan Wiederhold
- Fungus Testing Laboratory, University of Texas Health Science Center, San Antonio, TX, USA
| | - Tihana Bicanic
- Institute of Infection and Immunity, St George's University of London, London, UK
| | - Jagdish Chander
- Department of Microbiology, Government Medical College Hospital, Chandigarh, India
| | - Yee-Chun Chen
- Division of Infectious Diseases, Department of Internal Medicine, National Taiwan University College of Medicine, Taipeh, Taiwan; Department of Medicine, National Taiwan University College of Medicine, Taipeh, Taiwan
| | - Po-Ren Hsueh
- Division of Infectious Diseases, Department of Internal Medicine, National Taiwan University College of Medicine, Taipeh, Taiwan; Department of Laboratory Medicine, National Taiwan University College of Medicine, Taipeh, Taiwan
| | - Margaret Ip
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Patricia Munoz
- Infectious Diseases and Clinical Microbiology Department, Hospital General Universitario Gregorio Marañón, Servicio de Microbiología-Enfermedades Infecciosas, Madrid, Spain
| | - Isabel Spriet
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium; Pharmacy Department, University Hospitals Leuven, Leuven, Belgium
| | - Elvis Temfack
- Internal Medicine Unit, Douala General Hospital, Douala, Cameroon; National Public Health Laboratory, Yaounde, Cameroon
| | - Luis Thompson
- Clinica Alemana-Universidad del Desarrollo, Departamento de Medicina Interna, Unidad de Infectología, Santiago, Chile
| | - Anna Maria Tortorano
- Department of Biomedical Science for Research, Universita degli Studi di Milano, Milan, Italy
| | - Aristea Velegraki
- Mycology Research Laboratory and UOA/HCPF Culture Collection, Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Nelesh P Govender
- National Institute for Communicable Diseases (Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses), a Division of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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9
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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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10
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ElGindi M, Al-Baghdadi R, Jackman AB, Antonyan AS, McMahon DL, Taj-Aldeen SJ, Finkel JS. Where the infection is isolated rather than the specific species correlates with adherence strength, whereas biofilm density remains static in clinically isolated Candida and arthroconidial yeasts. Can J Microbiol 2021; 67:497-505. [PMID: 34232751 DOI: 10.1139/cjm-2020-0215] [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] [Indexed: 11/22/2022]
Abstract
To colonize and infect the host, arthroconidial yeasts must avoid being killed by the host's defenses. The formation of biofilms on implanted devices allows fungi to avoid host responses and to disseminate into the host. To better study the mechanisms of infection by arthroconidial yeasts, adherence and biofilm formation were assayed using patient samples collected over 10 years. In clinical samples, adherence varies within species, but the relative adherence is constant for those samples isolated from the same infection site. Herein we document, for the first time, in-vitro biofilm formation by Trichosporon dohaense, T. ovoides, T. japonicum, T. coremiiforme, Cutaneotrichosporon mucoides, Cutaneotrichosporon cutaneum, Galactomyces candidus, and Magnusiomyces capitatus on clinically relevant catheter material. Analysis of biofilm biomass assays indicated that biofilm mass changes less than 2-fold, regardless of the species. Our results support the hypothesis that most pathogenic fungi can form biofilms, and that biofilm formation is a source of systemic infections.
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Affiliation(s)
- Mei ElGindi
- Department of Biological Sciences, Carnegie Mellon University, Education City, PO Box 24866, Doha, Qatar
| | - Rula Al-Baghdadi
- Department of Biological Sciences, Carnegie Mellon University, Education City, PO Box 24866, Doha, Qatar
| | - Alex B Jackman
- Department of Biology, College of Engineering and Science, University of Detroit Mercy, 4001 W McNichols Road, Detroit, MI 48221-3038, USA
| | - Angelina S Antonyan
- Department of Biology, College of Engineering and Science, University of Detroit Mercy, 4001 W McNichols Road, Detroit, MI 48221-3038, USA
| | - Diana L McMahon
- Department of Biology, College of Engineering and Science, University of Detroit Mercy, 4001 W McNichols Road, Detroit, MI 48221-3038, USA
| | - Saad J Taj-Aldeen
- University of Babylon, Hilla, Iraq.,Microbiology Division, Department of Laboratory Medicine and Pathology, Mycology Unit, Hamad Medical Corporation, Doha, Qatar
| | - Jonathan S Finkel
- Department of Biological Sciences, Carnegie Mellon University, Education City, PO Box 24866, Doha, Qatar.,Department of Biology, College of Engineering and Science, University of Detroit Mercy, 4001 W McNichols Road, Detroit, MI 48221-3038, USA
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11
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Kangül H, Özcan N, Uzuner N, Mete M, Mert Erginer U. Saprochaete clavata ( Geotrichum clavatum) septicemia in a patient with multiple myeloma; An emerging case from Southeastern Turkey. Curr Med Mycol 2021; 6:66-69. [PMID: 34195463 PMCID: PMC8226052 DOI: 10.18502/cmm.6.4.5440] [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] [Indexed: 11/24/2022] Open
Abstract
Background and Purpose Invasive fungal infections (IFI) are life-threatening and can be seen in immuno-compromised patients with malignancy, those who undergo chemotherapy, or transplant recipients. The Candida and Aspergillus species are the most common IFI agents; however, infections can also be caused by rare fungal species. This case report is about a bloodstream infection due to Saprochaete clavata (formerly known as Geotrichum clavatum) in a woman with multiple myeloma. Case report A 59-years-old woman suffered from fever, widespread rashes, and diarrhea after an autologous bone marrow transplantation. Peripheral blood cultures were taken from the patient and sent to the microbiology laboratory. Cultures grew white to cream-colored cottony colonies. Moreover, septate and branched hyphae and arthroconidia were seen under a microscope by lactophenol blue staining. The fungi colonies were identified by Maldi Biotyper 3. 1. (manufactured by Bruker Daltonics, USA) as S. clavata (G. clavatum) with a reliable score. Antifungal susceptibility test was carried out by the concentration gradient strip Etest method. Minimal inhibitory concentrations of Amphotericin B, fluconazole, voriconazole, posaconazole, and anidulafungin were determined as 4, 3, 0.125, 0.125, and > 32 mg/dL, respectively. Despite amphotericin B treatment, the patient died three days after the identification of the fungi. Conclusion The IFIs are serious conditions that have high mortality rates. In the current case report, we aimed to draw attention to S. clavata which is a rare fungal agent.
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Affiliation(s)
- Handan Kangül
- Department of Medical Microbiology, Faculty of Medicine, Dicle University, Diyarbakır, Turkey
| | - Nida Özcan
- Department of Medical Microbiology, Faculty of Medicine, Dicle University, Diyarbakır, Turkey
| | - Nurullah Uzuner
- Department of Medical Microbiology, Faculty of Medicine, Dicle University, Diyarbakır, Turkey
| | - Mahmut Mete
- Department of Medical Microbiology, Faculty of Medicine, Dicle University, Diyarbakır, Turkey
| | - Ufuk Mert Erginer
- Department of Internal Medicine, Faculty of Medicine, Dicle University, Diyarbakır, Turkey
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12
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Boekhout T, Aime MC, Begerow D, Gabaldón T, Heitman J, Kemler M, Khayhan K, Lachance MA, Louis EJ, Sun S, Vu D, Yurkov A. The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks. FUNGAL DIVERS 2021; 109:27-55. [PMID: 34720775 PMCID: PMC8550739 DOI: 10.1007/s13225-021-00475-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.
