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Gonçalves C, Harrison MC, Steenwyk JL, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Rokas A. Diverse signatures of convergent evolution in cactus-associated yeasts. PLoS Biol 2024; 22:e3002832. [PMID: 39312572 PMCID: PMC11449361 DOI: 10.1371/journal.pbio.3002832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 10/03/2024] [Accepted: 09/05/2024] [Indexed: 09/25/2024] Open
Abstract
Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently approximately 17 times. Using a machine learning-based approach, we further found that cactophily can be predicted with 76% accuracy from both functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which we found to be likely associated with altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall-degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved independently through disparate molecular mechanisms. Notably, we found that multiple cactophilic species and their close relatives have been reported as emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle-and perhaps more generally lifestyles favoring thermotolerance-might preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high-throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.
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Affiliation(s)
- Carla Gonçalves
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- Associate Laboratory i4HB—Institute for Health and Bioeconomy and UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Dana A. Opulente
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Biology Department, Villanova University, Villanova, Pennsylvania, United States of America
| | - Abigail L. LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - John F. Wolters
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou, China
| | | | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
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Caldwell AT, Gabaldón T, Mixão V, Wengenack NL, Westley BP, Stevens RW. An inconspicuous identification: Isolation and identification of a novel Pichia species presenting as fungemia following cardiac surgery. Int J Infect Dis 2024; 143:107040. [PMID: 38580069 DOI: 10.1016/j.ijid.2024.107040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024] Open
Abstract
Fungemia is common in critically ill patient populations, and is associated with a high rate of mortality, especially when caused by nonalbicans Candida species. Herein, we describe a fatal case of fungemia following cardiothoracic surgery in which the organism, initially identified as Candida inconspicua, represents a novel species: Pichia alaskaensis.
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Affiliation(s)
- Allorie T Caldwell
- Department of Pharmacy, Providence Alaska Medical Center, Anchorage, AK, USA
| | - Toni Gabaldón
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain; Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Verónica Mixão
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain; Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
| | | | - Benjamin P Westley
- Division of Infectious Disease, Providence Alaska Medical Center, Anchorage, AK, USA
| | - Ryan W Stevens
- Department of Pharmacy, Mayo Clinic, Rochester, MN, USA.
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3
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Gonçalves C, Harrison MC, Steenwyk JL, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Rokas A. Diverse signatures of convergent evolution in cacti-associated yeasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557833. [PMID: 37745407 PMCID: PMC10515907 DOI: 10.1101/2023.09.14.557833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently ~17 times. Using machine-learning, we further found that cactophily can be predicted with 76% accuracy from functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which is likely associated with duplication and altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall-degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved through disparate molecular mechanisms. Remarkably, multiple cactophilic lineages and their close relatives are emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle-and perhaps more generally lifestyles favoring thermotolerance-may preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.
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Affiliation(s)
- Carla Gonçalves
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Present address: Associate Laboratory i4HB—Institute for Health and Bioeconomy and UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Present address: UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Marie-Claire Harrison
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Jacob L. Steenwyk
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Dana A. Opulente
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institu te, University of Wisconsin-Madison, Madison, WI 53726, USA
- Biology Department, Villanova University, Villanova, PA 19085, USA
| | - Abigail L. LaBella
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte NC 28223
| | - John F. Wolters
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institu te, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Xiaofan Zhou
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | | | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institu te, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Antonis Rokas
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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Kucukoglu O, Sariguzel FM, Koc AN, Parkan OM. Molecular epidemiology, virulence factors, and antifungal susceptibility of Candida inconspicua strains isolated from clinical samples in Turkey. Diagn Microbiol Infect Dis 2023; 106:115915. [PMID: 36947944 DOI: 10.1016/j.diagmicrobio.2023.115915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/26/2022] [Accepted: 01/30/2023] [Indexed: 02/09/2023]
Abstract
In this study, it was aimed to evaluate the molecular epidemiology, virulence factors, and antifungal susceptibility of clinical Candida inconspicua isolates. All isolates were identified by phenotypic methods and sequence analysis of ITS 1-2, D1/D2, EF-1 alpha. Proteinase, phospholipase, and esterase activities, biofilm formation, and antifungal susceptibilities were determined. All thirty isolates identified as Candida norvegensis by phenotypic methods were reidentified as C. inconspicua by sequence analysis, demonstrating the inadequacy of phenotypic methods to differentiate these 2 species. The gene regions examined in terms of determining evolutionary relatedness did not show intraspecies nucleotide variations. Therefore, different molecular approaches are needed to evaluate molecular epidemiology. Esterase, phospholipase, and biofilm formation were found to be positive in 100%, 100%, and 36.6% of the strains, respectively. The MIC50/MIC90 values for fluconazole and flucytosine were found to be higher than the other tested antifungals, which should be taken into account in the treatment.
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Affiliation(s)
- Osman Kucukoglu
- Department of Medical Microbiology, Erciyes University Medical Faculty, Kayseri, Turkey
| | - Fatma Mutlu Sariguzel
- Department of Medical Microbiology, Erciyes University Medical Faculty, Kayseri, Turkey.
| | - Ayse Nedret Koc
- Department of Medical Microbiology, Erciyes University Medical Faculty, Kayseri, Turkey
| | - Omur Mustafa Parkan
- Department of Medical Microbiology, Erciyes University Medical Faculty, Kayseri, Turkey
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Overview on the Infections Related to Rare Candida species. Pathogens 2022; 11:pathogens11090963. [PMID: 36145394 PMCID: PMC9505029 DOI: 10.3390/pathogens11090963] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/30/2022] Open
Abstract
Atypical Candida spp. infections are rising, mostly due to the increasing numbers of immunocompromised patients. The most common Candida spp. is still Candida albicans; however, in the last decades, there has been an increase in non-Candida albicans Candida species infections (e.g., Candida glabrata, Candida parapsilosis, and Candida tropicalis). Furthermore, in the last 10 years, the reports on uncommon yeasts, such as Candida lusitaniae, Candida intermedia, or Candida norvegensis, have also worryingly increased. This review summarizes the information, mostly related to the last decade, regarding the infections, diagnosis, treatment, and resistance of these uncommon Candida species. In general, there has been an increase in the number of articles associated with the incidence of these species. Additionally, in several cases, there was a suggestive antifungal resistance, particularly with azoles, which is troublesome for therapeutic success.
