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Luo Z, Ning Y, Yu S, Xiao M, Dai R, Chen X, Wang Y, Kang W, Jiang Y, Yu H, Liang H, Xu Y, Sun T, Zhang L. The first established microsatellite markers to distinguish Candida orthopsilosis isolates and detection of a nosocomial outbreak in China. J Clin Microbiol 2023; 61:e0080623. [PMID: 37877725 PMCID: PMC10662339 DOI: 10.1128/jcm.00806-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/11/2023] [Indexed: 10/26/2023] Open
Abstract
The infection proportion of Candida orthopsilosis, a member of the C. parapsilosis complex, has increased globally in recent years, and nosocomial outbreaks have been reported in several countries. This study aimed to establish microsatellite loci-based typing method that was able to effectively distinguish among C. orthopsilosis isolates. Three reference C. orthopsilosis genome sequences were analyzed to identify repeat loci. DNA sequences containing over eight bi- or more nucleotide repeats were selected. A total of 51 loci were initially identified, and locus-specific primers were designed and tested with 20 epidemiologically unrelated isolates. Four loci with excellent reproducibility, specificity, and resolution for molecular typing purposes were identified, and the combined discriminatory power (DP, based on 20 epidemiologically unrelated isolates) of these four loci was 1.0. Reproducibility was demonstrated by consistently testing three strains each in triplicate, and stability, demonstrated by testing 10 successive passages. Then, we collected 48 C. orthopsilosis non-duplicate clinical isolates from the China Hospital Invasive Fungal Surveillance Net study to compare the DP of the microsatellite-based typing with internal transcribed spacer (ITS) and amplified fragment length polymorphism (AFLP) typing analyses, using ATCC 96139 as a reference strain. These 49 isolates were subdivided into 12 microsatellite types (COMT1-12), six AFLP types, and three ITS types, while all the isolates with the same COMT belonged to consistent AFLP and ITS type, demonstrating the high DP of our microsatellite-type method. According to our results, COMT12 was found to be the predominant type in China, and COMT5 was the second largest and responsible for causing a nosocomial outbreak. This microsatellite-type method is a valuable tool for the differentiation of C. orthopsilosis and could be vital for epidemiological studies to determine strain relatedness and monitor transmission.
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Affiliation(s)
- Zhengyu Luo
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Yating Ning
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Shuying Yu
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Rongchen Dai
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinfei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Yao Wang
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Wei Kang
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Yan Jiang
- Department of Microbiology and Immunology, Guizhou Medical University Affiliated Hospital, Guiyang, China
| | - Hua Yu
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Hongjie Liang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, The First Affiliated Hospital of Guangxi Medical University, Guangxi, China
| | - Yingchun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Tianshu Sun
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Clinical Biobank, Medical Research Center, National Science and Technology Key Infrastructure on Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Li Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Hitchcock M, Xu J. Analyses of the Global Multilocus Genotypes of the Human Pathogenic Yeast Cryptococcus neoformans Species Complex. Genes (Basel) 2022; 13:2045. [PMID: 36360282 PMCID: PMC9691084 DOI: 10.3390/genes13112045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 12/18/2023] Open
Abstract
Cryptococcus neoformans species complex (CNSC) is a globally distributed human opportunistic yeast pathogen consisting of five major molecular types (VNI, VNII, VNB, VNIII and VNIV) belonging to two species, C. neoformans (VNI, VNII and VNB, collectively called serotype A) and C. deneoformans (VNIV, commonly called serotype D), and their hybrids (VNIII, serotype AD). Over the years, many studies have analyzed the geographical distribution and genetic diversity of CNSC. However, the global population structure and mode of reproduction remain incompletely described. In this study, we analyze the published multilocus sequence data at seven loci for CNSC. The combined sequences at the seven loci identified a total of 657 multilocus sequence types (STs), including 296 STs with known geographic information, representing 4200 non-redundant isolates from 31 countries and four continents. Among the 296 STs, 78 and 52 were shared among countries and continents, respectively, representing 3643 of the 4200 isolates. Except for the clone-corrected serotype D sample among countries, our analysis of the molecular variance of the 4200 isolates revealed significant genetic differentiations among countries and continents in populations of CNSC, serotype A, and serotype D. Phylogenetic analyses of the concatenated sequences of all 657 STs revealed several large clusters corresponding to the major molecular types. However, several rare but distinct STs were also found, representing potentially novel molecular types and/or hybrids of existing molecular types. Phylogenetic incompatibility analyses revealed evidence for recombination within all four major molecular types-VNI, VNII, VNIV and VNB-as well as within two VNB subclades, VNBI and VNBII, and two ST clusters around the most common STs, ST5 and ST93. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across most samples. Together, our results suggest evidence for historical differentiation, frequent recent gene flow, clonal expansion and recombination within and between lineages of the global CNSC population.
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Affiliation(s)
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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Bader O. Phylogenetic Distribution of csp1 Types in Aspergillus fumigatus and Their Correlates to Azole Antifungal Drug Resistance. Microbiol Spectr 2021; 9:e0121421. [PMID: 34787484 PMCID: PMC8597649 DOI: 10.1128/spectrum.01214-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/22/2021] [Indexed: 11/20/2022] Open
Abstract
In Aspergillus fumigatus, the repetitive region of the csp1 gene is one of the most frequently used loci for intraspecies typing of this human pathogenic mold. Using PCR amplification and Sanger sequencing of only a single marker, csp1 typing is readily available to most laboratories and highly reproducible. Here, I evaluate the usefulness of the csp1 marker for resistance detection and epidemiologic stratification among A. fumigatus isolates. After resolving nomenclature conflicts from published studies and adding novel csp1 types, the number of known types now adds up to 38. Their distribution mostly correlates with A. fumigatus population structure, and they are also meaningful for narrowly defined cases of azole resistance phenotypes. Isolates carrying the pandemic resistance allele TR34/L98H show signs of interclade crossing of strains with t02 or t04A, into the t11 clade. Furthermore, absolute differences in voriconazole MIC values between t02/t04B versus t11 TR34/L98H isolates indicate that the genetic background of resistance mutations may have a pivotal role in cross-resistance phenotypes and, thus, clinical outcome and environmental selection. Despite the general genetic similarity of isolates with identical csp1 types, outcrossing into other clades is also observed. The csp1 type alone, therefore, does not sufficiently discriminate genetic clades to be used as the sole marker in epidemiologic studies. IMPORTANCE Aspergillus fumigatus is a ubiquitously distributed saprophytic mold and a leading cause of invasive aspergillosis in human hosts. Pandemic azole-resistant strains have emerged on a global scale, which are thought to be propagated through use of azole-based fungicides in agriculture. To perform epidemiologic studies, genetic typing of large cohorts is key. Here, I evaluate the usefulness of the frequently used csp1 marker for resistance detection and epidemiologic stratification among A. fumigatus isolates. The phylogenetic distribution of csp1 types mostly correlates with A. fumigatus population structure and is also meaningful for narrowly defined cases of azole resistance phenotypes. Nevertheless, outcrossing of csp1 into other clades is also observed. The csp1 type alone, therefore, does not sufficiently discriminate genetic clades and should not be used as the sole marker in epidemiologic studies.