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Affiliation(s)
- Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - M. Catherine Aime
- Dept Botany and Plant Pathology, College of Agriculture, Purdue University, West Lafayette, IN 47907 USA
| | - Dominik Begerow
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC–CNS), Jordi Girona, 29, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Martin Kemler
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Kantarawee Khayhan
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, 56000 Thailand
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON N6A 5B7 Canada
| | - Edward J. Louis
- Department of Genetics and Genome Biology, Genetic Architecture of Complex Traits, University of Leicester, Leicester, LE1 7RH UK
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Andrey Yurkov
- German Collection of Microorganisms and Cell Cultures, Leibniz Institute DSMZ, Brunswick, Germany
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13
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Arastehfar A, de Almeida Júnior JN, Perlin DS, Ilkit M, Boekhout T, Colombo AL. Multidrug-resistant Trichosporon species: underestimated fungal pathogens posing imminent threats in clinical settings. Crit Rev Microbiol 2021; 47:679-698. [PMID: 34115962 DOI: 10.1080/1040841x.2021.1921695] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Species of Trichosporon and related genera are widely used in biotechnology and, hence, many species have their genome sequenced. Importantly, yeasts of the genus Trichosporon have been increasingly identified as a cause of life-threatening invasive trichosporonosis (IT) in humans and are associated with an exceptionally high mortality rate. Trichosporon spp. are intrinsically resistant to frontline antifungal agents, which accounts for numerous reports of therapeutic failure when echinocandins are used to treat IT. Moreover, these fungi have low sensitivity to polyenes and azoles and, therefore, are potentially regarded as multidrug-resistant pathogens. However, despite the clinical importance of Trichosporon spp., our understanding of their antifungal resistance mechanisms is quite limited. Furthermore, antifungal susceptibility testing is not standardized, and there is a lack of interpretive epidemiological cut-off values for minimal inhibitory concentrations to distinguish non-wild type Trichosporon isolates. The route of infection remains obscure and detailed clinical and environmental studies are required to determine whether the Trichosporon infections are endogenous or exogenous in nature. Although our knowledge on effective IT treatments is rather limited and future randomized clinical trials are required to identify the best antifungal agent, the current paradigm advocates the use of voriconazole, removal of central venous catheters and recovery from neutropenia.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - João N de Almeida Júnior
- Laboratorio de Micologia Medica (LIM 53), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil.,Laboratório Central (LIM 03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Macit Ilkit
- Division of Mycology, University of Çukurova, Adana, Turkey
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Arnaldo Lopes Colombo
- Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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14
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Lau AF. Matrix-Assisted Laser Desorption Ionization Time-of-Flight for Fungal Identification. Clin Lab Med 2021; 41:267-283. [PMID: 34020763 DOI: 10.1016/j.cll.2021.03.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many studies have shown successful performance of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for rapid yeast and mold identification, yet few laboratories have chosen to apply this technology into their routine clinical mycology workflow. This review provides an overview of the current status of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for fungal identification, including key findings in the literature, processing and database considerations, updates in technology, and exciting future prospects. Significant advances toward standardization have taken place recently; thus, accurate species-level identification of yeasts and molds should be highly attainable, achievable, and practical in most clinical laboratories.
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Affiliation(s)
- Anna F Lau
- Sterility Testing Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, 10 Center Drive, Room 2C306, Bethesda, MD 20892, USA.
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15
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Pawlak Z, Andrusiów S, Pajączkowska M, Janczura A. Identification of Fungi Isolated from Oral Cavity of Patients with HIV Using MALDI-TOF MS. J Clin Med 2021; 10:jcm10081570. [PMID: 33917925 PMCID: PMC8068364 DOI: 10.3390/jcm10081570] [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: 03/04/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND A growing incidence of invasive fungal infections, especially among immunocompromised patients, has given increased significance to microbiological diagnostics of yeast-like fungi. More accurate and faster fungi identification methods that can compete with classical methods are being searched for. In this paper, classical microbiological methods are compared to MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry). METHODS The diagnostic material was collected from buccal mucosa from 98 adults, including 69 with HIV. Only positive cultures were included in the study. RESULTS Matching results were obtained in 45 samples, and there were nonmatching results in 35 samples, with the majority of these in the study group, constituting 50% of identifications within this group. A particularly common mistake resulting from the use of classical methods is the false identification of C. dubliniensis as C. albicans. Additionally, C. tropicalis proves to be difficult to identify. CONCLUSIONS Our results and literature data suggest that MALDI-TOF MS should be considered an effective alternative to classical methods in terms of fungi identification, especially among HIV-positive patients, due to the different morphology of fungal colonies.
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Affiliation(s)
- Zuzanna Pawlak
- Students Scientific Society of Infectious Diseases, Liver Diseases and Acquired Immune Deficiencies, Faculty of Medicine, Wroclaw Medical University, 51-149 Wroclaw, Poland; (Z.P.); (S.A.)
| | - Szymon Andrusiów
- Students Scientific Society of Infectious Diseases, Liver Diseases and Acquired Immune Deficiencies, Faculty of Medicine, Wroclaw Medical University, 51-149 Wroclaw, Poland; (Z.P.); (S.A.)
| | - Magdalena Pajączkowska
- Department of Microbiology, Faculty of Medicine, Wroclaw Medical University, 50-368 Wroclaw, Poland;
| | - Adriana Janczura
- Department of Microbiology, Faculty of Medicine, Wroclaw Medical University, 50-368 Wroclaw, Poland;
- Correspondence:
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16
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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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17
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Almulhim AM, Vellozzi-Averhoff CM, Howard-Anderson J, Babiker A, Kraft CS. Answer to November 2020 Photo Quiz. J Clin Microbiol 2020; 58:e00454-20. [PMID: 33087545 PMCID: PMC7587088 DOI: 10.1128/jcm.00454-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Abdulaziz M Almulhim
- College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | | | - Jessica Howard-Anderson
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ahmed Babiker
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Colleen S Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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18
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Kabwe MH, Vikram S, Mulaudzi K, Jansson JK, Makhalanyane TP. The gut mycobiota of rural and urban individuals is shaped by geography. BMC Microbiol 2020; 20:257. [PMID: 32807105 PMCID: PMC7430031 DOI: 10.1186/s12866-020-01907-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/15/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Understanding the structure and drivers of gut microbiota remains a major ecological endeavour. Recent studies have shown that several factors including diet, lifestyle and geography may substantially shape the human gut microbiota. However, most of these studies have focused on the more abundant bacterial component and comparatively less is known regarding fungi in the human gut. This knowledge deficit is especially true for rural and urban African populations. Therefore, we assessed the structure and drivers of rural and urban gut mycobiota. RESULTS Our participants (n = 100) were balanced by geography and sex. The mycobiota of these geographically separated cohorts was characterized using amplicon analysis of the Internal Transcribed Spacer (ITS) gene. We further assessed biomarker species specific to rural and urban cohorts. In addition to phyla which have been shown to be ubiquitous constituents of gut microbiota, Pichia were key constituents of the mycobiota. We found that geographic location was a major driver of gut mycobiota. Other factors such as smoking where also determined gut mycobiota albeit to a lower extent, as explained by the small proportion of total variation. Linear discriminant and the linear discriminant analysis effect size analysis revealed several distinct urban and rural biomarkers. CONCLUSIONS Together, our analysis reveals distinct community structure in urban and rural South African individuals. Geography was shown to be a key driver of rural and urban gut mycobiota.
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Affiliation(s)
- Mubanga Hellen Kabwe
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynwood Road, Hatfield, Pretoria, 0028, South Africa
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynwood Road, Hatfield, Pretoria, 0028, South Africa
| | - Khodani Mulaudzi
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynwood Road, Hatfield, Pretoria, 0028, South Africa
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington, 99352, USA
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynwood Road, Hatfield, Pretoria, 0028, South Africa.
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19
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Duan PN, Hung NN, Nhu PT, Thien CD, Tran QC. Saprochaete Capitata Infection in an 80-Year Old Chronic Obstructive Pulmonary Disease (COPD) Patient: A Case Report. Open Access Maced J Med Sci 2019; 7:4329-4332. [PMID: 32215088 PMCID: PMC7084037 DOI: 10.3889/oamjms.2019.385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND: The fungal disease caused by invasive fungus Saprochaete capitata is becoming an increasingly popular infection. Fungal pathogens mainly occur in patients with immunocompromised disorders such as hematologic malignancies, acute myeloid leukemia, transplant patients. CASE REPORT: In this study, we presented a COPD patient infected with S. capitata. At the first check, the patient showed cough, dyspnea, chest pain on both sides. The clinical laboratory test result was characterized with high White blood cell (12.8 G/L), HIV negative. The X ray showed bronchitis and emphysema. Bronchoscopy illustrated bronchial mucositis. CT scanner demonstrated pneumonia with fuzzy nodular lesions and thick interstitial organization in both lungs. The patient was treated with ciprofloxacin 800 mg/day; cefuroxime 2250 mmg/day. However, the fever appeared 2 weeks thereafter. The S. capitata was discovered in the bronchial fluid. The patient was then treated with fluconazole 400 mg/day for 14 days. At the end of treatment, all signs and symptoms of S. capitata infection disappeared and the patient recovered. CONCLUSION: This case study showed that S. capitata infection can occur in the COPD patients and fluconazole is a pertinent drug for treatment of the infection.