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Willaert RG, Kayacan Y, Devreese B. The Flo Adhesin Family. Pathogens 2021; 10:pathogens10111397. [PMID: 34832553 PMCID: PMC8621652 DOI: 10.3390/pathogens10111397] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 12/14/2022] Open
Abstract
The first step in the infection of fungal pathogens in humans is the adhesion of the pathogen to host tissue cells or abiotic surfaces such as catheters and implants. One of the main players involved in this are the expressed cell wall adhesins. Here, we review the Flo adhesin family and their involvement in the adhesion of these yeasts during human infections. Firstly, we redefined the Flo adhesin family based on the domain architectures that are present in the Flo adhesins and their functions, and set up a new classification of Flo adhesins. Next, the structure, function, and adhesion mechanisms of the Flo adhesins whose structure has been solved are discussed in detail. Finally, we identified from Pfam database datamining yeasts that could express Flo adhesins and are encountered in human infections and their adhesin architectures. These yeasts are discussed in relation to their adhesion characteristics and involvement in infections.
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Affiliation(s)
- Ronnie G. Willaert
- Research Group Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium;
- Alliance Research Group VUB-UGent NanoMicrobiology (NAMI), 1050 Brussels, Belgium;
- International Joint Research Group VUB-EPFL NanoBiotechnology & NanoMedicine (NANO), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
- Correspondence: ; Tel.: +32-2629-1846
| | - Yeseren Kayacan
- Research Group Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium;
- Alliance Research Group VUB-UGent NanoMicrobiology (NAMI), 1050 Brussels, Belgium;
- International Joint Research Group VUB-EPFL NanoBiotechnology & NanoMedicine (NANO), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Bart Devreese
- Alliance Research Group VUB-UGent NanoMicrobiology (NAMI), 1050 Brussels, Belgium;
- International Joint Research Group VUB-EPFL NanoBiotechnology & NanoMedicine (NANO), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Laboratory for Microbiology, Gent University (UGent), 9000 Gent, Belgium
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Genome Assemblies of Two Rare Opportunistic Yeast Pathogens: Diutina rugosa (syn. Candida rugosa) and Trichomonascus ciferrii (syn. Candida ciferrii). G3-GENES GENOMES GENETICS 2019; 9:3921-3927. [PMID: 31575637 PMCID: PMC6893180 DOI: 10.1534/g3.119.400762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Infections caused by opportunistic yeast pathogens have increased over the last years. These infections can be originated by a large number of diverse yeast species of varying incidence, and with distinct clinically relevant phenotypic traits, such as different susceptibility profiles to antifungal drugs, which challenge diagnosis and treatment. Diutina rugosa (syn. Candida rugosa) and Trichomonascus ciferrii (syn. Candida ciferrii) are two opportunistic rare yeast pathogens, which low incidence (< 1%) limits available clinical experience. Furthermore, these yeasts have elevated Minimum Inhibitory Concentration (MIC) levels to at least one class of antifungal agents. This makes it more difficult to manage their infections, and thus they are associated with high rates of mortality and clinical failure. With the aim of improving our knowledge on these opportunistic pathogens, we assembled and annotated their genomes. A phylogenomics approach revealed that genes specifically duplicated in each of the two species are often involved in transmembrane transport activities. These genomes and the reconstructed complete catalog of gene phylogenies and homology relationships constitute useful resources for future studies on these pathogens.
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Fluconazole Resistance in Isolates of Uncommon Pathogenic Yeast Species from the United Kingdom. Antimicrob Agents Chemother 2019; 63:AAC.00211-19. [PMID: 31182537 DOI: 10.1128/aac.00211-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/07/2019] [Indexed: 01/12/2023] Open
Abstract
The triazole drug fluconazole remains one of the most commonly prescribed antifungal drugs, both for prophylaxis in high-risk patients and also as a second-line treatment option for invasive Candida infections. Established susceptibility profiles and clinical interpretive breakpoints are available for fluconazole with Candida albicans, Candida glabrata, Candida tropicalis, and Candida parapsilosis, which account for the majority of infections due to pathogenic yeast species. However, less common species for which only limited susceptibility data are available are increasingly reported in high-risk patients and from breakthrough infections. The UK National Mycology Reference Laboratory performs routine antifungal susceptibility testing of clinical isolates of pathogenic yeast submitted from across the United Kingdom. Between 2002 and 2016, ∼32,000 isolates were referred, encompassing 94 different yeast species. Here, we present fluconazole antifungal susceptibility data generated using a CLSI methodology over this 15-year period for 82 species (2,004 isolates) of less common yeast and yeast-like fungi, and amphotericin B, fluconazole, itraconazole, voriconazole, posaconazole, and anidulafungin, with members of the Nakaseomyces clade (C. glabrata, Candida nivariensis, and Candida bracarensis). At least 22 different teleomorph genera, comprising 45 species, exhibited high MICs when tested with fluconazole (>20% of isolates with MICs higher than the clinical breakpoint [≥8 mg/liter] proposed for C. albicans). Since several of these species have been reported anecdotally from breakthrough infections and therapeutic failures in patients receiving fluconazole, the current study underscores the importance of rapid and accurate yeast identification and may aid clinicians dealing with infections with rarer yeasts to decide whether fluconazole would be appropriate.
