Candida Species
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Identification and Phylogeny of Ascomycetous Yeasts from Analysis
Antonie van Leeuwenhoek 73: 331–371, 1998. 331 © 1998 Kluwer Academic Publishers. Printed in the Netherlands. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences Cletus P. Kurtzman∗ & Christie J. Robnett Microbial Properties Research, National Center for Agricultural Utilization Research, Agricultural Research Ser- vice, U.S. Department of Agriculture, Peoria, Illinois 61604, USA (∗ author for correspondence) E-mail: [email protected] Received 19 June 1998; accepted 19 June 1998 Key words: Ascomycetous yeasts, phylogeny, ribosomal DNA, systematics Abstract Approximately 500 species of ascomycetous yeasts, including members of Candida and other anamorphic genera, were analyzed for extent of divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA. Divergence in this domain is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species. Phylogenetic relationships among the ascomycetous yeasts were analyzed from D1/D2 sequence divergence. For comparison, the phylogeny of selected members of the Saccharomyces clade was determined from 18S rDNA sequences. Species relationships were highly concordant between the D1/D2 and 18S trees when branches were statistically well supported. Introduction lesser ranges of nDNA relatedness than those found among heterothallic species. Disadvantages of nDNA reassociation studies in- Procedures commonly used for yeast identification clude the need for pairwise comparisons of all isolates rely on the appearance of cellular morphology and dis- under study and that resolution is limited to the ge- tinctive reactions on a standardized set of fermentation netic distance of sister species, i.e., closely related and assimilation tests. -
The Phylogeny of Plant and Animal Pathogens in the Ascomycota
Physiological and Molecular Plant Pathology (2001) 59, 165±187 doi:10.1006/pmpp.2001.0355, available online at http://www.idealibrary.com on MINI-REVIEW The phylogeny of plant and animal pathogens in the Ascomycota MARY L. BERBEE* Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z4, Canada (Accepted for publication August 2001) What makes a fungus pathogenic? In this review, phylogenetic inference is used to speculate on the evolution of plant and animal pathogens in the fungal Phylum Ascomycota. A phylogeny is presented using 297 18S ribosomal DNA sequences from GenBank and it is shown that most known plant pathogens are concentrated in four classes in the Ascomycota. Animal pathogens are also concentrated, but in two ascomycete classes that contain few, if any, plant pathogens. Rather than appearing as a constant character of a class, the ability to cause disease in plants and animals was gained and lost repeatedly. The genes that code for some traits involved in pathogenicity or virulence have been cloned and characterized, and so the evolutionary relationships of a few of the genes for enzymes and toxins known to play roles in diseases were explored. In general, these genes are too narrowly distributed and too recent in origin to explain the broad patterns of origin of pathogens. Co-evolution could potentially be part of an explanation for phylogenetic patterns of pathogenesis. Robust phylogenies not only of the fungi, but also of host plants and animals are becoming available, allowing for critical analysis of the nature of co-evolutionary warfare. Host animals, particularly human hosts have had little obvious eect on fungal evolution and most cases of fungal disease in humans appear to represent an evolutionary dead end for the fungus. -
Of Candida Dubliniensis, Ireland* Isolate Source Year of Isolation Location DST† Mating Type TAG Reference SL411 Ixodes Uriae Ticks 2007 GSI 27 Aa + (5) SL422 I