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Affiliation(s)
- Pham Ngoc Duan
- Department of Parasitology, Hanoi Medical University, Hanoi, Vietnam.,Department of Microbiology and Parasitology, Hanoi Medical University Hospital, Hanoi, Vietnam
| | - Nguyen Nhu Hung
- Department of Microbiology, 74 Hospital, Phuc Yen, Vinh Phuc, Vietnam
| | | | - Chu Dinh Thien
- Institute for Research and Development, Duy Tan University, 03 Quang Trung, Danang, Vietnam
| | - Quang Canh Tran
- Center for Hygiene and Food Safety, Haiduong Medical Technical University, Hai Duong, Vietnam
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20
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A case report of catheter-related bloodstream infection due to Trichosporon coremiiforme in a patient with secondary neutropenia to HIV. J Mycol Med 2019; 30:100916. [PMID: 31843296 DOI: 10.1016/j.mycmed.2019.100916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/21/2019] [Accepted: 11/24/2019] [Indexed: 12/15/2022]
Abstract
Here, we describe an invasive infection due to Trichosporon coremiiforme in an HIV positive patient with neutropenia. The strain was first erroneously identified as Trichosporon asahii by conventional methods, but correctly identified by mass spectrometry using matrix-assisted laser desorption/ionization time-of-flight technology (MALDI-TOF MS) and ribosomal DNA sequencing. The infection was successfully resolved after antifungal treatment with amphotericin B and fluconazole. This case report is a contribution to the study of T. coremiiforme infections and reinforces its relevance as a species capable of causing invasive human infection in immunocompromised patients and also contributes to the study of its susceptibility profile against antifungal drugs.
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21
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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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22
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Gabaldón T. Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. FEMS Microbiol Rev 2019; 43:517-547. [PMID: 31158289 PMCID: PMC8038933 DOI: 10.1093/femsre/fuz015] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/31/2019] [Indexed: 12/29/2022] Open
Abstract
The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.
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Affiliation(s)
- Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- ICREA, Pg Lluís Companys 23, 08010 Barcelona, Spain
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23
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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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24
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Ceballos-Garzón A, Cortes G, Morio F, Zamora-Cruz EL, Linares MY, Ariza BE, Valderrama SL, Garzón JR, Alvarez-Moreno CA, Le Pape P, Parra-Giraldo CM. Comparison between MALDI-TOF MS and MicroScan in the identification of emerging and multidrug resistant yeasts in a fourth-level hospital in Bogotá, Colombia. BMC Microbiol 2019; 19:106. [PMID: 31122184 PMCID: PMC6533654 DOI: 10.1186/s12866-019-1482-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/07/2019] [Indexed: 02/07/2023] Open
Abstract
Background The introduction of MALDI-TOF MS in the clinical microbiology laboratory has modified the approaches for the identification of fungi. Thanks to this tool, it is possible to identify cryptic species, which possess critical susceptibility patterns. Clinical strains were identified using the MicroScan and MALDI-TOF MS systems. Discrepant results from both methods were investigated using ITS rDNA barcoding. Finally, these isolates were also tested for in vitro susceptibility. Results The percentage of agreement between both methods to 498 yeast isolates was of 93.6% (32 discrepant isolates). The concordance of ITS sequencing with MALDI-TOF MS was higher (99%) than that of MicroScan (94%). Several of these discordant yeasts displayed high MICs for antifungal agents. Conclusions Our study highlights the need of the MS and molecular approaches such as MALDI-TOF MS and ITS rDNA barcoding for the correct identification of emerging or cryptic yeast species; besides, some of these could be multidrug resistant. This work was the first experience in the implementation of the MALDI-TOF MS technology in Colombia. We found the first uncommon yeasts including Candida auris and we could identify Trichosporon faecalis. Our work highlights a clear necessity of an accurate yeast identification as a much more pertinent technique than the susceptibility profiles, because the most unusual yeasts exhibit resistance profiles to the few available antifungals.
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Affiliation(s)
- Andrés Ceballos-Garzón
- Departamento de Microbiología, Facultad de Ciencias, Unidad de Proteomica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Pontificia Universidad Javeriana, Bogotá, Colombia.,Grupo de Investigación en Enfermedades Infecciosas, Hospital Universitario San Ignacio, Bogotá, Colombia.,Department of Parasitology and Medical Mycology of the University of Nantes, Nantes Atlantique Universities, Faculty of Pharmacy, Nantes, France
| | - Gloria Cortes
- Laboratorio Clínico, Área de Microbiología, Hospital Universitario San Ignacio, Bogotá, Colombia.,Grupo de Investigación en Enfermedades Infecciosas, Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Florent Morio
- Department of Parasitology and Medical Mycology of the University of Nantes, Nantes Atlantique Universities, Faculty of Pharmacy, Nantes, France
| | - Edna L Zamora-Cruz
- Departamento de Microbiología, Facultad de Ciencias, Unidad de Proteomica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Melva Y Linares
- Departamento de Microbiología, Facultad de Ciencias, Unidad de Proteomica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Pontificia Universidad Javeriana, Bogotá, Colombia.,Grupo de Investigación en Enfermedades Infecciosas, Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Beatriz E Ariza
- Laboratorio Clínico, Área de Microbiología, Hospital Universitario San Ignacio, Bogotá, Colombia.,Grupo de Investigación en Enfermedades Infecciosas, Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Sandra L Valderrama
- Unidad de Infectología, Departamento de Medicina Interna, Facultad de Medicina, Hospital Universitario San Ignacio, Bogotá, Colombia.,Grupo de Investigación en Enfermedades Infecciosas, Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Javier R Garzón
- Unidad de Infectología, Departamento de Medicina Interna, Facultad de Medicina, Hospital Universitario San Ignacio, Bogotá, Colombia.,Grupo de Investigación en Enfermedades Infecciosas, Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Carlos A Alvarez-Moreno
- Grupo de Investigación en Enfermedades Infecciosas, Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Patrice Le Pape
- Department of Parasitology and Medical Mycology of the University of Nantes, Nantes Atlantique Universities, Faculty of Pharmacy, Nantes, France
| | - Claudia M Parra-Giraldo
- Departamento de Microbiología, Facultad de Ciencias, Unidad de Proteomica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Pontificia Universidad Javeriana, Bogotá, Colombia. .,Grupo de Investigación en Enfermedades Infecciosas, Hospital Universitario San Ignacio, Bogotá, Colombia.
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25
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Rapid and Simple Detection of Trichosporon asahii by Optimized Colony PCR. BIOMED RESEARCH INTERNATIONAL 2019; 2019:1803278. [PMID: 31218222 PMCID: PMC6537005 DOI: 10.1155/2019/1803278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/23/2019] [Indexed: 12/26/2022]
Abstract
Trichosporon asahii is the major pathogen causing invasive trichosporonosis. Conventional methods of its detection are time-consuming or costly and often require complex DNA extraction and purification steps, which hinders rapid clinical diagnosis. In this study, we evaluated colony PCR, which directly uses colonies or trace clinical samples as the template for amplification, for rapid detection of T. asahii infection. Four methods, namely, direct colony, freeze-thaw, glass beads, and enzymolysis, were compared to select the best DNA extraction strategy. We subsequently designed and screened species-specific primers targeting the intergenic spacer 1 (IGS1) of the ribosomal DNA of T. asahii and used them to detect mock infection clinical samples. The species-specific colony PCR based on glass beads proved advantageous, with short procedure time (154.8 ± 0.6 min), good sensitivity (detection limit, 102 CFU/mL), and specificity for T. asahii, indicating that this method can be used for the rapid and simple identification of clinical samples of T. asahii infection.