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Hoang MTV, Irinyi L, Chen SCA, Sorrell TC, Meyer W. Dual DNA Barcoding for the Molecular Identification of the Agents of Invasive Fungal Infections. Front Microbiol 2019; 10:1647. [PMID: 31379792 PMCID: PMC6657352 DOI: 10.3389/fmicb.2019.01647] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/03/2019] [Indexed: 12/27/2022] Open
Abstract
Invasive fungal infections, such as aspergillosis, candidiasis, and cryptococcosis, have significantly increased among immunocompromised people. To tackle these infections the first and most decisive step is the accurate identification of the causal pathogen. Routine identification of invasive fungal infections has progressed away from culture-dependent methods toward molecular techniques, including DNA barcoding, a highly efficient and widely used diagnostic technique. Fungal DNA barcoding previously relied on a single barcoding region, the internal transcribed spacer (ITS) region. However, this allowed only for 75% of all fungi to be correctly identified. As such, the translational elongation factor 1α (TEF1α) was recently introduced as the secondary barcode region to close the gap. Both loci together form the dual fungal DNA barcoding scheme. As a result, the ISHAM Barcoding Database has been expanded to include sequences for both barcoding regions to enable practical implementation of the dual barcoding scheme into clinical practice. The present study investigates the impact of the secondary barcode on the identification of clinically important fungal taxa, that have been demonstrated to cause severe invasive disease. Analysis of the barcoding regions was performed using barcoding gap analysis based on the genetic distances generated with the Kimura 2-parameter model. The secondary barcode demonstrated an improvement in identification for all taxa that were unidentifiable with the primary barcode, and when combined with the primary barcode ensured accurate identification for all taxa analyzed, making DNA barcoding an important, efficient and reliable addition to the diagnostic toolset of invasive fungal infections.
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Affiliation(s)
- Minh Thuy Vi Hoang
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- The Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Sharon C. A. Chen
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Tania C. Sorrell
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Research and Education Network, Westmead Hospital, Westmead, NSW, Australia
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Pérez-Hansen A, Lass-Flörl C, Lackner M, Aigner M, Alastruey-Izquierdo A, Arikan-Akdagli S, Bader O, Becker K, Boekhout T, Buzina W, Cornely OA, Hamal P, Kidd SE, Kurzai O, Lagrou K, Lopes Colombo A, Mares M, Masoud H, Meis JF, Oliveri S, Rodloff AC, Orth-Höller D, Guerrero-Lozano I, Sanguinetti M, Segal E, Taj-Aldeen SJ, Tortorano AM, Trovato L, Walther G, Willinger B. Antifungal susceptibility profiles of rare ascomycetous yeasts. J Antimicrob Chemother 2019; 74:2649-2656. [DOI: 10.1093/jac/dkz231] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/30/2019] [Accepted: 05/04/2019] [Indexed: 12/21/2022] Open
Abstract
AbstractObjectivesTo generate antifungal susceptibility patterns for Trichomonascus ciferrii (Candida ciferrii), Candida inconspicua (Torulopsis inconspicua) and Diutina rugosa species complex (Candida rugosa species complex), and to provide key parameters such as MIC50, MIC90 and tentative epidemiological cut-off values (TECOFFs).MethodsOur strain set included isolates of clinical origin: C. inconspicua (n = 168), D. rugosa species complex (n = 90) [Candida pararugosa (n = 60), D. rugosa (n = 26) and Candida mesorugosa (n = 4)], Pichia norvegensis (Candida norvegensis) (n = 15) and T. ciferrii (n = 8). Identification was performed by MALDI-TOF MS or internal transcribed spacer sequencing. Antifungal susceptibility patterns were generated for azoles, echinocandins and amphotericin B using commercial Etest and the EUCAST broth microdilution method v7.3.1. Essential agreement (EA) was calculated for Etest and EUCAST.ResultsC. inconspicua, C. pararugosa and P. norvegensis showed elevated azole MICs (MIC50 ≥0.06 mg/L), and D. rugosa and C. pararugosa elevated echinocandin MICs (MIC50 ≥0.06 mg/L). EA between methods was generally low (<90%); EA averaged 77.45%. TECOFFs were suggested for C. inconspicua and D. rugosa species complex.ConclusionsRare yeast species tested shared high fluconazole MICs. D. rugosa species complex displayed high echinocandin MICs, while C. inconspicua and P. norvegensis were found to have high azole MICs. Overall, the agreement between EUCAST and Etest was poor and therefore MIC values generated with Etest cannot be directly compared with EUCAST results.
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Affiliation(s)
- Antonio Pérez-Hansen
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, Austria
| | - Michaela Lackner
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, Austria
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11
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Mixão V, Hansen AP, Saus E, Boekhout T, Lass-Florl C, Gabaldón T. Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Candida inconspicua Uncovers Its Hybrid Origin. Front Genet 2019; 10:383. [PMID: 31105748 PMCID: PMC6494940 DOI: 10.3389/fgene.2019.00383] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/09/2019] [Indexed: 12/02/2022] Open
Abstract
Fungal infections such as those caused by Candida species are increasingly common complications in immunocompromised patients. The list of causative agents of candidiasis is growing and comprises a set of emerging species whose relative global incidence is rare but recurrent. This is the case of Candida inconspicua, which prevalence has increased 10-fold over the last years. To gain novel insights into the emergence of this opportunistic pathogen and its genetic diversity, we performed whole genome sequencing of the type strain (CBS180), and of 10 other clinical isolates. Our results revealed high levels of genetic heterozygosity structured in non-homogeneous patterns, which are indicative of a hybrid genome shaped by events of loss of heterozygosity (LOH). All analyzed strains were hybrids and could be clustered into two distinct clades. We found large variability across strains in terms of ploidy, patterns of LOH, and mitochondrial genome heterogeneity that suggest potential admixture between hybrids. Altogether, our results identify a new hybrid species with virulence potential toward humans and underscore the potential role of hybridization in the emergence of novel pathogenic lineages.