cans isolates from humans and animals (3,4). The purpose Genetic Differences of our study was to use MLST, the presence or absence of a previously identified polymorphism in the CDR1 gene (8), between Avian and and mating type analysis to determine genetic relatedness between avian-associated and human C. dubliniensis iso- Human Isolates lates and whether avian-associated isolates are a source of of Candida human opportunistic infections. dubliniensis The Study To obtain avian-associated C. dubliniensis isolates Brenda A. McManus, Derek J. Sullivan, from a novel geographic site, fresh seabird excrement Gary P. Moran, Christophe d’Enfert, was sampled from the campus of Trinity College Dublin, Marie-Elisabeth Bougnoux, Miles A. Nunn, ≈150 km north of Great Saltee Island by using nitrogen- and David C. Coleman gassed VI-PAK sterile swabs (Sarstedt-Drinagh, Wexford, Ireland). Samples were plated within 2 h of collection When Candida dubliniensis isolates obtained from on CHROMagar Candida medium (CHROMagar, Paris, seabird excrement and from humans in Ireland were com- France), incubated at 30°C for 48 h, and identified as de- pared by using multilocus sequence typing, 13 of 14 avian isolates were genetically distinct from human isolates. The scribed (7,9–12). Three new C. dubliniensis isolates were remaining avian isolate was indistinguishable from a human obtained from 134 fecal samples. Like isolates from Great isolate, suggesting that transmission may occur between Saltee Island (5), these 3 isolates obtained directly from humans and birds. freshly deposited herring gull (Larus argentatus) excre- ment were ITS genotype 1 (13). Because the isolates origi- nally described by Nunn et al. -
Fungal Phyla
ZOBODAT - www.zobodat.at Zoologisch-Botanische Datenbank/Zoological-Botanical Database Digitale Literatur/Digital Literature Zeitschrift/Journal: Sydowia Jahr/Year: 1984 Band/Volume: 37 Autor(en)/Author(s): Arx Josef Adolf, von Artikel/Article: Fungal phyla. 1-5 ©Verlag Ferdinand Berger & Söhne Ges.m.b.H., Horn, Austria, download unter www.biologiezentrum.at Fungal phyla J. A. von ARX Centraalbureau voor Schimmelcultures, P. O. B. 273, NL-3740 AG Baarn, The Netherlands 40 years ago I learned from my teacher E. GÄUMANN at Zürich, that the fungi represent a monophyletic group of plants which have algal ancestors. The Myxomycetes were excluded from the fungi and grouped with the amoebae. GÄUMANN (1964) and KREISEL (1969) excluded the Oomycetes from the Mycota and connected them with the golden and brown algae. One of the first taxonomist to consider the fungi to represent several phyla (divisions with unknown ancestors) was WHITTAKER (1969). He distinguished phyla such as Myxomycota, Chytridiomycota, Zygomy- cota, Ascomycota and Basidiomycota. He also connected the Oomycota with the Pyrrophyta — Chrysophyta —• Phaeophyta. The classification proposed by WHITTAKER in the meanwhile is accepted, e. g. by MÜLLER & LOEFFLER (1982) in the newest edition of their text-book "Mykologie". The oldest fungal preparation I have seen came from fossil plant material from the Carboniferous Period and was about 300 million years old. The structures could not be identified, and may have been an ascomycete or a basidiomycete. It must have been a parasite, because some deformations had been caused, and it may have been an ancestor of Taphrina (Ascomycota) or of Milesina (Uredinales, Basidiomycota). -
The Classification of Lower Organisms
The Classification of Lower Organisms Ernst Hkinrich Haickei, in 1874 From Rolschc (1906). By permission of Macrae Smith Company. C f3 The Classification of LOWER ORGANISMS By HERBERT FAULKNER COPELAND \ PACIFIC ^.,^,kfi^..^ BOOKS PALO ALTO, CALIFORNIA Copyright 1956 by Herbert F. Copeland Library of Congress Catalog Card Number 56-7944 Published by PACIFIC BOOKS Palo Alto, California Printed and bound in the United States of America CONTENTS Chapter Page I. Introduction 1 II. An Essay on Nomenclature 6 III. Kingdom Mychota 12 Phylum Archezoa 17 Class 1. Schizophyta 18 Order 1. Schizosporea 18 Order 2. Actinomycetalea 24 Order 3. Caulobacterialea 25 Class 2. Myxoschizomycetes 27 Order 1. Myxobactralea 27 Order 2. Spirochaetalea 28 Class 3. Archiplastidea 29 Order 1. Rhodobacteria 31 Order 2. Sphaerotilalea 33 Order 3. Coccogonea 33 Order 4. Gloiophycea 33 IV. Kingdom Protoctista 37 V. Phylum Rhodophyta 40 Class 1. Bangialea 41 Order Bangiacea 41 Class 2. Heterocarpea 44 Order 1. Cryptospermea 47 Order 2. Sphaerococcoidea 47 Order 3. Gelidialea 49 Order 4. Furccllariea 50 Order 5. Coeloblastea 51 Order 6. Floridea 51 VI. Phylum Phaeophyta 53 Class 1. Heterokonta 55 Order 1. Ochromonadalea 57 Order 2. Silicoflagellata 61 Order 3. Vaucheriacea 63 Order 4. Choanoflagellata 67 Order 5. Hyphochytrialea 69 Class 2. Bacillariacea 69 Order 1. Disciformia 73 Order 2. Diatomea 74 Class 3. Oomycetes 76 Order 1. Saprolegnina 77 Order 2. Peronosporina 80 Order 3. Lagenidialea 81 Class 4. Melanophycea 82 Order 1 . Phaeozoosporea 86 Order 2. Sphacelarialea 86 Order 3. Dictyotea 86 Order 4. Sporochnoidea 87 V ly Chapter Page Orders. Cutlerialea 88 Order 6. -