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26
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Indrawattana N, Pumipuntu N, Suriyakhun N, Jangsangthong A, Kulpeanprasit S, Chantratita N, Sookrung N, Chaicumpa W, Buranasinsup S. Staphylococcus argenteus from rabbits in Thailand. Microbiologyopen 2019; 8:e00665. [PMID: 29931813 PMCID: PMC6460352 DOI: 10.1002/mbo3.665] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/03/2018] [Accepted: 05/03/2018] [Indexed: 11/11/2022] Open
Abstract
Staphylococcus argenteus, a novel species of the genus Staphylococcus or a member of the S. aureus complex, is closely related to S. aureus and is usually misidentified. In this study, the presence of S. argenteus in isolated S. aureus was investigated in 67 rabbits with abscess lesions during 2014-2016. Among 19 S. aureus complex isolates, three were confirmed to be S. argenteus by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, nonribosomal peptide synthetase gene amplification, and multilocus sequence type. All S. aureus complex isolates, including the S. aureus isolates, were examined for their antimicrobial resistance phenotype by disk diffusion and for their resistance genotype by PCR assays. Among the S. argenteus isolates, one was susceptible to all antimicrobial drugs and the other two were resistant to penicillin and doxycycline. In contrast, most S. aureus isolates were resistant to penicillin (37.5%), and gentamicin (12.5%). Moreover, S. aureus isolates harbored the blaZ, mecA, aacA-aphD, and mrs(A) as well as mutations of gyrA and grlA, but S. argenteus isolates carried solely the blaZ. S. argenteus isolates were investigated for enterotoxin (sea-sed) and virulence genes by PCR. One isolate carried sea, sec, and sed, whereas the other two isolates carried only sea or sed. No isolate carried seb and see. All three S. argenteus isolates carried hla, hlb, and clfA, followed by pvl, whereas coa, spa (IgG-binding region), and spa (x region) were not detected in the three isolates. This paper presents the first identification of S. argenteus from rabbits in Thailand. S. argenteus might be pathogenic because the isolates carried virulence genes. Moreover, antimicrobial resistance was observed. Investigations of this new bacterial species should be conducted in other animal species as well as in humans.
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Affiliation(s)
- Nitaya Indrawattana
- Department of Microbiology and ImmunologyFaculty of Tropical MedicineMahidol UniversityBangkokThailand
| | - Natapol Pumipuntu
- Office of Academic AffairsFaculty of Veterinary SciencesMahasarakham UniversityMaha SarakhamThailand
| | - Nawarat Suriyakhun
- Prasu‐Arthorn Animal HospitalFaculty of Veterinary ScienceMahidol UniversityNakhon PathomThailand
| | - Arunee Jangsangthong
- Department of Pre‐Clinic and Applied Animal ScienceFaculty of Veterinary ScienceMahidol UniversityNakornpathomThailand
| | - Suphang Kulpeanprasit
- Department of Microbiology and ImmunologyFaculty of Tropical MedicineMahidol UniversityBangkokThailand
| | - Narisara Chantratita
- Department of Microbiology and ImmunologyFaculty of Tropical MedicineMahidol UniversityBangkokThailand
| | - Nitat Sookrung
- Laboratory for Research and Technology DevelopmentFaculty of MedicineSiriraj HospitalMahidol UniversityBangkokThailand
| | - Wanpen Chaicumpa
- Center of Excellence on Therapeutic Proteins and Antibody EngineeringDepartment of ParasitologyFaculty of MedicineSiriraj HospitalMahidol UniversityBangkokThailand
| | - Shutipen Buranasinsup
- Department of Pre‐Clinic and Applied Animal ScienceFaculty of Veterinary ScienceMahidol UniversityNakornpathomThailand
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27
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Genome Sequence of Flavor-Producing Yeast Saprochaete suaveolens NRRL Y-17571. Microbiol Resour Announc 2019; 8:MRA00094-19. [PMID: 30834381 PMCID: PMC6395866 DOI: 10.1128/mra.00094-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/04/2019] [Indexed: 12/01/2022] Open
Abstract
Saprochaete suaveolens is an ascomycetous yeast that produces a range of fruity flavors and fragrances. Here, we report the high-contiguity genome sequence of the ex-holotype strain, NRRL Y-17571 (CBS 152.25). Saprochaete suaveolens is an ascomycetous yeast that produces a range of fruity flavors and fragrances. Here, we report the high-contiguity genome sequence of the ex-holotype strain, NRRL Y-17571 (CBS 152.25). The nuclear genome sequence contains 24.4 Mbp and codes for 8,119 predicted proteins.
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28
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Arastehfar A, Daneshnia F, Kord M, Roudbary M, Zarrinfar H, Fang W, Hashemi SJ, Najafzadeh MJ, Khodavaisy S, Pan W, Liao W, Badali H, Rezaie S, Zomorodian K, Hagen F, Boekhout T. Comparison of 21-Plex PCR and API 20C AUX, MALDI-TOF MS, and rDNA Sequencing for a Wide Range of Clinically Isolated Yeast Species: Improved Identification by Combining 21-Plex PCR and API 20C AUX as an Alternative Strategy for Developing Countries. Front Cell Infect Microbiol 2019; 9:21. [PMID: 30828570 PMCID: PMC6385604 DOI: 10.3389/fcimb.2019.00021] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/22/2019] [Indexed: 12/31/2022] Open
Abstract
Occurrence of non-Candida albicans Candida (NCAC) species that are associated with elevated MIC values and therapeutic failures are increasing. As a result, timely and accurate means of identification to the species level is becoming an essential part of diagnostic practices in clinical settings. In this study, 301 clinically isolated yeast strains recovered from various anatomical sites [Blood (n = 145), other sites (n = 156)] were used to assess the accuracy and practicality of API 20C AUX and 21-plex PCR compared to MALDI-TOF MS and large subunit rDNA (LSU rDNA). MALDI-TOF MS correctly identified 98.33% of yeast isolates, 100% of top five Candida species, 95.7% of rare yeast species, while 1.3% of isolates were misidentified. API 20C AUX correctly identified 83.7% of yeast isolates, 97.2% of top five Candida species, 61.8% of rare yeast species, while 16.2% of yeast isolates were misidentified. The 21-plex PCR, accurately identified 87.3% of yeast isolates, 100% of top five Candida species, 72% of rare yeast species, but it misidentified 1.3% of rare yeast species while 9.9% of whole yeast isolates were not identified. The combination of rapidity of 21-plex PCR and comprehensiveness of API 20C AUX, led to correct identification of 92% of included yeast isolates. Due to expensiveness of MALDI-TOF MS and sequencing, this combination strategy could be the most accurate and inexpensive alternative identification strategy for developing countries. Moreover, by the advent and development of cost-effective, reliable, and rapid PCR machines that cost 130 US dollars, 21-plex could be integrated in routine laboratories of developing and resource-limited countries to specifically identify 95% causative agents of yeast-related infections in human. Databases of MALDI-TOF MS, API 20C AUX, and the number of target species identified by 21-plex require further improvement to keep up with the diverse spectrum of yeast species.
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Affiliation(s)
- Amir Arastehfar
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Farnaz Daneshnia
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Mohammad Kord
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Roudbary
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Sayed Jamal Hashemi
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran.,Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran.,Zoonoses Research Center, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Hamid Badali
- Department of Medical Mycology, Invasive Fungi Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sassan Rezaie
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamiar Zomorodian
- Department of Medical Mycology and Parasitology, Basic Sciences in Infectious Diseases Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ferry Hagen
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Teun Boekhout
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Yeast Biodiversity Department, Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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29
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Zhao Y, Tsang CC, Xiao M, Chan JFW, Lau SKP, Kong F, Xu Y, Woo PCY. Yeast identification by sequencing, biochemical kits, MALDI-TOF MS and rep-PCR DNA fingerprinting. Med Mycol 2018; 56:816-827. [PMID: 29228397 DOI: 10.1093/mmy/myx118] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 10/12/2017] [Indexed: 01/14/2023] Open
Abstract
No study has comprehensively evaluated the performance of 28S nrDNA and ITS sequencing, commercial biochemical test kits, MALDI-TOF MS platforms, and the emerging rep-PCR DNA fingerprinting technology using a cohort of yeast strains collected from a clinical microbiology laboratory. In this study, using 71 clinically important yeast isolates (excluding Candida albicans) collected from a single centre, we determined the concordance of 28S nrDNA and ITS sequencing and evaluated the performance of two commercial test kits, two MALDI-TOF MS platforms, and rep-PCR DNA fingerprinting. 28S nrDNA and ITS sequencing showed complete agreement on the identities of the 71 isolates. Using sequencing results as the standard, 78.9% and 71.8% isolates were correctly identified using the API 20C AUX and Vitek 2 YST ID Card systems, respectively; and 90.1% and 80.3% isolates were correctly identified using the Bruker and Vitek MALDI-TOF MS platforms, respectively. Of the 18 strains belonging to the Candida parapsilosis species complex tested by DiversiLab automated rep-PCR DNA fingerprinting, all were identified only as Candida parapsilosis with similarities ≥93.2%, indicating the misidentification of Candida metapsilosis and Candida orthopsilosis. However, hierarchical cluster analysis of the rep-PCR DNA fingerprints of these three species within this species complex formed three different discrete clusters, indicating that this technology can potentially differentiate the three species. To achieve higher accuracies of identification, the databases of commercial biochemical test kits, MALDI-TOF MS platforms, and DiversiLab automated rep-PCR DNA fingerprinting needs further enrichment, particularly for uncommonly encountered yeast species.