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Affiliation(s)
- Verónica Mixão
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Antonio Perez Hansen
- Division of Hygiene and Medical Microbiology, Innsbruck Medical University, Innsbruck, Austria
| | - Ester Saus
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Cornelia Lass-Florl
- Division of Hygiene and Medical Microbiology, Innsbruck Medical University, Innsbruck, Austria
| | - Toni Gabaldón
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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12
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Evaluation of the ePlex Blood Culture Identification Panels for Detection of Pathogens in Bloodstream Infections. J Clin Microbiol 2019; 57:JCM.01597-18. [PMID: 30487304 PMCID: PMC6355516 DOI: 10.1128/jcm.01597-18] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/20/2018] [Indexed: 01/05/2023] Open
Abstract
Rapid identification and susceptibility testing results are of importance for the early appropriate therapy of bloodstream infections. The ePlex (GenMark Diagnostics) blood culture identification (BCID) panels are fully automated PCR-based assays designed to identify Gram-positive and Gram-negative bacteria, fungi, and bacterial resistance genes within 1.5 h from positive blood culture. Rapid identification and susceptibility testing results are of importance for the early appropriate therapy of bloodstream infections. The ePlex (GenMark Diagnostics) blood culture identification (BCID) panels are fully automated PCR-based assays designed to identify Gram-positive and Gram-negative bacteria, fungi, and bacterial resistance genes within 1.5 h from positive blood culture. Consecutive non-duplicate positive blood culture episodes were tested by the ePlex system prospectively. The choice of panel(s) (Gram-positive, Gram-negative, and/or fungal pathogens) was defined by Gram-stained microscopy of blood culture-positive bottles (BacT/Alert; bioMérieux). Results with the ePlex panels were compared to the identification results obtained by standard culture-based workflow. In total, 216 positive blood culture episodes were evaluable, yielding 263 identification results. The sensitivity/positive predictive value for detection by the ePlex panels of targeted cultured isolates were 97% and 99% for the Gram-positive panel and 99% and 96% for the Gram-negative panel, resulting in overall agreement rates of 96% and 94% for the Gram-positive and Gram-negative panel, respectively. All 26 samples with targeted resistance results were correctly detected by the ePlex panels. The ePlex panels provided highly accurate results and proved to be an excellent diagnostic tool for the rapid identification of pathogens causing bloodstream infections. The short time to results may be of added value for optimizing the clinical management of patients with sepsis.
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13
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Panpetch W, Somboonna N, Palasuk M, Hiengrach P, Finkelman M, Tumwasorn S, Leelahavanichkul A. Oral Candida administration in a Clostridium difficile mouse model worsens disease severity but is attenuated by Bifidobacterium. PLoS One 2019; 14:e0210798. [PMID: 30645630 PMCID: PMC6333342 DOI: 10.1371/journal.pone.0210798] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 01/02/2019] [Indexed: 12/13/2022] Open
Abstract
Gut fungi may influence the course of Clostridium difficile infection either positively or negatively for the host. Fungi are not prominent in the mouse gut, and C. albicans, the major human gastrointestinal commensal yeast, is in low abundance or absent in mice. Bifidobacterium is one of the probiotics that may attenuate the severity of C. difficile infection. Inflammatory synergy between C. albicans and C. difficile, in gut, may provide a state that more closely resembles human infection and be more suitable for testing probiotic effects. We performed fecal mycobiota analysis and administered C. albicans at 1 day prior to C. difficile dosing. Fecal eukaryotic 18S rDNA analysis demonstrated the presence of Ascomycota, specifically, Candida spp., after oral antibiotics, despite negative fecal fungal culture. C. albicans administration enhanced the severity of the C. difficile infection model as determined by mortality rate, weight loss, gut leakage (FITC-dextran assay), and serum and intestinal tissue cytokines. This occurred without increased fecal C. difficile or bacteremia, in comparison with C. difficile gavage alone. Candida lysate with C. difficile increased IL-8 production from HT-29 and Caco-2 human intestinal epithelial cell-lines. Bifidobacterium attenuated the disease severity of the C. difficile plus Candida model. The reduced severity was associated with decreased Candida burdens in feces. In conclusion, gut C. albicans worsened C. difficile infection, possibly through exacerbation of inflammation. Hence, a mouse model of Clostridium difficile infection with C. albicans present in the gut may better model the human patient condition. Gut fungal mycobiome investigation in patients with C. difficile is warranted and may suggest therapeutic targets.
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Affiliation(s)
- Wimonrat Panpetch
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Matanee Palasuk
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Pratsanee Hiengrach
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Somying Tumwasorn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Asada Leelahavanichkul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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14
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Virulence factors and determination of antifungal susceptibilities of Candida species isolated from palm wine and sorghum beer. Microb Pathog 2018; 124:5-10. [PMID: 30092261 DOI: 10.1016/j.micpath.2018.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/04/2018] [Accepted: 08/05/2018] [Indexed: 01/09/2023]
Abstract
Since it has been considered that Candida species in food or drinks may, following ingestion, enter the bloodstream and cause fungaemia, the presence of these yeast species in traditional alcoholic beverages may be of some clinical significance. Thus we attempted to assess virulence factors and antifungal susceptibility profile of Candida strains and other potential pathogenic yeasts isolated from palm wine and sorghum beer (tchapalo). Of the 23 yeast isolates from palm wine, phospholipase, esterase and haemolysin production was revealed amongst 69.6%, 65.2% and 100% isolates respectively with high activity belonging to Candida tropicalis strains. All the isolates were biofilm producers at variable degree but none showed proteinase activity. When the isolates were tested for their susceptibility to five antifungal agents, we found that ketoconazole (91.3%) followed by fluconazole (78.3%) and amphotericin B (73.9%) were the most potent agents. Of the 14 isolates from tchapalo, 57.1%, 87.5% and 57.1% exhibited phospholipase, haemolysin and esterase activity respectively. They did not also show proteinase activity while 87.5% produced biofilm. The majority of the isolates were susceptible to azoles (92.7%) and amphotericin B (85.3%) but they were 5-flucytosine resistant like palm wine strains.