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Affiliation(s)
- Oliver Bader
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
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Ma H, Yang J, Chen X, Jiang X, Su Y, Qiao S, Zhong G. Deep convolutional neural network: a novel approach for the detection of Aspergillus fungi via stereomicroscopy. J Microbiol 2021; 59:563-572. [PMID: 33779956 DOI: 10.1007/s12275-021-1013-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/10/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Fungi of the genus Aspergillus are ubiquitously distributed in nature, and some cause invasive aspergillosis (IA) infections in immunosuppressed individuals and contamination in agricultural products. Because microscopic observation and molecular detection of Aspergillus species represent the most operator-dependent and time-intensive activities, automated and cost-effective approaches are needed. To address this challenge, a deep convolutional neural network (CNN) was used to investigate the ability to classify various Aspergillus species. Using a dissecting microscopy (DM)/stereomicroscopy platform, colonies on plates were scanned with a 35× objective, generating images of sufficient resolution for classification. A total of 8,995 original colony images from seven Aspergillus species cultured in enrichment medium were gathered and autocut to generate 17,142 image crops as training and test datasets containing the typical representative morphology of conidiophores or colonies of each strain. Encouragingly, the Xception model exhibited a classification accuracy of 99.8% on the training image set. After training, our CNN model achieved a classification accuracy of 99.7% on the test image set. Based on the Xception performance during training and testing, this classification algorithm was further applied to recognize and validate a new set of raw images of these strains, showing a detection accuracy of 98.2%. Thus, our study demonstrated a novel concept for an artificial-intelligence-based and cost-effective detection methodology for Aspergillus organisms, which also has the potential to improve the public's understanding of the fungal kingdom.
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Affiliation(s)
- Haozhong Ma
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Jinshan Yang
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xiaolu Chen
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xinyu Jiang
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yimin Su
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Shanlei Qiao
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Guowei Zhong
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
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Irwin NAT, Twynstra CS, Mathur V, Keeling PJ. The molecular phylogeny of Chionaster nivalis reveals a novel order of psychrophilic and globally distributed Tremellomycetes (Fungi, Basidiomycota). PLoS One 2021; 16:e0247594. [PMID: 33760841 PMCID: PMC7990227 DOI: 10.1371/journal.pone.0247594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/09/2021] [Indexed: 12/04/2022] Open
Abstract
Snow and ice present challenging substrates for cellular growth, yet microbial snow communities not only exist, but are diverse and ecologically impactful. These communities are dominated by green algae, but additional organisms, such as fungi, are also abundant and may be important for nutrient cycling, syntrophic interactions, and community structure in general. However, little is known about these non-algal community members, including their taxonomic affiliations. An example of this is Chionaster nivalis, a unicellular fungus that is morphologically enigmatic and frequently observed in snow communities globally. Despite being described over one hundred years ago, the phylogeny and higher-level taxonomic classifications of C. nivalis remain unknown. Here, we isolated and sequenced the internal transcribed spacer (ITS) and the D1-D2 region of the large subunit ribosomal RNA gene of C. nivalis, providing a molecular barcode for future studies. Phylogenetic analyses using the ITS and D1-D2 region revealed that C. nivalis is part of a novel lineage in the class Tremellomycetes (Basidiomycota, Agaricomycotina) for which a new order Chionasterales ord. nov. (MB838717) and family Chionasteraceae fam. nov. (MB838718) are proposed. Comparisons between C. nivalis and sequences generated from environmental surveys revealed that the Chionasterales are globally distributed and probably psychrophilic, as they appear to be limited to the high alpine and arctic regions. These results highlight the unexplored diversity that exists within these extreme habitats and emphasize the utility of single-cell approaches in characterizing these complex algal-dominated communities.
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Affiliation(s)
- Nicholas A. T. Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Merton College, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Chantelle S. Twynstra
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J. Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Houdelet C, Bocquet M, Bulet P. Matrix-assisted laser desorption/ionization mass spectrometry biotyping, an approach for deciphering and assessing the identity of the honeybee pathogen Nosema. Rapid Commun Mass Spectrom 2021; 35:e8980. [PMID: 33063365 DOI: 10.1002/rcm.8980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/29/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE The microsporidia are obligate intracellular pathogenic fungi that parasitize a wide range of invertebrate and vertebrate hosts and have important impacts on health, food security and the economy. In this paper, we focus on Nosema ceranae and N. apis, which chronically infect the digestive tract of honeybees, altering their physiology and lifespan. METHODS We applied matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for rapid molecular profiling of extracts of Nosema spores in order to identify the species and the geographical origin, and assess the viability status of Nosema microsporidia in conjunction with a flow cytometric approach. Pure solutions of spores were prepared for flow cytometric analysis and MALDI-MS profiling. A mechanical extraction of viable or heat-killed Nosema spores was conducted to obtain mass fingerprints of peptides/proteins for samples of microsporidia from different geographical origins (MBO.NC01, MBO.NC02 and MBO.NA01). RESULTS A distinction in the peptide/protein profiles between two isolates with different geographical origins was observed. Mass fingerprints of viable and experimentally killed spores were also clearly distinguishable, regardless of Nosema species. Finally, using our computational models on the different Nosema species, we were able to classify five independent isolates of Nosema microsporidia. CONCLUSIONS We have shown that MALDI-MS is a rapid, cost-effective and simple method for identifying Nosema species. We demonstrated that MALDI Biotyping could represent a valuable surveillance tool of nosemosis in apiaries for sanitary services and beekeepers.
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Affiliation(s)
- Camille Houdelet
- Institute for Advanced Biosciences, CR Inserm U1209, CNRSUMR 5309, University of Grenoble-Alpes, Grenoble, France
- Platform BioPark Archamps, Archamps, France
| | | | - Philippe Bulet
- Institute for Advanced Biosciences, CR Inserm U1209, CNRSUMR 5309, University of Grenoble-Alpes, Grenoble, France
- Platform BioPark Archamps, Archamps, France
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Cardot Martin E, Renaux C, Catherinot E, Limousin L, Couderc LJ, Vasse M. Rapid identification of fungi from respiratory samples by Bruker Biotyper matrix-assisted laser desorption/ionisation time-of-flight using ID-FUNGI plates. Eur J Clin Microbiol Infect Dis 2021; 40:391-395. [PMID: 32808108 DOI: 10.1007/s10096-020-04007-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/11/2020] [Indexed: 12/27/2022]
Abstract
Identification of moulds is crucial for the clinical management of patients. The goal of this study was to evaluate the new ID-FUNGI plate (IDFP) for the identification of moulds by MALDI Biotyper. IDFP was compared with Sabouraud with gentamicin and chloramphenicol plate (SAB) for the identification of 80 moulds from respiratory samples and eight reference strains. With the direct transfer method, species identification rose from 6% with SAB to 68% with IDFP using score cut-off 2 and from 20 to 75% using cut-off 1.7 (p < 0.001). Our study highlights that the new IDFP improves mycological diagnostic and workflow in laboratories.