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Affiliation(s)
- Ying Zhao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Chi-Ching Tsang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jasper F W Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
| | - Susanna K P Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.,Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research - Pathology West, Westmead Hospital, Westmead, New South Wales, Australia
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Patrick C Y Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.,Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
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Arastehfar A, Fang W, Pan W, Liao W, Yan L, Boekhout T. Identification of nine cryptic species of Candida albicans, C. glabrata, and C. parapsilosis complexes using one-step multiplex PCR. BMC Infect Dis 2018; 18:480. [PMID: 30253748 PMCID: PMC6156947 DOI: 10.1186/s12879-018-3381-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 09/13/2018] [Indexed: 01/24/2023] Open
Abstract
Background Candida albicans, Candida glabrata, and Candida parapsilosis are three prevalent causes of candidiasis, worldwide. These species are considered as nine medically important complex species. Limited knowledge about these newly recognized species prompted us to develop a one-step, multiplex PCR to detect and identify them in clinical settings. Methods Primers targeting Hyphal Wall Protein I gene for the C. albicans, C. dubliniensis, C. africana, Intergenic Spacer for the C. glabrata, C. nivariensis, C. bracarensis, and Intein and ITS rDNA for the C. parapsilosis, C. orthopsilosis, and C. metapsilosis were designed. Using 168 CBS reference strains and 280 clinical isolates, the specificity and reproducibility of the developed assay were evaluated. Results Our developed assay successfully identified and distinguished all the nine species. No cross-reaction with closely- and distantly-related yeast species, Aspergillus species and human DNA was observed, resulting in 100% specificity. The ambiguous results obtained by MALDI-TOF for C. albicans and C. africana were corrected by our 9-plex PCR assay. This assay identified all the cryptic complex species from two test sets from Iran and China, correctly. Conclusions Our developed multiplex assay is accurate, specific, cost/time-saving, and works without the tedious DNA extraction steps. It could be integrated into routine clinical laboratories and as a reliable identification tool and has the potential to be implemented into epidemiological studies to broaden the limited knowledge of cryptic species complexes. Electronic supplementary material The online version of this article (10.1186/s12879-018-3381-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht, 3584, the Netherlands
| | - Wenjie Fang
- Westerdijk Fungal Biodiversity Institute, Utrecht, 3584, the Netherlands.,Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China.
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - Liang Yan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, 3584, the Netherlands. .,Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China. .,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, 1012 WX, the Netherlands.
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Yu SY, Guo LN, Xiao M, Kudinha T, Kong F, Wang H, Cheng JW, Zhou ML, Xu H, Xu YC. Trichosporon dohaense, a rare pathogen of human invasive infections, and literature review. Infect Drug Resist 2018; 11:1537-1547. [PMID: 30288064 PMCID: PMC6160283 DOI: 10.2147/idr.s174301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Background Trichosporon dohaense is a rare fungal species that has not been described in human invasive infections. Patients and methods In this study, we investigated two T. dohaense isolates from patients with invasive infections in two hospitals in China, as part of the China Hospital Invasive Fungal Surveillance Net (CHIF-NET) program. Both patients were under immunocompromised conditions. Results On chromogenic agar, T. dohaense isolates were dark blue, similar to the color of Candida. tropicalis, but the characteristic moist colony appearance was quite different from that of T. asahii. The two isolates were misidentified as T. asahii and T. inkin by the VITEK 2 YST system. The rDNA internal transcribed spacer (ITS) region and the D1/D2 domain sequences of the two T. dohaense isolates were 100% identical to T. dohaense type strain CBS10761T. The sequence of the intergenic spacer region-1 also clearly distinguished the species. Of the three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry systems, Bruker Biotyper and Autobio MS correctly identified the two isolates to species level, whereas Vitek MS systems misidentified them as T. ovoides or T. asteroides. Echinocandins exhibited no in vitro activities against the two T. dohaense isolates. In addition, the isolates exhibited intermediate susceptibility to fluconazole (with minimal inhibitory concentrations [MICs] of 8 and 16 µg/mL) and itraconazole, voriconazole, and posaconazole (MICs of 0.25-1 µg/mL). T. dohaense demonstrated susceptibility to amphotericin B with MIC of 1 µg/mL. The MICs of fluconazole and voriconazole in our study were higher than the MIC50 of 62 for T. asahii isolates (4 and 0.064 µg/mL) in the CHIF-NET program. Conclusion This case study points to a possible emergence of T. dohaense as an opportunistic human invasive fungal pathogen, and the reduced susceptibility should be noted.
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Affiliation(s)
- Shu-Ying Yu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China, .,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China, .,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China,
| | - Li-Na Guo
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China, .,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China,
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China, .,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China,
| | - Timothy Kudinha
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, University of Sydney, Westmead Hospital, Westmead, NSW, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, Westmead Hospital, Westmead, NSW, Australia
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, University of Sydney, Westmead Hospital, Westmead, NSW, Australia
| | - He Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China, .,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China,
| | - Jing-Wei Cheng
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China, .,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China, .,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China,
| | - Meng-Lan Zhou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China, .,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China, .,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China,
| | - Hui Xu
- Department of Clinical Laboratory, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China,
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China, .,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China, .,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China,
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Molecular Analysis of Resistance and Detection of Non-Wild-Type Strains Using Etest Epidemiological Cutoff Values for Amphotericin B and Echinocandins for Bloodstream Candida Infections from a Tertiary Hospital in Qatar. Antimicrob Agents Chemother 2018; 62:AAC.00214-18. [PMID: 29941644 DOI: 10.1128/aac.00214-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 06/05/2018] [Indexed: 11/20/2022] Open
Abstract
A total of 301 Candida bloodstream isolates collected from 289 patients over 5 years at a tertiary hospital in Qatar were evaluated. Out of all Candida infections, 53% were diagnosed in patients admitted to the intensive care units. Steady increases in non-albicans Candida species were reported from 2009 to 2014 (30.2% for Candida albicans versus 69.8% for the other Candida species). Etest antifungal susceptibility testing was performed on all recovered clinical isolates to determine echinocandin (micafungin and anidulafungin) and amphotericin B susceptibilities and assess non-wild-type (non-WT) strains (strains for which MICs were above the epidemiological cutoff values). DNA sequence analysis was performed on all isolates to assess the presence of FKS mutations, which confer echinocandin resistance in Candida species. A total of 3.9% of isolates (12/301) among strains of C. albicans and C. orthopsilosis contained FKS hot spot mutations, including heterozygous mutations in FKS1 For C. tropicalis, the Etest appeared to overestimate strains non-WT for micafungin, anidulafungin, and amphotericin B, as 14%, 11%, and 35% of strains, respectively, had values above the epidemiological cutoff value. However, no FKS mutations were identified in this species. For all other species, micafungin best reported the echinocandin non-WT strains relative to the FKS genotype, as anidulafungin tended to overestimate non-wild-type strains. Besides C. tropicalis, few strains were classified as non-WT for amphotericin B.