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15
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Egue LAN, N'guessan FK, Aka-Gbezo S, Bouatenin JPKM, Koussemon-Camara M. Candida species in tchapalo and bangui, two traditional alcoholic beverages from Côte d'Ivoire. Fungal Biol 2018; 122:283-292. [PMID: 29665954 DOI: 10.1016/j.funbio.2018.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/15/2018] [Accepted: 01/16/2018] [Indexed: 01/05/2023]
Abstract
The increase of infections due to non-Candida albicans species made it very necessary to conduct adequate characterization to be able to identify the species of Candida isolated from traditional fermented foods. In this study, based on their hue on Candida Chromogenic Agar medium, a total of 136 yeast strains were isolated from tchapalo and bangui. Molecular identification based on PCR-RFLP of internal transcribed spacers of rDNA (ITS) and sequencing of the ITS and the D1/D2 regions allowed us to assign these isolates to seven species: Candida tropicalis, Candida inconspicua, Candida rugosa, Saccharomyces cerevisiae, Kluyveromyces marxianus, Hanseniaspora guilliermondii, Trichosporon asahii. With the respect to each beverage, six species were found among with four species are regarded as opportunistic pathogens. From these, C. tropicalis, C. inconspicua and K. marxianus were the most commonly encountered. The enzyme activities of the potential pathogens assessed using API ZYM system showed that almost strains had esterase, esterase lipase, valine and cystine arylamidase, alpha chymotrypsin, alkaline phosphatase and naphthol phosphohydrolase activities. The activity of α-glucosidase was found only in C. tropicalis and C. inconspicua strains isolated from tchapalo while β-glucosidase activity was found in all strains from tchapalo and only in C. inconspicua isolated from bangui.
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Affiliation(s)
- Laurence A N Egue
- Nangui Abrogoua University, Laboratory of Biotechnology and Food Microbiology, Department of Food Science and Technology (UFR-STA), 02 BP 801 Abidjan 02, Cote d'Ivoire.
| | - Florent K N'guessan
- Nangui Abrogoua University, Laboratory of Biotechnology and Food Microbiology, Department of Food Science and Technology (UFR-STA), 02 BP 801 Abidjan 02, Cote d'Ivoire
| | - Solange Aka-Gbezo
- Nangui Abrogoua University, Laboratory of Biotechnology and Food Microbiology, Department of Food Science and Technology (UFR-STA), 02 BP 801 Abidjan 02, Cote d'Ivoire; Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), 01 BP 1303 Abidjan 01, Cote d'Ivoire
| | - Jean-Paul K M Bouatenin
- Nangui Abrogoua University, Laboratory of Biotechnology and Food Microbiology, Department of Food Science and Technology (UFR-STA), 02 BP 801 Abidjan 02, Cote d'Ivoire
| | - Marina Koussemon-Camara
- Nangui Abrogoua University, Laboratory of Biotechnology and Food Microbiology, Department of Food Science and Technology (UFR-STA), 02 BP 801 Abidjan 02, Cote d'Ivoire
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16
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Clark-Ordóñez I, Callejas-Negrete OA, Aréchiga-Carvajal ET, Mouriño-Pérez RR. Candida species diversity and antifungal susceptibility patterns in oral samples of HIV/AIDS patients in Baja California, Mexico. Med Mycol 2017; 55:285-294. [PMID: 27630251 DOI: 10.1093/mmy/myw069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 08/01/2016] [Indexed: 12/11/2022] Open
Abstract
Candidiasis is the most common opportunistic fungal infection in HIV patients. The aims of this study were to identify the prevalence of carriers of Candida, Candida species diversity, and in vitro susceptibility to antifungal drugs. In 297 HIV/AIDS patients in Baja California, Mexico, Candida strains were identified by molecular methods (PCR-RFLP) from isolates of oral rinses of patients in Tijuana, Mexicali, and Ensenada. 56.3% of patients were colonized or infected with Candida. In Tijuana, there was a significantly higher percentage of carriers (75.5%). Out of the 181 strains that were isolated, 71.8% were Candida albicans and 28.2% were non-albicans species. The most common non-albicans species was Candida tropicalis (12.2%), followed by Candida glabrata (8.3%), Candida parapsilosis (2.2%), Candida krusei (1.7%), and Candida guilliermondii (1.1%). Candida dubliniensis was not isolated. Two associated species were found in 11 patients. In Mexicali and Ensenada, there was a lower proportion of Candida carriers compared to other regions in Mexico and worldwide, however, in Tijuana, a border town with many peculiarities, a higher carrier rate was found. In this population, only a high viral load was associated with oral Candida carriers. Other factors such as gender, use of antiretroviral therapy, CD4+ T-lymphocyte levels, time since diagnosis, and alcohol/ tobacco consumption, were not associated with Candida carriers.