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Affiliation(s)
| | - Claudine Renaux
- Department of Microbiology, Foch Hospital, 92150, Suresnes, France
| | | | - Lucie Limousin
- Department of Microbiology, Foch Hospital, 92150, Suresnes, France
| | - Louis Jean Couderc
- Department of Pneumonology, Foch Hospital, 92150, Suresnes, France
- UPRES EA 220, Department of Pneumonology, Faculty of Life Sciences Simone Veil, University Paris-Saclay, 91190, Saint-Aubin, France
| | - Marc Vasse
- Department of Microbiology, Foch Hospital, 92150, Suresnes, France
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Inglis PW, Mello SCM, Martins I, Silva JBT, Macêdo K, Sifuentes DN, Valadares-Inglis MC. Trichoderma from Brazilian garlic and onion crop soils and description of two new species: Trichoderma azevedoi and Trichoderma peberdyi. PLoS One 2020; 15:e0228485. [PMID: 32130211 PMCID: PMC7055844 DOI: 10.1371/journal.pone.0228485] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/15/2020] [Indexed: 01/05/2023] Open
Abstract
Fifty four Trichoderma strains were isolated from soil samples collected from garlic and onion crops in eight different sites in Brazil and were identified using phylogenetic analysis based on combined ITS region, tef1-α, cal, act and rpb2 sequences. The genetic variability of the recovered Trichoderma species was analysed by AFLP and their phenotypic variability determined using MALDI-TOF. The strain clusters from both typing techniques coincided with the taxonomic determinations made from phylogenetic analysis. The phylogenetic analysis showed the occurrence of Trichoderma asperellum, Trichoderma asperelloides, Trichoderma afroharzianum, Trichoderma hamatum, Trichoderma lentiforme, Trichoderma koningiopsis, Trichoderma longibrachiatum and Trichoderma erinaceum, in the soil samples. We also identified and describe two new Trichoderma species, both in the harzianum clade of section Pachybasium, which we have named Trichoderma azevedoi sp. nov. and Trichoderma peberdyi sp. nov. The examined strains of both T. azevedoi (three strains) and T. peberdyi (12 strains) display significant genotypic and phenotypic variability, but form monophyletic clades with strong bootstrap and posterior probability support and are morphologically distinct from their respective most closely related species.
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Affiliation(s)
- Peter W. Inglis
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | | | - Irene Martins
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | | | - Kamilla Macêdo
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
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Yin M, Jing C, Li H, Deng Q, Wang S. Surface chemistry modified upconversion nanoparticles as fluorescent sensor array for discrimination of foodborne pathogenic bacteria. J Nanobiotechnology 2020; 18:41. [PMID: 32111217 PMCID: PMC7049179 DOI: 10.1186/s12951-020-00596-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/20/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The identification of foodborne pathogenic bacteria types plays a crucial role in food safety and public health. In consideration of long culturing times, tedious operations and the desired specific recognition elements in conventional methods, the alternative fluorescent sensor arrays can offer a high-effective approach in bacterial identification by using multiple cross-reactive receptors. Herein, we achieve this goal by constructing an upconversion fluorescent sensor array based on anti-stokes luminogens featuring a series of functional lanthanide-doped upconversion nanoparticles (UCNPs) with phenylboronic acid, phosphate groups, or imidazole ionic liquid. The prevalent spotlight effect of microorganism and the electrostatic interaction between UCNPs and bacteria endow such sensor array an excellent discrimination property. RESULTS Seven common foodborne pathogenic bacteria including two Gram-positive bacteria (Staphylococcus aureus and Listeria monocytogenes) and five Gram-negative bacteria (Escherichia coli, Salmonella, Cronobacter sakazakii, Shigella flexneri and Vibrio parahaemolyticus) are precisely identified with 100% accuracy via linear discriminant analysis (LDA). Furthermore, blends of bacteria have been identified accurately. Bacteria in real samples (tap water, milk and beef) have been effectively discriminated with 92.1% accuracy. CONCLUSIONS Current fluorescence sensor array is a powerful tool for high-throughput bacteria identification, which overcomes the time-consuming bacteria culture and heavy dependence of specific recognition elements. The high efficiency of whole bacterial cell detection and the discrimination capability of life and death bacteria can brighten the application of fluorescence sensor array.
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Affiliation(s)
- Mingyuan Yin
- State Key Laboratory of Food Nutrition and Safety, School of Food Engineering and Biotechnology, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Chuang Jing
- State Key Laboratory of Food Nutrition and Safety, School of Food Engineering and Biotechnology, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Haijie Li
- State Key Laboratory of Food Nutrition and Safety, School of Food Engineering and Biotechnology, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Qiliang Deng
- State Key Laboratory of Food Nutrition and Safety, School of Food Engineering and Biotechnology, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Shuo Wang
- State Key Laboratory of Food Nutrition and Safety, School of Food Engineering and Biotechnology, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, 300071, People's Republic of China.
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Er H, Koyuncu-Ozyurt O, Ozhak B, Yazisiz H, Eres-Saritas Z, Cetinkaya O, Ongut G, Ogunc D. Evaluation of an Automated Yeasts Identification System for Identification of Yeast Isolates. Clin Lab 2020; 66. [PMID: 32013368 DOI: 10.7754/clin.lab.2019.190636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Invasive candidiasis is the most important health-care-associated fungal infection worldwide. In the last two decades, the cause of the increase of fungal infections is immunosuppression or serious underlying diseases. Additionally, Rhodotorula species, Blastoschizomyces capitatus, and Trichosporon species are emerging as important human pathogens in immunocompromised patients with hematological malignancy. METHODS Between January 2012 and January 2018, a total of 603 fungal organisms were isolated from blood culture samples and included in the study. All of the isolates were identified by using standard mycological methods, MALDI TOF MS system, and the Phoenix system. Sequence analysis was performed on yeasts that could not be definitively identified by using SMM and incompatible according to the results with Phoenix and MALDI-TOF MS analysis. RESULTS 603 fungal isolates including 594 Candida spp. and 9 other yeasts like species were analyzed. C. albicans was the most frequently isolated species. The results of identification by conventional methods and MALDI TOF MS were compared to the results of the Phoenix system. The observed concordance was 99.2%. The compatibility with other systems of the Phoenix system was 100%, 100%, 97.3%, 100%, and 96.9% for C. albicans, C. parapsilosis, C. tropicalis, C. glabrata, and C. krusei, respectively. CONCLUSIONS The BD Phoenix system was found to be a simple, reliable, and effective method to identify the main species of the genus Candida in our study.
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Shokoohi GR, Ansari S, Abolghazi A, Gramishoar M, Nouripour-Sisakht S, Mirhendi H, Makimura K. The first case of fingernail onychomycosis due to Neoscytalidium novaehollandiae, molecular identification and antifungal susceptibility. J Mycol Med 2019; 30:100920. [PMID: 31892498 DOI: 10.1016/j.mycmed.2019.100920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023]
Abstract
Onychomycosis is considered a fungal nail infection caused mainly by dermatophytes, yeasts and non-dermatophyte molds including dematiaceous fungi. Onychomycosis caused by non-dermatophyte molds is a health problem in the medical environment as the patients frequently return to outpatient clinics seeking new therapeutic modalities. Here, we report the first case of onychomycosis caused by a black fungus, Neoscytalidium novaehollandiae, in the right hand finger nail of a 52-year-old Iranian female with no history of immunodeficiency and underlying disease. The pattern of nail involvement was recognized as total dystrophic onychomycosis. Examination of nail scrapings with potassium hydroxide revealed brown, septate and branching sub-hyaline to dark-colored hyphae. The black fungus isolated in culture was identified as Neoscytalidium novaehollandiae by molecular analysis. The patient received oral terbinafine plus ciclopirox nail lacquer twice a week and began responding to the treatment three months after initial antifungal therapy. Additional four weeks' use of terbinafine plus ciclopirox nail lacquer completely resolved the clinical manifestations of onychomycosis. After four months, both microscopy and culture were negative.