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[Identification of Candida yeasts: Conventional methods and MALDI-TOF MS]. Rev Iberoam Micol 2018; 35:151-154. [PMID: 30078526 DOI: 10.1016/j.riam.2018.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 01/22/2018] [Accepted: 02/26/2018] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Invasive fungal infections are increasing, and Candida yeasts are the main cause. Species other than Candida albicans are becoming more frequent, and some of them may have variable patterns of susceptibility to antifungal agents, making it important to identify them correctly. Conventional identification methods used by most laboratories may present with drawbacks. Mass spectrometry (MALDI-TOF MS) has emerged as an alternative method. AIMS The aim of this study was to evaluate the concordance of the identification, at species level, by conventional methods (API) and MALDI-TOF MS. METHODS The following species and number of isolates were studied: Candida parapsilosis (28), Candida glabrata (34), Candida krusei (24), Candida tropicalis (45), Candida guilliermondii (30), C. albicans (28), Candida dubliniensis (6), Candida kefyr (1), and Candida lipolytica (1) from the strain collection of Autonomous City of Buenos Aires Mycology Network (RMCABA). The strains C. parapsilosis 22019, C. glabrata 90030, C. krusei 6258 and C. albicans 68548 from the American Type Culture Collection (ATCC) were also included. Discrepancies were resolved by genotyping. RESULTS AND CONCLUSIONS The direct concordance between the conventional identification method and MALDI-TOF MS was 92.5% (186/201).
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Abstract
Limited data are available on micafungin breakthrough fungemia (MBF), fungemia that develops on administration of micafungin, in patients with hematological disorders. We reviewed medical and microbiological records of patients with hematological disorders who developed MBF between January 2008 and June 2015. A total of 39 patients with MBF were identified, and Candida (30 strains) and non-Candida (9 strains) fungal species were recognized as causative strains. Among 35 stored strains, Candida parapsilosis (14 strains), Trichosporon asahii (7 strains), Candida glabrata (5 strains), and other fungal species (9 strains) were identified by sequencing. Neutropenia was identified as an independent predictor of non-Candida fungemia (P = 0.023). T. asahii was the most common causative strain (7/19) during neutropenia. The 14-day crude mortality rate of patients treated with early micafungin change (EMC) to other antifungal agents was lower than that of the patients not treated with EMC (14% versus 43%, P = 0.044). Most of the stored causative Candida strains were susceptible (80%) or showed wild-type susceptibility (72%) to micafungin. The MICs of voriconazole for T. asahii were low (range, 0.015 to 0.12 μg/ml), whereas the MICs of amphotericin B for T. asahii were high (range, 2 to 4 μg/ml). MBF caused by non-Candida fungus should be considered, especially in patients with neutropenia. EMC could improve early mortality. Based on epidemiology and drug susceptibility profiling, empirical voriconazole-containing therapy might be suitable for treating MBF during neutropenia to cover for T. asahii.
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Shao J, Wan Z, Li R, Yu J. Species Identification and Delineation of Pathogenic Mucorales by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2018; 56:e01886-17. [PMID: 29436422 PMCID: PMC5869826 DOI: 10.1128/jcm.01886-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/29/2018] [Indexed: 11/20/2022] Open
Abstract
This study aimed to validate the effectiveness of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification of filamentous fungi of the order Mucorales. A total of 111 isolates covering six genera preserved at the Research Center for Medical Mycology of Peking University were selected for MALDI-TOF MS analysis. We emphasized the study of 23 strains of Mucor irregularis predominantly isolated from patients in China. We first used the Bruker Filamentous Fungi library (v1.0) to identify all 111 isolates. To increase the identification rate, we created a compensatory in-house database, the Beijing Medical University (BMU) database, using 13 reference strains covering 6 species, including M. irregularis, Mucor hiemalis, Mucor racemosus, Cunninghamella bertholletiae, Cunninghamella phaeospora, and Cunninghamella echinulata All 111 isolates were then identified by MALDI-TOF MS using a combination of the Bruker library and BMU database. MALDI-TOF MS identified 55 (49.5%) and 74 (66.7%) isolates at the species and genus levels, respectively, using the Bruker Filamentous Fungi library v1.0 alone. A combination of the Bruker library and BMU database allowed MALDI-TOF MS to identify 90 (81.1%) and 111 (100%) isolates at the species and genus levels, respectively, with a significantly increased accuracy rate. MALDI-TOF MS poorly identified Mucorales when the Bruker library was used alone due to its lack of some fungal species. In contrast, this technique perfectly identified M. irregularis after main spectrum profiles (MSPs) of relevant reference strains were added to the Bruker library. With an expanded Bruker library, MALDI-TOF MS is an effective tool for the identification of pathogenic Mucorales.
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Affiliation(s)
- Jin Shao
- Department of Dermatology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
| | - Zhe Wan
- Department of Dermatology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
| | - Ruoyu Li
- Department of Dermatology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
| | - Jin Yu
- Department of Dermatology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
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Rico-Munoz E, Samson RA, Houbraken J. Mould spoilage of foods and beverages: Using the right methodology. Food Microbiol 2018; 81:51-62. [PMID: 30910088 DOI: 10.1016/j.fm.2018.03.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 11/19/2022]
Abstract
Fungal spoilage of products manufactured by the food and beverage industry imposes significant annual global revenue losses. Mould spoilage can also be a food safety issue due to the production of mycotoxins by these moulds. To prevent mould spoilage, it is essential that the associated mycobiota be adequately isolated and accurately identified. The main fungal groups associated with spoilage are the xerophilic, heat-resistant, preservative-resistant, anaerobic and psychrophilic fungi. To assess mould spoilage, the appropriate methodology and media must be used. While classic mycological detection methods can detect a broad range of fungi using well validated protocols, they are time consuming and results can take days or even weeks. New molecular detection methods are faster but require good DNA isolation techniques, expensive equipment and may detect viable and non-viable fungi that probably will not spoil a specific product. Although there is no complete and easy method for the detection of fungi in food it is important to be aware of the limitation of the methodology. More research is needed on the development of methods of detection and identification that are both faster and highly sensitive.
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Affiliation(s)
- Emilia Rico-Munoz
- BCN Research Laboratories, Inc., 2491 Stock Creek Blvd., Rockford, TN 37853, USA.
| | - Robert A Samson
- Westerdijk Fungal Biodiversity Institute, Dept. Applied and Industrial Mycology, Uppsalalaan 8, Utrecht, CT 3584, The Netherlands
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Dept. Applied and Industrial Mycology, Uppsalalaan 8, Utrecht, CT 3584, The Netherlands
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Quintilla R, Kolecka A, Casaregola S, Daniel HM, Houbraken J, Kostrzewa M, Boekhout T, Groenewald M. MALDI-TOF MS as a tool to identify foodborne yeasts and yeast-like fungi. Int J Food Microbiol 2018; 266:109-118. [DOI: 10.1016/j.ijfoodmicro.2017.11.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/23/2017] [Accepted: 11/20/2017] [Indexed: 01/09/2023]
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Borges FM, de Paula TO, Sarmiento MRA, de Oliveira MG, Pereira MLM, Toledo IV, Nascimento TC, Ferreira-Machado AB, Silva VL, Diniz CG. Fungal Diversity of Human Gut Microbiota Among Eutrophic, Overweight, and Obese Individuals Based on Aerobic Culture-Dependent Approach. Curr Microbiol 2018; 75:726-735. [PMID: 29368026 DOI: 10.1007/s00284-018-1438-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 01/16/2018] [Indexed: 12/14/2022]
Abstract
Fungi have a complex role in the intestinal tract, influencing health and disease, with dysbiosis contributing to obesity. Our objectives were to investigate fungal diversity in human gut microbiota among eutrophic, overweight, and obese. Epidemiological and nutritional information were collected from adult individuals, as well as stool samples processed for selective fungi isolation and identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (yeasts) or microculture (filamentous fungi). Further 18S rDNA sequencing was performed to confirm identification. The mean count of fungi was 241 CFU/g of feces. Differences in the population level of the filamentous fungi were observed within eutrophic and obese groups. Overall, 34 genera were identified. The predominant phylum was Ascomycota with 20 different genera, followed by Basidiomycota and Zygomycota. As for Ascomycota, the most prevalent species were Paecilomyces sp., Penicillium sp., Candida sp., Aspergillus sp., Fonsecaea sp., and Geotrichum sp. (76.39, 65.28, 59.72, 58.33, 12.50, and 9.72%, respectively). As for Basidiomycota, Trichosporon sp. and Rhodotorula sp. were the most prevalent (30.56 and 15.28%, respectively), and for Zygomycota, Rhizopus sp. and Mucor sp. were the most numerous (15.28 and 9.72%, respectively). As expected there is a mycobiota shift towards obesity, with slightly higher diversity associated to eutrophic individuals. This mycobiota shift seems also to be related to the nutritional behavior of the individuals, as observed that the macronutrients intake may be positively related to the different fungi occurrences. Other studies are needed to better understand relationships between mycobiota and obesity, which could be used in future obesity treatments.