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Affiliation(s)
- Isadora Clark-Ordóñez
- Departamento de Microbiología. Centro de Investigación Científica y de Educación Superior de Ensenada. Ensenada B. C.,Facultad de Medicina. Universidad Autónoma de Baja California. Mexicali, B. C
| | - Olga A Callejas-Negrete
- Departamento de Microbiología. Centro de Investigación Científica y de Educación Superior de Ensenada. Ensenada B. C
| | - Elva T Aréchiga-Carvajal
- Departamento de Microbiología e Inmunología. Facultad de Ciencias Biológicas. Universidad Autónoma de Nuevo León. Monterrey, N. L
| | - Rosa R Mouriño-Pérez
- Departamento de Microbiología. Centro de Investigación Científica y de Educación Superior de Ensenada. Ensenada B. C
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17
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Bretagne S, Renaudat C, Desnos-Ollivier M, Sitbon K, Lortholary O, Dromer F. Predisposing factors and outcome of uncommon yeast species-related fungaemia based on an exhaustive surveillance programme (2002–14). J Antimicrob Chemother 2017; 72:1784-1793. [DOI: 10.1093/jac/dkx045] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/24/2017] [Indexed: 01/05/2023] Open
Affiliation(s)
- Stéphane Bretagne
- Institut Pasteur, CNRS, Molecular Mycology Unit, French National Reference Center for Invasive Mycoses & Antifungals, URA3012, Paris, France
- Parasitology-Mycology Laboratory, Saint Louis hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Charlotte Renaudat
- Institut Pasteur, CNRS, Molecular Mycology Unit, French National Reference Center for Invasive Mycoses & Antifungals, URA3012, Paris, France
| | - Marie Desnos-Ollivier
- Institut Pasteur, CNRS, Molecular Mycology Unit, French National Reference Center for Invasive Mycoses & Antifungals, URA3012, Paris, France
| | - Karine Sitbon
- Institut Pasteur, CNRS, Molecular Mycology Unit, French National Reference Center for Invasive Mycoses & Antifungals, URA3012, Paris, France
| | - Olivier Lortholary
- Institut Pasteur, CNRS, Molecular Mycology Unit, French National Reference Center for Invasive Mycoses & Antifungals, URA3012, Paris, France
- Paris Descartes University, Necker Pasteur Center for Infectious Diseases and Tropical Medicine, Necker Enfants Malades Hospital, Paris, France
| | - Françoise Dromer
- Institut Pasteur, CNRS, Molecular Mycology Unit, French National Reference Center for Invasive Mycoses & Antifungals, URA3012, Paris, France
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18
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Castillo-Castillo Y, Ruiz-Barrera O, Burrola-Barraza ME, Marrero-Rodriguez Y, Salinas-Chavira J, Angulo-Montoya C, Corral-Luna A, Arzola-Alvarez C, Itza-Ortiz M, Camarillo J. Isolation and characterization of yeasts from fermented apple bagasse as additives for ruminant feeding. Braz J Microbiol 2016; 47:889-895. [PMID: 27520528 PMCID: PMC5052383 DOI: 10.1016/j.bjm.2016.07.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/06/2016] [Indexed: 10/26/2022] Open
Abstract
Solid-state fermentation can be used to produce feeds for ruminants, which can provide an enriched population of yeasts to improve ruminal fermentation. Fermentation of apple bagasse was performed to obtain a yeast-rich product, with the objective of isolating, identifying, and characterizing yeast strains and testing their capability to enhance in vitro ruminal fermentation of fibrous feeds. Yeasts were isolated from apple bagasse fermented under in vitro conditions, using rumen liquor obtained from cannulated cows and alfalfa as a fibrous substrate. A total of 16 new yeast strains were isolated and identified by biochemical and molecular methods. The strains were designated Levazot, followed by the isolate number. Their fermentative capacity was assessed using an in vitro gas production method. Strain Levazot 15 (Candida norvegensis) showed the greatest increase in gas production (p<0.05) compared with the yeast-free control and positively affected in vitro ruminal fermentation parameters of alfalfa and oat straw. Based on these results, it was concluded that the Levazot 15 yeast strain could be potentially used as an additive for ruminants consuming high-fiber diets. However, further studies of effects of these additives on rumen digestion, metabolism, and productive performance of ruminants are required.
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Affiliation(s)
- Y Castillo-Castillo
- Universidad Autonoma de Cd. Juarez, Division Multidisciplinaria, Departamento de Medicina Veterinaria, Nuevo Casas Grandes, Mexico
| | - O Ruiz-Barrera
- Universidad Autonoma de Chihuahua, Facultad de Zootecnia y Ecologia, Chihuahua, Mexico.
| | - M E Burrola-Barraza
- Universidad Autonoma de Chihuahua, Facultad de Zootecnia y Ecologia, Chihuahua, Mexico
| | | | - J Salinas-Chavira
- Universidad Autonoma de Tamaulipas, Facultad de Medicina Veterinaria y Zootecnia, Cd. Victoria, Mexico
| | - C Angulo-Montoya
- Universidad Autonoma de Sinaloa, Culiacan, Facultad de Medicina Veterinaria y Zootecnia, Sin, Mexico
| | - A Corral-Luna
- Universidad Autonoma de Chihuahua, Facultad de Zootecnia y Ecologia, Chihuahua, Mexico
| | - C Arzola-Alvarez
- Universidad Autonoma de Chihuahua, Facultad de Zootecnia y Ecologia, Chihuahua, Mexico
| | - M Itza-Ortiz
- Universidad Autonoma de Cd. Juarez, Division Multidisciplinaria, Departamento de Medicina Veterinaria, Nuevo Casas Grandes, Mexico
| | - J Camarillo
- Universidad Autonoma de Chihuahua, Facultad de Zootecnia y Ecologia, Chihuahua, Mexico
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19
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Tadec L, Talarmin JP, Gastinne T, Bretonnière C, Miegeville M, Le Pape P, Morio F. Epidemiology, risk factor, species distribution, antifungal resistance and outcome of Candidemia at a single French hospital: a 7-year study. Mycoses 2016; 59:296-303. [PMID: 26806101 DOI: 10.1111/myc.12470] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 11/27/2022]
Abstract
Candidemia remains a major cause of disease worldwide and is associated with a high mortality rate. We conducted a retrospective study of candidemia at Nantes Hospital, France, between 2004 and 2010. A total of 191 episodes (n = 188 patients) were reviewed. Incidence, demographics, risk factors, antifungal management, species identification, in vitro susceptibility and 12 weeks survival were analysed. Global incidence of candidemia was 0.37‰ admissions. Higher incidences were observed in haematology (6.65‰) and intensive care units (2‰). Central venous catheter and antibiotic exposure were the most frequent risk factors (77% and 76% respectively). Candida albicans was the predominant species (51.8%) followed by C. parapsilosis (14.5%), C. glabrata (9.8%), C. tropicalis (9.8%) and C. krusei (4.1%). However, species distribution differed significantly between medical units with frequency of C. tropicalis being higher in haematology compared to other medical units. Fluconazole and caspofungin were the main antifungals given as first-line therapy. Although not significant, 12 weeks mortality rate was 30.9%, being higher for C. tropicalis (44.4%) than for C. parapsilosis (16%). Acquired azole or echinocandin resistance was noted in some isolates, underlining the need for systematic antifungal susceptibility testing in patients with candidemia. These epidemiological findings will be of interest for antifungal stewardship at our hospital.