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Affiliation(s)
- G R Shokoohi
- Department of Medical Parasitology and Mycology, School of Medicine, Jahrom University of Medical Sciences, Jahrom, Iran
| | - S Ansari
- Department of Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - A Abolghazi
- Department of Medical Parasitology and Mycology, School of Medicine, Jahrom University of Medical Sciences, Jahrom, Iran
| | - M Gramishoar
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - S Nouripour-Sisakht
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - H Mirhendi
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - K Makimura
- Medical Mycology, Graduate School of Medicine, Teikyo University, Tokyo, Japan
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Conti M, Cinget B, Vivancos J, Oudemans P, Bélanger RR. A Molecular Assay Allows the Simultaneous Detection of 12 Fungi Causing Fruit Rot in Cranberry. Plant Dis 2019; 103:2843-2850. [PMID: 31469361 DOI: 10.1094/pdis-03-19-0531-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cranberry fruit rot (CFR) is arguably one of the most limiting factors of cranberry (Vaccinium macrocarpon) production throughout its growing areas. The disease is caused by a group of closely related fungi that require identification using long and cumbersome steps of isolation and microscopic observations of structural features. The objective of this study was to develop a molecular assay to simultaneously detect and discriminate 12 of the most important fungal species reported to be pathogenic on cranberry fruit to facilitate the diagnosis of CFR. As the first approach, internal transcribed spacers and large subunit regions of all fungi were sequenced and confirmed with sequences available in the NCBI database. These data were used to develop primers able to differentiate seven of the 12 species. The five remaining species, including three in the Phacidiaceae family and two in the Glomerellaceae family, were differentiated on the basis of a more discriminant marker, the translation elongation factor 1-α. Two PCR reactions were optimized to clearly delineate the 12 species. The multiplex test was first validated using pure fungal cultures; it was subsequently validated using fruit collected in cranberry beds in eastern Canada. In the latter case, the test was rigorous enough to clearly discriminate the fungal pathogens from contaminants. Within the tested samples, Physalospora vaccinii and Coleophoma empetri were most commonly found. This molecular test offers scientists, diagnosticians, and growers a powerful tool that can rapidly and precisely identify fungi causing CFR so they can implement appropriate control methods.
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Affiliation(s)
- Matteo Conti
- Centre de Recherche en Innovation des Végétaux, Université Laval, Quebec City, Québec, Canada
| | - Benjamin Cinget
- Centre de Recherche en Innovation des Végétaux, Université Laval, Quebec City, Québec, Canada
| | - Julien Vivancos
- Laboratoire d'expertise et de Diagnostic en Phytoprotection, Quebec City, Québec, Canada
| | - Peter Oudemans
- Philip E. Marucci Center for Blueberry and Cranberry Research and Extension, The State University of New Jersey, Chatsworth, NJ, U.S.A
| | - Richard R Bélanger
- Centre de Recherche en Innovation des Végétaux, Université Laval, Quebec City, Québec, Canada
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Abstract
The yeast Candida glabrata has emerged, second only to Candida albicans, to be one of the most frequently isolated fungi in clinical specimen from human. Its frequent resistance towards azole antifungal drugs and the high capacity to form biofilms on indwelling catheters of individual isolates render it an often difficult to treat pathogen. Hence, there is a notably increasing scientific and clinical interest in this species. This has led to the development of a variety of molecular tools for genetic modification, strain collections, and last but not least different approaches to analyse the population structure among isolates of different geographical and clinical contexts. Often, these are used to study correlations (or the absence thereof) with different pathogenicity, virulence, or drug resistance traits. Three molecular methods have been used to type within the C. glabrata population on a genetic level by multiple studies: multi-locus sequence typing, microsatellite length polymorphisms, and clustering of whole-genome sequencing data, and these are subject of this review.
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Affiliation(s)
- Toni Gabaldón
- Comparative Genomics Group, Life Science Programme, Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute of Research in Biomedicine (IRB), Barcelona, Spain
- Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Emilia Gómez-Molero
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, 37075, Göttingen, Germany
| | - Oliver Bader
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, 37075, Göttingen, Germany.
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Lemma T, Wang J, Arstila K, Hytönen VP, Toppari JJ. Identifying yeasts using surface enhanced Raman spectroscopy. Spectrochim Acta A Mol Biomol Spectrosc 2019; 218:299-307. [PMID: 31005737 DOI: 10.1016/j.saa.2019.04.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/05/2019] [Accepted: 04/07/2019] [Indexed: 06/09/2023]
Abstract
The molecular fingerprints of yeasts Saccharomyces cerevisiae, Dekkera bruxellensis, and Wickerhamomyces anomalus (former name Pichia anomala) have been examined using surface-enhanced Raman spectroscopy (SERS) and helium ion microscopy (HIM). The SERS spectra obtained from cell cultures (lysate and non-treated cells) distinguish between these very closely related fungal species. Highly SERS active silver nano-particles suitable for detecting complex biomolecules were fabricated using a simple synthesis route. The yeast samples mixed with aggregated Ag nanoparticles yielded highly enhanced and reproducible Raman signal owing to the high density of the hot spots at the junctions of two or more Ag nanoparticles and enabled to differentiate the three species based on their unique features (spectral fingerprint). We also collected SERS spectra of the three yeast species in beer medium to demonstrate the potential of the method for industrial application. These findings demonstrate the great potential of SERS for detection and identification of fungi species based on the biochemical compositions, even in a chemically complex sample.
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Affiliation(s)
- Tibebe Lemma
- Faculdade de Clências e Tecnologia (FCT)-Universidade Estadual Paulista (UNESP)-Presidente Prudente, SP 19060-900, Brazil.
| | - Jin Wang
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China
| | - Kai Arstila
- NanoScience Center, Department of Physics, P.O. Box 35 (YN), FI-40014, University of Jyväskylä, Finland
| | - Vesa P Hytönen
- Faculty of Medicine and Health Technology, BioMediTech, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland; Fimlab Laboratories, Biokatu 4, FI-33520 Tampere, Finland
| | - J Jussi Toppari
- NanoScience Center, Department of Physics, P.O. Box 35 (YN), FI-40014, University of Jyväskylä, Finland
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Trabelsi H, Neji S, Hadrich I, Khemakhem N, Sellami H, Makni F, Ayadi A. Contribution of the internal transcribed spacer regions to the detection and identification of human fungal pathogens. Curr Res Transl Med 2019; 67:100-106. [PMID: 30975553 DOI: 10.1016/j.retram.2019.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/25/2019] [Accepted: 04/02/2019] [Indexed: 11/17/2022]
Abstract
Fungi are morphologically and phylogenetically diverse. There identification is largely based on phenotypic methods. Thus, related species, phenotypic variants and rare species may be unidentified. So, molecular methods have been introduced for identification of pathogenic molds to overcome these problems. In this study, we report the contribution of molecular tools (PCR sequencing) to identify fungal pathogens in both clinical and environmental samples. A total of 82 mold isolates were used (50 clinical samples and 32 environmental samples). PCR and direct sequencing, targeting the internal transcribed spacer (ITS) regions, were performed. We employed comparative sequence analysis to identify molds by using the GenBank database. 89% of isolates were identified by phenotypic methods. PCR- sequencing allowed the fungal identification in all cases. The concordance between molecular and morphological identification was obtained for 33 cases (40.2%). In 36 cases (43.9%), the molecular study gave the exact species identification. PCR sequencing allowed as revising mycological identification for 13 fungi strains (15.9%). The concordance of identification at species level by phenotypic method and by sequence analysis was obtained for 28% of clinical samples and for 59% of environmental samples. The phylogenetic tree for the ITS sequences showed six different clusters that are composed of isolates belonging to the same genus or species. PCR sequencing has been shown to be useful for the detection of the presence of fungal DNA in both environmental and clinical samples. It is rapid and more sensitive for the identification of medically important fungi.