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Affiliation(s)
- Francis M Borges
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Thaís O de Paula
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Marjorie R A Sarmiento
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Maycon G de Oliveira
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Maria L M Pereira
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Isabela V Toledo
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Thiago C Nascimento
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Alessandra B Ferreira-Machado
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Vânia L Silva
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Cláudio G Diniz
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil.
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Shokohi T, Aslani N, Ahangarkani F, Meyabadi MF, Hagen F, Meis JF, Boekhout T, Kolecka A, Badali H. Candida infanticola and Candida spencermartinsiae yeasts: Possible emerging species in cancer patients. Microb Pathog 2017; 115:353-357. [PMID: 29292174 DOI: 10.1016/j.micpath.2017.12.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 11/22/2017] [Accepted: 12/28/2017] [Indexed: 02/05/2023]
Abstract
Opportunistic infections due to Candida species occur frequently in intensive care settings. We investigated the prevalence of Candida species among 65 clinical specimens obtained from 200 cancer patients by phenotypic and molecular (ITS sequencing and AFLP) methods. Among the 65 yeast isolates, Candida albicans was the most commonly isolated species (n = 34, 52.3%), whereas other Candida species comprised 47.7% (n = 31) and consisted of Candida glabrata (n = 14, 21.5%), Candida tropicalis (n = 5, 7.7%) and uncommon Candida species (n = 12, 18.5%) such as Candida pelliculosa (n = 3, 4.6%), Pichia kudriavzevii (= Candida krusei, n = 2, 3.1%), Candida orthopsilosis (n = 2, 3.1%), Candida parapsilosis (n = 1, 1.5%), Candida infanticola (n = 2, 3.1%), Candida spencermartinsiae (n = 1, 1.5%), and Kluyveromyces marxianus (=Candida kefyr, n = 1, 1.5%). Candida infanticola and Candida spencermartinsiae were recovered from oral lesions of cancer patients. Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) easily confirmed these isolates as less common Candida isolates (4.6%). The in vitro antifungal susceptibilities of C. spencermartinsiae and the two strains of C. infanticola were determined according to CLSI guidelines (M27-A3). MIC results among these isolates showed they were susceptible to isavuconazole, posaconazole and voriconazole, however, fluconazole and caspofungin had high MIC values. These Candida species that may occur more commonly in infections remain unnoticed using commonly used phenotypical methods in routine microbiology laboratories. MALDI-TOF MS proved to be a more fast and robust diagnostic technique for identification of the yeasts isolated from different clinical specimens of cancer patients.
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Affiliation(s)
- Tahereh Shokohi
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Narges Aslani
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Fatemeh Ahangarkani
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Masoumeh Fatahi Meyabadi
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands; Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital (CWZ), and Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital (CWZ), and Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands; Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands; Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Anna Kolecka
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Hamid Badali
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
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Iatta R, Battista M, Miragliotta G, Boekhout T, Otranto D, Cafarchia C. Blood culture procedures and diagnosis of Malassezia furfur bloodstream infections: Strength and weakness. Med Mycol 2017; 56:828-833. [DOI: 10.1093/mmy/myx122] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/12/2017] [Indexed: 01/26/2023] Open
Affiliation(s)
- Roberta Iatta
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari “Aldo Moro”, Italy
| | | | - Giuseppe Miragliotta
- Dipartimento Interdisciplinare di Medicina, Università degli Studi di Bari “Aldo Moro”, Italy
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Centre, Uppsalalaan, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Domenico Otranto
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari “Aldo Moro”, Italy
| | - Claudia Cafarchia
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari “Aldo Moro”, Italy
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41
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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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42
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A Comprehensive Analysis of MALDI-TOF MS and Ribosomal DNA Sequencing for Identification of Clinical Yeasts. CURRENT FUNGAL INFECTION REPORTS 2017. [DOI: 10.1007/s12281-017-0297-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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43
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AbdulWahab A, Salah H, Chandra P, Taj-Aldeen SJ. Persistence of Candida dubliniensis and lung function in patients with cystic fibrosis. BMC Res Notes 2017; 10:326. [PMID: 28747217 PMCID: PMC5530559 DOI: 10.1186/s13104-017-2656-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/21/2017] [Indexed: 01/03/2023] Open
Abstract
Objectives Candida dubliniensis is an emerging yeast and demonstrated a high adherence property to cystic fibrosis respiratory tract. Therefore, it is important to determine the persistence of C. dubliniensis and to assess the possible relationship to the body mass index (BMI) and forced expiratory volume in 1st second (FEV1). Results Candida isolates were identified by MALDI-TOF MS to species level from 40/52 (76.9%) cystic fibrosis patients. C. dubliniensis was the most common organism isolated from 50/77 (65%) lower respiratory specimens of 29 patients. Patients with persistent C. dubliniensis isolates have higher mean BMI in comparison to intermittent C. dubliniensis group. However, this difference did not reach statistical significance (P = 0.539). In contrast, patients with persistent C. dubliniensis isolates have significantly lower FEV1% mean in comparison to intermittent C. dubliniensis group particularly at initial two visits (P < 0.05); however, at subsequent visit the difference observed was not statistically significant (P = 0.456). The persistence of C. dubliniensis is more frequent in adults having more advanced disease, co-infections with chronic P. aeruginosa, cystic fibrosis related diabetes, long-term nebulized tobramycin and oral Zithromax therapy than patients with intermittent C. dubliniensis. Patients with persistent C. dubliniensis have lower FEV1 percentage and higher BMI than the intermittent C. dubliniensis.
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Affiliation(s)
- Atqah AbdulWahab
- Departments of Pediatrics, Hamad Medical Corporation, Doha, Qatar. .,Weill Cornell Medicine, Doha, Qatar.
| | - Husam Salah
- Microbiology Division, Laboratory of Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar.,CBS Fungal Biodiversity Center, Utrecht, The Netherlands
| | - Prem Chandra
- Department of Medical Research, Hamad Medical Corporation, Doha, Qatar
| | - Saad J Taj-Aldeen
- Weill Cornell Medicine, Doha, Qatar.,Microbiology Division, Laboratory of Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
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44
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Cavanna C, Lallitto F, Mangione F, Tamarozzi F, Marone P, Ceriana P. Fungemia due to Saprochaete capitata in a non-neutropenic patient hospitalized in an intensive care unit after cardiac surgery. J Mycol Med 2017; 27:281-284. [DOI: 10.1016/j.mycmed.2017.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/28/2016] [Accepted: 01/13/2017] [Indexed: 11/16/2022]
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45
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Wilson DA, Young S, Timm K, Novak-Weekley S, Marlowe EM, Madisen N, Lillie JL, Ledeboer NA, Smith R, Hyke J, Griego-Fullbright C, Jim P, Granato PA, Faron ML, Cumpio J, Buchan BW, Procop GW. Multicenter Evaluation of the Bruker MALDI Biotyper CA System for the Identification of Clinically Important Bacteria and Yeasts. Am J Clin Pathol 2017; 147:623-631. [PMID: 28505220 DOI: 10.1093/ajcp/aqw225] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES A report on the multicenter evaluation of the Bruker MALDI Biotyper CA System (MBT-CA; Bruker Daltonics, Billerica, MA) for the identification of clinically important bacteria and yeasts. METHODS In total, 4,399 isolates of medically important bacteria and yeasts were assessed in the MBT-CA. These included 2,262 aerobic gram-positive (AGP) bacteria, 792 aerobic gram-negative (AGN) bacteria 530 anaerobic (AnA) bacteria, and 815 yeasts (YSTs). Three processing methods were assesed. RESULTS Overall, 98.4% (4,329/4,399) of all bacterial and yeast isolates were correctly identified to the genus and species/species complex level, and 95.7% of isolates were identified with a high degree of confidence. The percentage correctly identified and the percentage identified correctly with a high level of confidence, respectively, were as follows: AGP bacteria (98.6%/96.5%), AGN bacteria (98.5%/96.8%), AnA bacteria (98.5%/97.4%), and YSTs (97.8%/87.6%). The extended direct transfer method was only minimally superior to the direct transfer method for bacteria (89.9% vs 86.8%, respectively) but significantly superior for yeast isolates (74.0% vs 48.9%, respectively). CONCLUSIONS The Bruker MALDI Biotyper CA System accurately identifies most clinically important bacteria and yeasts and has optional processing methods to improve isolate characterization.