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Affiliation(s)
- Laurent Tadec
- Département de Parasitologie et Mycologie Médicale, EA1155 - IICiMed, Faculté de Pharmacie, Université de Nantes, Nantes Atlantique Universités, Nantes, France.,Laboratoire de Parasitologie-Mycologie, CHU de Nantes, Nantes, France
| | | | - Thomas Gastinne
- Service d'Hématologie Clinique, CHU de Nantes, Nantes, France
| | | | - Michel Miegeville
- Département de Parasitologie et Mycologie Médicale, EA1155 - IICiMed, Faculté de Pharmacie, Université de Nantes, Nantes Atlantique Universités, Nantes, France.,Laboratoire de Parasitologie-Mycologie, CHU de Nantes, Nantes, France
| | - Patrice Le Pape
- Département de Parasitologie et Mycologie Médicale, EA1155 - IICiMed, Faculté de Pharmacie, Université de Nantes, Nantes Atlantique Universités, Nantes, France.,Laboratoire de Parasitologie-Mycologie, CHU de Nantes, Nantes, France
| | - Florent Morio
- Département de Parasitologie et Mycologie Médicale, EA1155 - IICiMed, Faculté de Pharmacie, Université de Nantes, Nantes Atlantique Universités, Nantes, France.,Laboratoire de Parasitologie-Mycologie, CHU de Nantes, Nantes, France
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20
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Galán F, García-Agudo L, Guerrero I, Marín P, García-Tapia A, García-Martos P, Rodríguez-Iglesias M. Evaluación de la espectrometría de masas en la identificación de levaduras de interés clínico. Enferm Infecc Microbiol Clin 2015; 33:372-8. [DOI: 10.1016/j.eimc.2014.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/29/2014] [Accepted: 10/01/2014] [Indexed: 10/24/2022]
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21
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Candida inconspicua and Candida norvegensis: new insights into identification in relation to sexual reproduction and genome organization. J Clin Microbiol 2015; 53:1655-61. [PMID: 25762773 DOI: 10.1128/jcm.02913-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/05/2015] [Indexed: 01/22/2023] Open
Abstract
Candida inconspicua and Candida (Pichia) norvegensis are two emerging pathogenic species that exhibit reduced susceptibility to azole derivatives. Conventional (biochemical) approaches do not readily differentiate between the two species. The first aim of this work was to analyze the performance of biochemical, proteomic (matrix-assisted laser desorption ionization-time of flight [MALDI-TOF]), and molecular approaches in the precise identification of these species. These results then led us to sequence 3 genomic loci, i.e., the internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA), the D1/D2 domain of the 28S rDNA, and the elongation factor 1α (EF-1α) gene, either directly or following cloning, of 13 clinical isolates and 9 reference strains belonging to the 5 species included in the Pichia cactophila clade, namely, Pichia cactophila, Pichia insulana, C. inconspicua, C. norvegensis, and P. pseudocactophila. Finally, isolates of C. inconspicua were challenged for sexual reproduction on the appropriate medium. Our results show that EF-1α sequencing and proteic profiling by MALDI-TOF are the two most efficient approaches to distinguish between C. norvegensis and C. inconspicua. As a characteristic of the P. cactophila clade, we found multiple alleles of the rDNA regions in certain strains belonging to the tested species, making ITS or D1/D2 sequencing not appropriate for identification. Whatever the method of identification, including MALDI-TOF and EF-1α sequencing, none could differentiate C. inconspicua from P. cactophila. The results of phylogenetic analysis and the generation of asci from pure cultures of all C. inconspicua strains both support the identification of P. cactophila as the teleomorph of C. inconspicua.