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Affiliation(s)
- H Trabelsi
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - S Neji
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - I Hadrich
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - N Khemakhem
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - H Sellami
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - F Makni
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - A Ayadi
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.
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Xanthopoulou A, Ganopoulos I, Tryfinopoulou P, Panagou EZ, Osanthanunkul M, Madesis P, Kizis D. Rapid and accurate identification of black aspergilli from grapes using high-resolution melting (HRM) analysis. J Sci Food Agric 2019; 99:309-314. [PMID: 29876941 DOI: 10.1002/jsfa.9189] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Aspergillus is a diverse genus of fungi with high economic and social impact. Various species that belong to section Nigri (black aspergilli) are common agents of grape spoilage and potent producers of ochratoxin A (OTA), a mycotoxin associated with various nephrotoxic and immunotoxic effects in humans. Black aspergilli are difficult to classify following only phenotypic criteria; thus chemotaxonomic and molecular methods are employed in parallel with phenotypic ones for species characterization. These approaches, though accurate and replicable, require more than one individual step and are to a certain extent laborious when a rapid identification of these species is required. RESULTS The aim of this study was to develop a high-resolution melting polymerase chain reaction (HRM-PCR) assay as a rapid method for identification of Aspergillus spp. section Nigri isolates and their detection in grape samples. Melt curve analysis of amplicons originating from the internal transcribed spacer 2 (ITS2) ribosomal region generated species-specific HRM curve profiles, enabling the accurate differentiation of the analyzed genotypes. Furthermore, the assay was able to identify A. carbonarius, A. tubingensis, A. niger, A. ibericus and A. japonicus in grape samples artificially inoculated with conidia of these fungi. CONCLUSION To our knowledge this is the first report on the development of an HRM-PCR assay for the identification of black Aspergillus species in grape samples. © 2018 Society of Chemical Industry.
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Affiliation(s)
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources ELGO-DEMETER, Thessaloniki, Greece
| | - Paschalitsa Tryfinopoulou
- Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Efstathios Z Panagou
- Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Maslin Osanthanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | - Dimosthenis Kizis
- Laboratory of Mycology, Department of Phytopathology, Benaki Phytopathological Institute, Athens, Greece
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Morales-Cruz A, Figueroa-Balderas R, García JF, Tran E, Rolshausen PE, Baumgartner K, Cantu D. Profiling grapevine trunk pathogens in planta: a case for community-targeted DNA metabarcoding. BMC Microbiol 2018; 18:214. [PMID: 30547761 PMCID: PMC6295080 DOI: 10.1186/s12866-018-1343-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/15/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND DNA metabarcoding, commonly used in exploratory microbial ecology studies, is a promising method for the simultaneous in planta-detection of multiple pathogens associated with disease complexes, such as the grapevine trunk diseases. Profiling of pathogen communities associated with grapevine trunk diseases is particularly challenging, due to the presence within an individual wood lesion of multiple co-infecting trunk pathogens and other wood-colonizing fungi, which span a broad range of taxa in the fungal kingdom. As such, we designed metabarcoding primers, using as template the ribosomal internal transcribed spacer of grapevine trunk-associated ascomycete fungi (GTAA) and compared them to two universal primer widely used in microbial ecology. RESULTS We first performed in silico simulations and then tested the primers by high-throughput amplicon sequencing of (i) multiple combinations of mock communities, (ii) time-course experiments with controlled inoculations, and (iii) diseased field samples from vineyards under natural levels of infection. All analyses showed that GTAA had greater affinity and sensitivity, compared to those of the universal primers. Importantly, with GTAA, profiling of mock communities and comparisons with shotgun-sequencing metagenomics of field samples gave an accurate representation of genera of important trunk pathogens, namely Phaeomoniella, Phaeoacremonium, and Eutypa, the abundances of which were over- or under-estimated with universal primers. CONCLUSIONS Overall, our findings not only demonstrate that DNA metabarcoding gives qualitatively and quantitatively accurate results when applied to grapevine trunk diseases, but also that primer customization and testing are crucial to ensure the validity of DNA metabarcoding results.
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Affiliation(s)
- Abraham Morales-Cruz
- Department of Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616 USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616 USA
| | - Jadran F. García
- Department of Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616 USA
| | - Eric Tran
- Department of Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616 USA
| | - Philippe E. Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
| | - Kendra Baumgartner
- United States Department of Agriculture, Agricultural Research Service, Crops Pathology and Genetics Research Unit, Davis, CA 95616 USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616 USA
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Trobajo-Sanmartín C, Ezpeleta G, Pais C, Eraso E, Quindós G. Design and validation of a multiplex PCR protocol for microsatellite typing of Candida parapsilosis sensu stricto isolates. BMC Genomics 2018; 19:718. [PMID: 30268088 PMCID: PMC6162959 DOI: 10.1186/s12864-018-5065-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 09/11/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Analysis of polymorphic microsatellite markers (STR) is a helpful genotyping technique to differentiate Candida parapsilosis sensu stricto isolates. The aim of this study is to develop and perform an initial validation of an alternative protocol for the reliable and accurate microsatellite genotyping of C. parapsilosis sensu stricto isolates using high-throughput multiplex PCR. To achieve this, the results obtained using the new protocol were compared to the ones obtained using a previously described reference method. To that end, diagnostic accuracy, informativeness and discrimination parameters were estimated. RESULTS Our results showed good concordance between both methods (Kappa index: 0.920), leading to a high sensitivity (1; CI(95%) (0.991-1)) and specificity (1; CI(95%) (0.772-1)) after the validation of the new protocol. Moreover, the electropherograms profiles obtained with the new PCR scheme showed a high signal to noise ratio (SNR). CONCLUSIONS The new multiplex protocol is valuable for the differentiation of C. parapsilosis sensu stricto, with direct clinical applications. Besides, the new protocol represents a shortening the hands-on time, reducing the sample manipulation (dismissing the possibility of cross-contamination), maintaining the quality of the results (when compared to the ones obtained with the reference method), and helping to the standardization and simplification of the genotyping scheme.
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Affiliation(s)
- Camino Trobajo-Sanmartín
- Laboratorio de Micología Médica, Departamento de Inmunología, Microbiología y Parasitología, UFI11/25 (Microbios y Salud), Facultad de Medicina y Enfermería, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Apartado 699, E-48080 Bilbao, Spain
| | - Guillermo Ezpeleta
- Departamento de Medicina Preventiva y Salud Pública, Facultad de Medicina y Enfermería, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Bilbao, Spain
- Servicio de Medicina Preventiva e Higiene Hospitalaria, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Célia Pais
- Centro de Biologia Molecular e Ambiental (CBMA), Departamento de Biologia, Universidade do Minho, Braga, Portugal
| | - Elena Eraso
- Laboratorio de Micología Médica, Departamento de Inmunología, Microbiología y Parasitología, UFI11/25 (Microbios y Salud), Facultad de Medicina y Enfermería, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Apartado 699, E-48080 Bilbao, Spain
| | - Guillermo Quindós
- Laboratorio de Micología Médica, Departamento de Inmunología, Microbiología y Parasitología, UFI11/25 (Microbios y Salud), Facultad de Medicina y Enfermería, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Apartado 699, E-48080 Bilbao, Spain
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De la Torre González FJ, Avendaño DOG, Mathis ACG, Kirchmayr MR. Evaluation of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for differentiation of Pichia kluyveri strains isolated from traditional fermentation processes. Rapid Commun Mass Spectrom 2018; 32:1514-1520. [PMID: 29873842 DOI: 10.1002/rcm.8192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/18/2018] [Accepted: 05/28/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Non-Saccharomyces yeasts are widespread microorganisms that nowadays have gained importance for their ability to produce volatile compounds which in alcoholic beverages improve aromatic complexity and therefore the overall quality. Their rapid identification and differentiation in fermentation processes is vital for timely decision making. METHODS A total of 19 strains of Pichia kluyveri isolated from mezcal, tejuino and cacao fermentations were analyzed with rep-PCR fingerprinting using the primer (GTG)5 and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) on a Microflex LT mass spectrometer using Biotyper 3.1 software (Bruker Daltonics). RESULTS The comparative analysis between MS spectra and rep-PCR patterns obtained from these strains showed a high similarity between both methods. However, minimal differences between the obtained rep-PCR and MALDI-TOF MS clusters could be observed, especially by the presence and/or absence of one or more discriminating peaks even when they have similarities in their main spectra projection, observing that isolates from the same fermentative process were grouped into the same sub-cluster based on their MALDI-TOF MS profiles. CONCLUSIONS The data shown suggests that MALDI-TOF MS is a promising alternative technique for rapid, reliable and cost-effective differentiation of native yeast strains isolated from different traditional fermented foods and beverages.