Identification of Culture-Negative Fungi in Blood and Respiratory Samples
IDENTIFICATION OF CULTURE-NEGATIVE FUNGI IN BLOOD AND RESPIRATORY SAMPLES Farida P. Sidiq A Dissertation Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY May 2014 Committee: Scott O. Rogers, Advisor W. Robert Midden Graduate Faculty Representative George Bullerjahn Raymond Larsen Vipaporn Phuntumart © 2014 Farida P. Sidiq All Rights Reserved iii ABSTRACT Scott O. Rogers, Advisor Fungi were identified as early as the 1800’s as potential human pathogens, and have since been shown as being capable of causing disease in both immunocompetent and immunocompromised people. Clinical diagnosis of fungal infections has largely relied upon traditional microbiological culture techniques and examination of positive cultures and histopathological specimens utilizing microscopy. The first has been shown to be highly insensitive and prone to result in frequent false negatives. This is complicated by atypical phenotypes and organisms that are morphologically indistinguishable in tissues. Delays in diagnosis of fungal infections and inaccurate identification of infectious organisms contribute to increased morbidity and mortality in immunocompromised patients who exhibit increased vulnerability to opportunistic infection by normally nonpathogenic fungi. In this study we have retrospectively examined one-hundred culture negative whole blood samples and one-hundred culture negative respiratory samples obtained from the clinical microbiology lab at the University of Michigan Hospital in Ann Arbor, MI. Samples were obtained from randomized, heterogeneous patient populations collected between 2005 and 2006. Specimens were tested utilizing cetyltrimethylammonium bromide (CTAB) DNA extraction and polymerase chain reaction amplification of internal transcribed spacer (ITS) regions of ribosomal DNA utilizing panfungal ITS primers. -
The Presence of Fluconazole-Resistant Candida Dubliniensis Strains
44 Rev Iberoam Micol 2002; 19: 44-48 Original The presence of fluconazole-resistant Candida dubliniensis strains among Candida albicans isolates from immu- nocompromised or otherwise debili- tated HIV-negative Turkish patients A. Serda Kantarcıoglu & Ayhan Yücel Department of Microbiology and Clinical Microbiology, Cerrahpasa School of Medicine, Istanbul University, Cerrahpasa, Istanbul, Turkey Summary The newly described species Candida dubliniensis phenotypically resembles Candida albicans in many respects and so it could be easily misidentified. The present study aimed at determining the frequency at which this new Candida species was not recognized in the authors’ university hospital clinical laboratory and to assess antifungal susceptibility. In this study six identification methods based on significant phenotypic characteristics each proposed as reliable tests applicable in mycology laboratories for the differentiation of the two species were performed together to assess the clinical strains that were initially identified as C. albicans. Only the isolates which have had the parallel results in all methods were assessed as C. dubliniensis. One hundred and twentynine C. albicans strains isolated from deep mycosis suspected patients were further examined. Three of 129 C. albicans ( two from oral cavity, one from sputum) were reidenti- fied as C. dubliniensis. One of the strains isolated from oral cavity and that from sputum were obtained at two months intervals from the same patient with acute myeloid leukemia, while the other oral cavity strain was obtained from a patient who had previously been irradiated for a laryngeal malignancy. Isolates were all susceptible in vitro to amphotericin B, with the MIC range 0.125 to 0.5 µg/ml, resistant to fluconazole, with the MICs ≥ 64 µg/ml, and resistant to ketoconazole, with the MICs ≥ 16 µg/ml, dose-dependent to itraconazole with the MIC range 0.25-0.5 µg/ml, and susceptible to flucytosine, with the MIC range 1-4 µg/ml. -
Inhibition of MRN Activity by a Telomere Protein Motif