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22
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Virgilio E, Mercantini P, Ferri M, Cavallini M, Teggi A, Ziparo V. Coexistence of diffuse malignant peritoneal mesothelioma and Candida norvegensis peritonitis. Surg Infect (Larchmt) 2014; 15:660-1. [PMID: 25314348 DOI: 10.1089/sur.2014.088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Edoardo Virgilio
- 1 Department of Medical and Surgical Sciences and Translational Medicine, Faculty of Medicine and Psychology "Sapienza," Rome, Italy
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23
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Dorn-In S, Fahn C, Hölzel CS, Wenz S, Hartwig I, Schwaiger K, Bauer J. Reconstruction of the original mycoflora in pelleted feed by PCR-SSCP and qPCR. FEMS Microbiol Lett 2014; 359:182-92. [PMID: 25088501 DOI: 10.1111/1574-6968.12552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/30/2014] [Accepted: 07/30/2014] [Indexed: 11/28/2022] Open
Abstract
Ground feeds for pigs were investigated for fungal contamination before and after pelleting (subsamples in total n = 24) by cultural and molecular biological methods. A fungal-specific primer pair ITS1/ITS5.8R was used to amplify fungal DNA; PCR products were processed for the PCR-SSCP method. In the resulting acrylamide gel, more than 85% of DNA bands of ground feeds were preserved after pelleting. Twenty-two DNA bands were sequenced; all represented fungal DNA. The level of fungal DNA in ground feed samples was equivalent to 4.77-5.69 log10 CFU g(-1) , calculated by qPCR using a standard curve of Aspergillus flavus. In pelleted feed, the level of fungal DNA was in average ± 0.07 log10 different from ground feed. Quantified by cultural methods, the fresh ground feeds contained up to 4.51 log10 CFU g(-1) culturable fungi, while there was < 2.83 log10 CFU g(-1) detected in pelleted feeds. This result shows that, while the process of pelleting reduced the amount of living fungi dramatically, it did not affect the total fungal DNA in feed. Thus, the described methodology was able to reconstruct the fungal microbiota in feeds and reflected a considerable fungal contamination of raw materials such as grains.
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Maubon D, Garnaud C, Calandra T, Sanglard D, Cornet M. Resistance of Candida spp. to antifungal drugs in the ICU: where are we now? Intensive Care Med 2014; 40:1241-55. [PMID: 25091787 DOI: 10.1007/s00134-014-3404-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 07/10/2014] [Indexed: 12/11/2022]
Abstract
Current increases in antifungal drug resistance in Candida spp. and clinical treatment failures are of concern, as invasive candidiasis is a significant cause of mortality in intensive care units (ICUs). This trend reflects the large and expanding use of newer broad-spectrum antifungal agents, such as triazoles and echinocandins. In this review, we firstly present an overview of the mechanisms of action of the drugs and of resistance in pathogenic yeasts, subsequently focusing on recent changes in the epidemiology of antifungal resistance in ICU. Then, we emphasize the clinical impacts of these current trends. The emergence of clinical treatment failures due to resistant isolates is described. We also consider the clinical usefulness of recent advances in the interpretation of antifungal susceptibility testing and in molecular detection of the mutations underlying acquired resistance. We pay particular attention to practical issues relating to ICU patient management, taking into account the growing threat of antifungal drug resistance.
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Affiliation(s)
- Danièle Maubon
- Parasitologie-Mycologie, Institut de Biologie et de Pathologie, CHU de Grenoble, Grenoble, France,
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Epidemiology and antifungal susceptibilities of yeasts causing vulvovaginitis in a teaching hospital. Mycopathologia 2014; 178:251-8. [PMID: 25005365 DOI: 10.1007/s11046-014-9780-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 06/26/2014] [Indexed: 10/25/2022]
Abstract
Vulvovaginal candidiasis is one of the most common mycosis. However, the information about antifungal susceptibilities of the yeasts causing this infection is scant. We studied 121 yeasts isolated from 118 patients with vulvovaginal candidiasis. The isolates were identified by phenotypic and molecular methods, including four phenotypic methods described to differentiate Candida albicans from C. dubliniensis. Antifungal susceptibility testing was performed according to CLSI documents M27A3 and M27S4 using the drugs available as treatment option in the hospital. Diabetes, any antibacterial and amoxicillin treatment were statistically linked with vulvovaginal candidiasis, while oral contraceptives were not considered a risk factor. Previous azole-based over-the-counter antifungal treatment was statistically associated with non-C.albicans yeasts infections. The most common isolated yeast species was C. albicans (85.2 %) followed by C. glabrata (5 %), Saccharomyces cerevisiae (3.3 %), and C. dubliniensis (2.5 %). Fluconazole- and itraconazole-reduced susceptibility was observed in ten and in only one C. albicans strains, respectively. All the C. glabrata isolates showed low fluconazole MICs. Clotrimazole showed excellent potency against all but seven isolates (three C. glabrata, two S. cerevisiae, one C. albicans and one Picchia anomala). Any of the strains showed nystatin reduced susceptibility. On the other hand, terbinafine was the less potent drug. Antifungal resistance is still a rare phenomenon supporting the use of azole antifungals as empirical treatment of vulvovaginal candidiasis.
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Musso M, Giannella M, Antonini M, Bordi E, Ettorre GM, Tessitore L, Mariano A, Capone A. Invasive Candidiasis due to Candida Norvegensis in a Liver Transplant Patient: Case Report and Literature Review. Infect Dis Rep 2014; 6:5374. [PMID: 25002960 PMCID: PMC4083299 DOI: 10.4081/idr.2014.5374] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/16/2014] [Accepted: 04/17/2014] [Indexed: 11/23/2022] Open
Abstract
Candida norvegensis is an emerging fluconazole-resistant pathogen isolated in most cases from skin and mucous membranes of immunocompromized patients. Documented invasive candidiasis (IC) due to C. norvegensis has been rarely reported, thus the clinical features of patients at risk for this pathogen are poorly defined. We report a liver transplant patient who developed IC due to C. norvegensis and review other cases of C. norvegensis IC published in the literature.
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Affiliation(s)
- Maria Musso
- Second Division of Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani , Rome
| | | | - Mario Antonini
- Intensive Care Unit and Anesthesia, National Institute for Infectious Diseases Lazzaro Spallanzani , Rome
| | - Eugenio Bordi
- Microbiology Unit, National Institute for Infectious Diseases Lazzaro Spallanzani , Rome
| | | | - Loretta Tessitore
- Neurosurgical Intensive Care Unit, S. Camillo-Forlanini Hospital , Rome
| | - Andrea Mariano
- First Division of Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani , Rome, Italy
| | - Alessandro Capone
- Second Division of Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani , Rome
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