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Affiliation(s)
- Francisco Javier De la Torre González
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Camino Arenero 1227, El Bajío del Arenal, 45019, Zapopan, Jalisco, México
| | - Daniel Oswaldo Gutiérrez Avendaño
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Camino Arenero 1227, El Bajío del Arenal, 45019, Zapopan, Jalisco, México
| | - Anne Christine Gschaedler Mathis
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Camino Arenero 1227, El Bajío del Arenal, 45019, Zapopan, Jalisco, México
| | - Manuel Reinhart Kirchmayr
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Camino Arenero 1227, El Bajío del Arenal, 45019, Zapopan, Jalisco, México
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Cordeiro RA, Sales JA, Ponte YBD, Mendes PBL, Serpa R, Evangelista AJ, Alencar LPD, Pereira-Neto WDA, Brilhante RSN, Sidrim JJC, Castelo-Branco DSCM, Rocha MFG. Phenotype-driven strategies for screening Candida parapsilosis complex for molecular identification. Braz J Microbiol 2018; 49 Suppl 1:193-198. [PMID: 29548715 PMCID: PMC6328843 DOI: 10.1016/j.bjm.2017.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/12/2017] [Accepted: 11/16/2017] [Indexed: 11/21/2022] Open
Abstract
In this study, phenotypic methods presented >80% agreement with the molecular identification of 59 Candida parapsilosis complex. Growth at 15% NaCl or pH 7.0 significantly reduced cfu-counts of Candida orthopsilosis, suggesting these conditions may support the development of phenotypic methods for the differentiation of the cryptic species of C. parapsilosis complex.
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Affiliation(s)
- Rossana A Cordeiro
- Universidade Federal do Ceará, Departmento de Patologia e Medicina Legal, Programa de Pós-Graduação em Microbiologia Médica, Centro Médico Especializado em Micologia, Fortaleza, CE, Brazil
| | - Jamille A Sales
- Universidade Estatual do Ceará, Escola de Medicina Veterinária, Programa de Pós-Graduação em Ciências Veterinárias, Fortaleza, CE, Brazil
| | - Yago B de Ponte
- Universidade Estatual do Ceará, Escola de Medicina Veterinária, Programa de Pós-Graduação em Ciências Veterinárias, Fortaleza, CE, Brazil
| | - Patrícia B L Mendes
- Universidade Federal do Ceará, Departmento de Patologia e Medicina Legal, Programa de Pós-Graduação em Microbiologia Médica, Centro Médico Especializado em Micologia, Fortaleza, CE, Brazil
| | - Rosana Serpa
- Universidade Federal do Ceará, Departmento de Patologia e Medicina Legal, Programa de Pós-Graduação em Microbiologia Médica, Centro Médico Especializado em Micologia, Fortaleza, CE, Brazil
| | - Antônio J Evangelista
- Universidade Federal do Ceará, Departmento de Patologia e Medicina Legal, Programa de Pós-Graduação em Microbiologia Médica, Centro Médico Especializado em Micologia, Fortaleza, CE, Brazil
| | - Lucas P de Alencar
- Universidade Federal do Ceará, Departmento de Patologia e Medicina Legal, Programa de Pós-Graduação em Microbiologia Médica, Centro Médico Especializado em Micologia, Fortaleza, CE, Brazil
| | - Waldemiro de A Pereira-Neto
- Universidade Federal do Ceará, Departmento de Patologia e Medicina Legal, Programa de Pós-Graduação em Microbiologia Médica, Centro Médico Especializado em Micologia, Fortaleza, CE, Brazil
| | - Raimunda S N Brilhante
- Universidade Federal do Ceará, Departmento de Patologia e Medicina Legal, Programa de Pós-Graduação em Microbiologia Médica, Centro Médico Especializado em Micologia, Fortaleza, CE, Brazil.
| | - José J C Sidrim
- Universidade Federal do Ceará, Departmento de Patologia e Medicina Legal, Programa de Pós-Graduação em Microbiologia Médica, Centro Médico Especializado em Micologia, Fortaleza, CE, Brazil
| | - Débora S C M Castelo-Branco
- Universidade Federal do Ceará, Departmento de Patologia e Medicina Legal, Programa de Pós-Graduação em Microbiologia Médica, Centro Médico Especializado em Micologia, Fortaleza, CE, Brazil
| | - Marcos F G Rocha
- Universidade Federal do Ceará, Departmento de Patologia e Medicina Legal, Programa de Pós-Graduação em Microbiologia Médica, Centro Médico Especializado em Micologia, Fortaleza, CE, Brazil; Universidade Estatual do Ceará, Escola de Medicina Veterinária, Programa de Pós-Graduação em Ciências Veterinárias, Fortaleza, CE, Brazil
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23
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Luethy PM, Zelazny AM. Rapid one-step extraction method for the identification of molds using MALDI-TOF MS. Diagn Microbiol Infect Dis 2018; 91:130-135. [PMID: 29454652 DOI: 10.1016/j.diagmicrobio.2018.01.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/21/2017] [Accepted: 01/18/2018] [Indexed: 11/18/2022]
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized fungal identification. Previously, we developed a MALDI-TOF MS mold extraction procedure and comprehensive database. While MALDI-TOF MS has become routine in a few laboratories, it has not yet become widespread. A major obstacle is the lack of a simple, reproducible and uniform protein extraction procedure. In this study, we developed and validated a rapid one-step protein extraction protocol for filamentous fungi. Excised molds were placed into tubes containing zirconia-silica beads and extraction solution without washing or ethanol inactivation steps. Extraction solutions containing different ratios of acetonitrile and formic acid were evaluated. Samples were then processed using a PowerLyzer high power bead based homogenizer and supernatants spotted for MALDI-TOF MS. The rapid method was evaluated prospectively and in parallel to our current mold extraction protocol for 3 months. Analysis of 106 clinical mold isolates resulted in an improved performance and a decrease in extraction time by 30 minutes to a total of 5 minutes of hands-on time. Acceptable identification scores (≥ 2.00) were achieved for up to 63.0% of mold isolates by the rapid method compared with 52.8% of isolates by the current routine protocol. Score comparisons between duplicate spots showed higher reproducibility of the rapid method as compared to the routine method. The rapid extraction method allows efficient analysis of clinical mold isolates both in scheduled batch runs and on an in-demand basis while providing a simple starting platform for laboratories adopting MALDI-TOF MS for mold identification.