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Affiliation(s)
| | - Stephen Young
- Tricore Reference Laboratories, Albuquerque, NM
- Department of Pathology, The University of New Mexico Health Sciences Center, Albuquerque
| | - Karen Timm
- Tricore Reference Laboratories, Albuquerque, NM
| | - Susan Novak-Weekley
- Kaiser Permanente Southern California Permanente Medical Group Regional Reference Laboratories, North Hollywood, CA
| | - Elizabeth M Marlowe
- Kaiser Permanente Southern California Permanente Medical Group Regional Reference Laboratories, North Hollywood, CA
| | | | | | - Nathan A Ledeboer
- Wisconsin Diagnostic Laboratory, Milwaukee
- Medical College of Wisconsin, Milwaukee
| | | | - Josh Hyke
- Wisconsin Diagnostic Laboratory, Milwaukee
| | | | | | - Paul A Granato
- Laboratory Alliance of Central New York, Fayetteville
- SUNY Upstate Medical University, Syracuse, NY
| | | | - Joven Cumpio
- Kaiser Permanente Southern California Permanente Medical Group Regional Reference Laboratories, North Hollywood, CA
| | - Blake W Buchan
- Wisconsin Diagnostic Laboratory, Milwaukee
- Medical College of Wisconsin, Milwaukee
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46
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Evaluating and Improving Vitek MS for Identification of Clinically Relevant Species of Trichosporon and the Closely Related Genera Cutaneotrichosporon and Apiotrichum. J Clin Microbiol 2017; 55:2439-2444. [PMID: 28539340 DOI: 10.1128/jcm.00461-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 05/16/2017] [Indexed: 12/27/2022] Open
Abstract
Trichosporon species are relevant etiologic agents of hospital-acquired infections. High mortality rates are attributed to Trichosporon deep-seated infections in immunocompromised individuals, making fast and accurate species identification relevant for hastening the discovery of best-targeted therapy. Recently, Trichosporon taxonomy has been reassessed, and three genera have been proposed for the pathogenic species: Trichosporon, Cutaneotrichosporon, and Apiotrichum Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has replaced old phenotypic methods for microorganism identification in clinical laboratories, but spectral profile databases have to be evaluated and improved for optimal species identification performance. Vitek MS (bioMérieux) is one of the commercially available MALDI-TOF MS platforms for pathogen identification, and its spectral profile databases remain poorly evaluated for Trichosporon, Cutaneotrichosporon, and Apiotrichum species identification. We herein evaluated and improved Vitek MS for the identification of the main clinical relevant species of Trichosporon, Cutaneotrichosporon, and Apiotrichum using a large set of strains and isolates belonging to different yeast collections in Brazil and France.
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47
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Hazirolan G, Aypak A, Aksu N. An unusual case of urinary tract infection caused by Saprochaete capitata under anidulafungin treatment. J Mycol Med 2017; 27:387-390. [PMID: 28478968 DOI: 10.1016/j.mycmed.2017.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/09/2017] [Accepted: 04/04/2017] [Indexed: 11/28/2022]
Abstract
Saprochaete capitata may cause uncommon severe infections, especially in immunocompromised patients. Here, we describe a rare case of urinary tract infection by S. capitata in a chronic kidney disease and diabetes mellitus patient, which occur during anidulafungin therapy. Mycological examinations of urine were positive to S. capitata identified by mass spectrometry and confirmed by ITS sequencing. Minimum inhibitory concentration (MIC) of the isolate for amphotericin B, fluconazole, itraconazole, voriconazole and, anidulafungin were 2, 16, 1, 1, and 8μg/mL, respectively. Presence of S. capitata infection was not known. Clinicians should be aware about these rare opportunistic fungal pathogens, particularly those with intrinsic or variable resistance to antifungals including echinocandins.
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Affiliation(s)
- G Hazirolan
- Medical microbiology, Ankara Numune training and research hospital, Ulku Mahallesi Talatpasa Bulvari No. 5 Altindag, 06100 Ankara, Turkey.
| | - A Aypak
- Clinical microbiology and infectious disease department, Ankara Numune training and research hospital, Ulku Mahallesi Talatpasa Bulvari, No. 5 Altindag, 06100 Ankara, Turkey
| | - N Aksu
- Medical microbiology, Ankara Numune training and research hospital, Ulku Mahallesi Talatpasa Bulvari No. 5 Altindag, 06100 Ankara, Turkey
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48
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Huang Y, Wang J, Zhang M, Zhu M, Wang M, Sun Y, Gu H, Cao J, Li X, Zhang S, Lu X. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for rapid identification of fungal rhinosinusitis pathogens. J Med Microbiol 2017; 66:328-333. [PMID: 28100314 DOI: 10.1099/jmm.0.000435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yanfei Huang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, PR China
| | - Mingxin Zhang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Min Zhu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Mei Wang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Yufeng Sun
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Haitong Gu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Jingjing Cao
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Xue Li
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Shaoya Zhang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Xinxin Lu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
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Durán Graeff L, Seidel D, Vehreschild MJGT, Hamprecht A, Kindo A, Racil Z, Demeter J, De Hoog S, Aurbach U, Ziegler M, Wisplinghoff H, Cornely OA. Invasive infections due toSaprochaeteandGeotrichumspecies: Report of 23 cases from the FungiScope Registry. Mycoses 2017; 60:273-279. [DOI: 10.1111/myc.12595] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 12/07/2016] [Accepted: 12/07/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Luisa Durán Graeff
- Division of Infectious Diseases; Department I of Internal Medicine; University Hospital Cologne; Cologne Germany
| | - Danila Seidel
- Division of Infectious Diseases; Department I of Internal Medicine; University Hospital Cologne; Cologne Germany
| | - Maria J. G. T. Vehreschild
- Division of Infectious Diseases; Department I of Internal Medicine; University Hospital Cologne; Cologne Germany
| | - Axel Hamprecht
- Institute for Medical Microbiology, Immunology and Hygiene; University Hospital of Cologne; Cologne Germany
| | - Anupma Kindo
- Department of Microbiology; Sri Ramachandra Medical College and Research Institute; Chennai India
| | - Zdenek Racil
- Department of Internal Medicine, Hematology and Oncology; Masaryk University and University Hospital Brno; Brno Czech Republic
| | - Judit Demeter
- First Department of Internal Medicine; Division of Hematology; Semmelweis University; Budapest Hungary
| | - Sybren De Hoog
- CBS-KNAW; Fungal Biodiversity Centre; Utrecht Netherlands
| | - Ute Aurbach
- Laboratory Dr. Wisplinghoff; Cologne Germany
| | | | - Hilmar Wisplinghoff
- Institute for Medical Microbiology, Immunology and Hygiene; University Hospital of Cologne; Cologne Germany
- Laboratory Dr. Wisplinghoff; Cologne Germany
- Institute for Virology and Medical Microbiology; University Witten/Herdecke; Witten Germany
| | - Oliver A. Cornely
- Division of Infectious Diseases; Department I of Internal Medicine; University Hospital Cologne; Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); Cologne Germany
- German Centre for Infection Research; Partner Site Bonn-Cologne; Cologne Germany
- Clinical Trials Centre Cologne; ZKS Köln; Cologne Germany
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50
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Cassagne C, Normand AC, L'Ollivier C, Ranque S, Piarroux R. Performance of MALDI-TOF MS platforms for fungal identification. Mycoses 2016; 59:678-690. [DOI: 10.1111/myc.12506] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 03/04/2016] [Accepted: 03/12/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Carole Cassagne
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Anne-Cécile Normand
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
| | - Coralie L'Ollivier
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Stéphane Ranque
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Renaud Piarroux
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
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