ARTICLE https://doi.org/10.1038/s41467-021-24047-2 OPEN Inhibition of MRN activity by a telomere protein motif Freddy Khayat1,6, Elda Cannavo2,6, Majedh Alshmery1, William R. Foster1, Charly Chahwan 1,4, Martino Maddalena1,5, Christopher Smith 1, Antony W. Oliver 1, Adam T. Watson1, Antony M. Carr 1, ✉ Petr Cejka2,3 & Alessandro Bianchi 1 The MRN complex (MRX in Saccharomyces cerevisiae, made of Mre11, Rad50 and Nbs1/Xrs2) 1234567890():,; initiates double-stranded DNA break repair and activates the Tel1/ATM kinase in the DNA damage response. Telomeres counter both outcomes at chromosome ends, partly by keeping MRN-ATM in check. We show that MRX is disabled by telomeric protein Rif2 through an N- terminal motif (MIN, MRN/X-inhibitory motif). MIN executes suppression of Tel1, DNA end- resection and non-homologous end joining by binding the Rad50 N-terminal region. Our data suggest that MIN promotes a transition within MRX that is not conductive for endonuclease activity, DNA-end tethering or Tel1 kinase activation, highlighting an Achilles’ heel in MRN, which we propose is also exploited by the RIF2 paralog ORC4 (Origin Recognition Complex 4) in Kluyveromyces lactis and the Schizosaccharomyces pombe telomeric factor Taz1, which is evolutionarily unrelated to Orc4/Rif2. This raises the possibility that analogous mechanisms might be deployed in other eukaryotes as well. 1 Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK. 2 Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Universitàdella Svizzera italiana (USI), Bellinzona, Switzerland. 3 Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland. -
Reexamining the Phylogeny of Clinically Relevant Candida Species
RESEARCH ARTICLE Re-examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analyses Clement K.M. Tsui1, Heide-Marie Daniel2, Vincent Robert3 & Wieland Meyer1,4 1Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Hospital, Westmead Millennium Institute, Westmead, NSW, Australia; 2BCCM/MUCL culture collection, Universite´ Catholique de Louvain, Unite´ de Microbiologie, Louvain-la-Neuve, Belgium; 3Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands; and 4Western Clinical School, Department of Medicine, The University of Sydney, Sydney, Australia Correspondence: Wieland Meyer, Molecular Abstract Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Yeasts of the artificial genus Candida include plant endophytes, insect symbionts, Westmead Hospital, Westmead Millennium and opportunistic human pathogens. Phylogenies based on rRNA gene and actin Institute, Westmead, NSW 2145, Australia. sequences confirmed that the genus is not monophyletic, and the relationships Tel.: 161 2 98456895; fax: 161 2 98915317; among Candida species and allied teleomorph genera are not clearly resolved. e-mail: [email protected] Protein-coding genes have been useful to resolve taxonomic positions among a broad range of fungi. Over 70 taxa of the genus Candida and its allied sexually Received 10 August 2007; revised 18 November reproducing genera were therefore selected, and their phylogenetic relationships 2007; accepted 20 November 2007. were investigated using nuclear sequences of the largest subunit and second largest First published online 31 January 2008. subunit of RNA polymerase II gene, actin, the second subunit of the mitochondrial DOI:10.1111/j.1567-1364.2007.00342.x cytochrome oxidase gene, and D1/D2 LSU rRNA gene. -
Molecular Markers of Antifungal Resistance: Potential Uses in Routine Practice and Future Perspectives
Journal of Fungi Review Molecular Markers of Antifungal Resistance: Potential Uses in Routine Practice and Future Perspectives Guillermo Garcia-Effron 1,2 1 Laboratorio de Micología y Diagnóstico Molecular, Cátedra de Parasitología y Micología, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe CP3000, Argentina; [email protected]; Tel.: +54-9342-4575209 (ext. 135) 2 Consejo Nacional de Investigaciones Científicas y Tecnológicas, Santa Fe CP3000, Argentina Abstract: Antifungal susceptibility testing (AST) has come to establish itself as a mandatory routine in clinical practice. At the same time, the mycological diagnosis seems to have headed in the direction of non-culture-based methodologies. The downside of these developments is that the strains that cause these infections are not able to be studied for their sensitivity to antifungals. Therefore, at present, the mycological diagnosis is correctly based on laboratory evidence, but the antifungal treatment is undergoing a growing tendency to revert back to being empirical, as it was in the last century. One of the explored options to circumvent these problems is to couple non-cultured based diagnostics with molecular-based detection of intrinsically resistant organisms and the identification of molecular mechanisms of resistance (secondary resistance). The aim of this work is to review the available molecular tools for antifungal resistance detection, their limitations, and their advantages. A comprehensive description of commercially available and in-house methods is included. In addition, gaps in the development of these molecular technologies are discussed. Citation: Garcia-Effron, G. Molecular Keywords: antifungal resistance; molecular tools; intrinsic resistance; secondary resistance; Cyp51A; Markers of Antifungal Resistance: FKS; Candida; Aspergillus Potential Uses in Routine Practice and Future Perspectives. -