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Affiliation(s)
- Paul M Luethy
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Adrian M Zelazny
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA.
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Castaño C, Oliva J, Martínez de Aragón J, Alday JG, Parladé J, Pera J, Bonet JA. Mushroom Emergence Detected by Combining Spore Trapping with Molecular Techniques. Appl Environ Microbiol 2017; 83:e00600-17. [PMID: 28432095 PMCID: PMC5478987 DOI: 10.1128/aem.00600-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 04/12/2017] [Indexed: 11/20/2022] Open
Abstract
Obtaining reliable and representative mushroom production data requires time-consuming sampling schemes. In this paper, we assessed a simple methodology to detect mushroom emergence by trapping the fungal spores of the fruiting body community in plots where mushroom production was determined weekly. We compared the performance of filter paper traps with that of funnel traps and combined these spore trapping methods with species-specific quantitative real-time PCR and Illumina MiSeq to determine the spore abundance. Significantly more MiSeq proportional reads were generated for both ectomycorrhizal and saprotrophic fungal species using filter traps than were obtained using funnel traps. The spores of 37 fungal species that produced fruiting bodies in the study plots were identified. Spore community composition changed considerably over time due to the emergence of ephemeral fruiting bodies and rapid spore deposition (lasting from 1 to 2 weeks), which occurred in the absence of rainfall events. For many species, the emergence of epigeous fruiting bodies was followed by a peak in the relative abundance of their airborne spores. There were significant positive relationships between fruiting body yields and spore abundance in time for five of seven fungal species. There was no relationship between fruiting body yields and their spore abundance at plot level, indicating that some of the spores captured in each plot were arriving from the surrounding areas. Differences in fungal detection capacity by spore trapping may indicate different dispersal ability between fungal species. Further research can help to identify the spore rain patterns for most common fungal species.IMPORTANCE Mushroom monitoring represents a serious challenge in economic and logistical terms because sampling approaches demand extensive field work at both the spatial and temporal scales. In addition, the identification of fungal taxa depends on the expertise of experienced fungal taxonomists. Similarly, the study of fungal dispersal has been constrained by technological limitations, especially because the morphological identification of spores is a challenging and time-consuming task. Here, we demonstrate that spores from ectomycorrhizal and saprotrophic fungal species can be identified using simple spore traps together with either MiSeq fungus-specific amplicon sequencing or species-specific quantitative real-time PCR. In addition, the proposed methodology can be used to characterize the airborne fungal community and to detect mushroom emergence in forest ecosystems.
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Affiliation(s)
- Carles Castaño
- Forest Bioengineering Solutions S.A., Solsona, Spain
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-AGROTECNIO, Lleida, Spain
| | - Jonàs Oliva
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-AGROTECNIO, Lleida, Spain
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Juan Martínez de Aragón
- Forest Bioengineering Solutions S.A., Solsona, Spain
- Centre Tecnològic Forestal de Catalunya, CTFC-CEMFOR, Solsona, Spain
| | - Josu G Alday
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-AGROTECNIO, Lleida, Spain
| | - Javier Parladé
- Protecció Vegetal Sostenible, IRTA, Centre de Cabrils, Barcelona, Spain
| | - Joan Pera
- Protecció Vegetal Sostenible, IRTA, Centre de Cabrils, Barcelona, Spain
| | - José Antonio Bonet
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-AGROTECNIO, Lleida, Spain
- Centre Tecnològic Forestal de Catalunya, CTFC-CEMFOR, Solsona, Spain
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25
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Chen SCA, Meyer W, Pashley CH. Challenges in Laboratory Detection of Fungal Pathogens in the Airways of Cystic Fibrosis Patients. Mycopathologia 2017; 183:89-100. [PMID: 28589247 DOI: 10.1007/s11046-017-0150-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 05/20/2017] [Indexed: 12/11/2022]
Abstract
Study of the clinical significance of fungal colonization/infection in the airways of cystic fibrosis (CF) patients, especially by filamentous fungi, is challenged by the absence of standardized methodology for the detection and identification of an ever-broadening range of fungal pathogens. Culture-based methods remain the cornerstone diagnostic approaches, but current methods used in many clinical laboratories are insensitive and unstandardized, rendering comparative studies unfeasible. Guidelines for standardized processing of respiratory specimens and for their culture are urgently needed and should include recommendations for specific processing procedures, inoculum density, culture media, incubation temperature and duration of culture. Molecular techniques to detect fungi directly from clinical specimens include panfungal PCR assays, multiplex or pathogen-directed assays, real-time PCR, isothermal methods and probe-based assays. In general, these are used to complement culture. Fungal identification by DNA sequencing methods is often required to identify cultured isolates, but matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is increasingly used as an alternative to DNA sequencing. Genotyping of isolates is undertaken to investigate relatedness between isolates, to pinpoint the infection source and to study the population structure. Methods range from PCR fingerprinting and amplified fragment length polymorphism analysis, to short tandem repeat typing, multilocus sequencing typing (MLST) and whole genome sequencing (WGS). MLST is the current preferred method, whilst WGS offers best case resolution but currently is understudied.
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Affiliation(s)
- Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, Westmead Hospital, 3rd Level ICPMR Building, Westmead, NSW, 2145, Australia.
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia.
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Catherine H Pashley
- Department of Infection, Immunity and Inflammation, Institute for Lung Health, University of Leicester, Leicester, LE1 9HN, UK
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26
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Ashtiani NM, Kachuei R, Yalfani R, Harchegani AB, Nosratabadi M. Identification of Aspergillus sections Flavi, Nigri, and Fumigati and their differentiation using specific primers. Infez Med 2017; 25:127-132. [PMID: 28603231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Aspergillus species are important in medicine, agriculture and various industries. The sections Fumigati, Flavi, and Nigri are the most important members of the Aspergillus genus. This study intended to identify and separate these three Aspergillus sections and to differentiate among them using specific primers. A bioinformatics study was initially performed to analyse the sequences of five genes, namely, beta-tubulin, calmodulin, the pre-rRNA processing protein Tsr1, the DNA-replication licensing factor Mcm7, and RNA polymerase II second largest subunit (RPB2) in the three Aspergillus sections using MEGA6 software and the NCBI database. Primers were designed to select genes for each of the Aspergillus sections being analysed. A total of 134 environmental and clinical Aspergillus species were isolated, purified and initially identified by colony morphology.. Subsequently, DNA was extracted using the phenol-chloroform method, specific primers were synthesized, PCR was performed for DNA from all isolates, and the results were compared to morphological characteristics. Of the 134 isolates tested, 56 were Nigri, 32 were Fumigati, 32 were Flavi, and the rest (14 isolates) belonged to other sections. The beta-tubulin and calmodulin genes were found to be the most suitable for differentiating among these three groups; the beta-tubulin gene was used for molecular identification of Aspergillus section Fumigati, and the calmodulin gene for identifying sections Flavi and Nigri.