Validation of a Simplex PCR Assay Enabling Reliable Identification Of
Fidler et al. BMC Infectious Diseases (2018) 18:393 https://doi.org/10.1186/s12879-018-3283-6 RESEARCH ARTICLE Open Access Validation of a simplex PCR assay enabling reliable identification of clinically relevant Candida species Gabor Fidler1, Eva Leiter2, Sandor Kocsube3, Sandor Biro1 and Melinda Paholcsek1* Abstract Background: Fungal bloodstream infections (BSI) may be serious and are associated with drastic rise in mortality and health care costs. Candida spp. are the predominant etiological agent of fungal sepsis. The prompt and species-level identification of Candida may influence patient outcome and survival. The aim of this study was to develop and evaluate the CanTub-simplex PCR assay coupled with Tm calling and subsequent high resolution melting (HRM) analysis to barcode seven clinically relevant Candida species. Methods: Efficiency, coefficient of correlation and the limit of reliable detection were estimated on purified Candida EDTA-whole blood (WB) reference panels seeded with Candida albicans, Candida glabrata, Candida parapsilosis, Candida tropicalis, Candida krusei, Candida guilliermondii, Candida dubliniensis cells in a 6-log range. Discriminatory power was measured on EDTA-WB clinical panels on three different PCR platforms; LightCycler®96, LightCycler® Nano, LightCycler® 2.0. Inter- and intra assay consistencies were also calculated. Results: The limit of reliable detection proved to be 0.2–2 genomic equivalent and the method was reliable on broad concentration ranges (106–10 CFU) providing distinctive melting peaks and characteristic HRM curves. The diagnostic accuracy of the discrimination proved to be the best on Roche LightCycler®2.0 platform. Repeatability was tested and proved to be % C.V.: 0.14 ± 0.06 on reference- and % C.V.: 0.14 ± 0.02 on clinical-plates accounting for a very high accuracy. -
Monilochaetes and Allied Genera of the Glomerellales, and a Reconsideration of Families in the Microascales
available online at www.studiesinmycology.org StudieS in Mycology 68: 163–191. 2011. doi:10.3114/sim.2011.68.07 Monilochaetes and allied genera of the Glomerellales, and a reconsideration of families in the Microascales M. Réblová1*, W. Gams2 and K.A. Seifert3 1Department of Taxonomy, Institute of Botany of the Academy of Sciences, CZ – 252 43 Průhonice, Czech Republic; 2Molenweg 15, 3743CK Baarn, The Netherlands; 3Biodiversity (Mycology and Botany), Agriculture and Agri-Food Canada, Ottawa, Ontario, K1A 0C6, Canada *Correspondence: Martina Réblová, [email protected] Abstract: We examined the phylogenetic relationships of two species that mimic Chaetosphaeria in teleomorph and anamorph morphologies, Chaetosphaeria tulasneorum with a Cylindrotrichum anamorph and Australiasca queenslandica with a Dischloridium anamorph. Four data sets were analysed: a) the internal transcribed spacer region including ITS1, 5.8S rDNA and ITS2 (ITS), b) nc28S (ncLSU) rDNA, c) nc18S (ncSSU) rDNA, and d) a combined data set of ncLSU-ncSSU-RPB2 (ribosomal polymerase B2). The traditional placement of Ch. tulasneorum in the Microascales based on ncLSU sequences is unsupported and Australiasca does not belong to the Chaetosphaeriaceae. Both holomorph species are nested within the Glomerellales. A new genus, Reticulascus, is introduced for Ch. tulasneorum with associated Cylindrotrichum anamorph; another species of Reticulascus and its anamorph in Cylindrotrichum are described as new. The taxonomic structure of the Glomerellales is clarified and the name is validly published. As delimited here, it includes three families, the Glomerellaceae and the newly described Australiascaceae and Reticulascaceae. Based on ITS and ncLSU rDNA sequence analyses, we confirm the synonymy of the anamorph generaDischloridium with Monilochaetes.