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Affiliation(s)
- Nafiseh Mohebbi Ashtiani
- Department of Biology, School of Basic Science, Islamic Azad University-Pishva Varamin Branch, Tehran, Iran
| | - Reza Kachuei
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Roozbeh Yalfani
- Department of Nursery, Faculty of Nursery and Midwifery, Islamic Azad University-Pishva Varamin Branch, Tehran, Iran
| | - Asghar Beigi Harchegani
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohsen Nosratabadi
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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27
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Maeda Y, Dobashi H, Sugiyama Y, Saeki T, Lim TK, Harada M, Matsunaga T, Yoshino T, Tanaka T. Colony fingerprint for discrimination of microbial species based on lensless imaging of microcolonies. PLoS One 2017; 12:e0174723. [PMID: 28369067 PMCID: PMC5378366 DOI: 10.1371/journal.pone.0174723] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/14/2017] [Indexed: 11/18/2022] Open
Abstract
Detection and identification of microbial species are crucial in a wide range of industries, including production of beverages, foods, cosmetics, and pharmaceuticals. Traditionally, colony formation and its morphological analysis (e.g., size, shape, and color) with a naked eye have been employed for this purpose. However, such a conventional method is time consuming, labor intensive, and not very reproducible. To overcome these problems, we propose a novel method that detects microcolonies (diameter 10–500 μm) using a lensless imaging system. When comparing colony images of five microorganisms from different genera (Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa, Staphylococcus aureus, and Candida albicans), the images showed obvious different features. Being closely related species, St. aureus and St. epidermidis resembled each other, but the imaging analysis could extract substantial information (colony fingerprints) including the morphological and physiological features, and linear discriminant analysis of the colony fingerprints distinguished these two species with 100% of accuracy. Because this system may offer many advantages such as high-throughput testing, lower costs, more compact equipment, and ease of automation, it holds promise for microbial detection and identification in various academic and industrial areas.
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Affiliation(s)
- Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hironori Dobashi
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Yui Sugiyama
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Tatsuya Saeki
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | | | | | - Tadashi Matsunaga
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
- * E-mail:
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28
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Badotti F, de Oliveira FS, Garcia CF, Vaz ABM, Fonseca PLC, Nahum LA, Oliveira G, Góes-Neto A. Effectiveness of ITS and sub-regions as DNA barcode markers for the identification of Basidiomycota (Fungi). BMC Microbiol 2017; 17:42. [PMID: 28228107 PMCID: PMC5322588 DOI: 10.1186/s12866-017-0958-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/14/2017] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Fungi are among the most abundant and diverse organisms on Earth. However, a substantial amount of the species diversity, relationships, habitats, and life strategies of these microorganisms remain to be discovered and characterized. One important factor hindering progress is the difficulty in correctly identifying fungi. Morphological and molecular characteristics have been applied in such tasks. Later, DNA barcoding has emerged as a new method for the rapid and reliable identification of species. The nrITS region is considered the universal barcode of Fungi, and the ITS1 and ITS2 sub-regions have been applied as metabarcoding markers. In this study, we performed a large-scale analysis of all the available Basidiomycota sequences from GenBank. We carried out a rigorous trimming of the initial dataset based in methodological principals of DNA Barcoding. Two different approaches (PCI and barcode gap) were used to determine the performance of the complete ITS region and sub-regions. RESULTS For most of the Basidiomycota genera, the three genomic markers performed similarly, i.e., when one was considered a good marker for the identification of a genus, the others were also; the same results were observed when the performance was insufficient. However, based on barcode gap analyses, we identified genomic markers that had a superior identification performance than the others and genomic markers that were not indicated for the identification of some genera. Notably, neither the complete ITS nor the sub-regions were useful in identifying 11 of the 113 Basidiomycota genera. The complex phylogenetic relationships and the presence of cryptic species in some genera are possible explanations of this limitation and are discussed. CONCLUSIONS Knowledge regarding the efficiency and limitations of the barcode markers that are currently used for the identification of organisms is crucial because it benefits research in many areas. Our study provides information that may guide researchers in choosing the most suitable genomic markers for identifying Basidiomycota species.
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Affiliation(s)
- Fernanda Badotti
- Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Departamento de Química, 30.421-169 Belo Horizonte, MG Brazil
| | | | - Cleverson Fernando Garcia
- Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Departamento de Química, 30.421-169 Belo Horizonte, MG Brazil
| | - Aline Bruna Martins Vaz
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, Av. Antônio Carlos, Belo Horizonte, 6627, 31270-901 MG Brazil
- Faculdade de Minas (FAMINAS), 66055-090 Belo Horizonte, MG Brazil
| | - Paula Luize Camargos Fonseca
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, Av. Antônio Carlos, Belo Horizonte, 6627, 31270-901 MG Brazil
| | - Laila Alves Nahum
- Fundação Oswaldo Cruz (FIOCRUZ), Centro de Pesquisas René Rachou – CPqRR, 30190-002 Belo Horizonte, MG Brazil
- Faculdade Promove de Tecnologia, 30140-061 Belo Horizonte, MG Brazil
| | - Guilherme Oliveira
- Fundação Oswaldo Cruz (FIOCRUZ), Centro de Pesquisas René Rachou – CPqRR, 30190-002 Belo Horizonte, MG Brazil
- Instituto Tecnológico Vale, 66055-090 Belém, PA Brazil
| | - Aristóteles Góes-Neto
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, Av. Antônio Carlos, Belo Horizonte, 6627, 31270-901 MG Brazil
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Drumonde-Neves J, Franco-Duarte R, Lima T, Schuller D, Pais C. Association between Grape Yeast Communities and the Vineyard Ecosystems. PLoS One 2017; 12:e0169883. [PMID: 28085916 PMCID: PMC5234834 DOI: 10.1371/journal.pone.0169883] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/24/2016] [Indexed: 11/19/2022] Open
Abstract
The grape yeast biota from several wine-producing areas, with distinct soil types and grapevine training systems, was assessed on five islands of Azores Archipelago, and differences in yeast communities composition associated with the geographic origin of the grapes were explored. Fifty-seven grape samples belonging to the Vitis vinifera grapevine cultivars Verdelho dos Açores (Verdelho), Arinto da Terceira (Arinto) and Terrantez do Pico (Terrantez) were collected in two consecutive years and 40 spontaneous fermentations were achieved. A total of 1710 yeast isolates were obtained from freshly crushed grapes and 1200 from final stage of fermentations. Twenty-eight species were identified, Hanseniaspura uvarum, Pichia terricola and Metschnikowia pulcherrima being the three most representative species isolated. Candida carpophila was encountered for the first time as an inhabitant of grape or wine-associated environments. In both sampling years, a higher proportion of H. uvarum in fresh grapes from Verdelho cultivar was observed, in comparison with Arinto cultivar. Qualitatively significant differences were found among yeast communities from several locations on five islands of the Archipelago, particularly in locations with distinctive agro-ecological compositions. Our results are in agreement with the statement that grape-associated microbial biogeography is non-randomly associated with interactions of climate, soil, cultivar, and vine training systems in vineyard ecosystems. Our observations strongly support a possible linkage between grape yeast and wine typicality, reinforcing the statement that different viticultural terroirs harbor distinctive yeast biota, in particular in vineyards with very distinctive environmental conditions.
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Affiliation(s)
- João Drumonde-Neves
- CITAA—Research Center for Agricultural Technology of Azores, University of Azores, Angra do Heroísmo, Portugal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Ricardo Franco-Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Teresa Lima
- CITAA—Research Center for Agricultural Technology of Azores, University of Azores, Angra do Heroísmo, Portugal
| | - Dorit Schuller
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Célia Pais
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
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30
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Affiliation(s)
- Andrew M Borman
- Public Health England National Mycology Reference Laboratory, Bristol, UK
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31
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Wang G, Cao X, Ma X, Guo M, Liu C, Yan L, Bian Y. Diversity and effect of Trichoderma spp. associated with green mold disease on Lentinula edodes in China. Microbiologyopen 2016; 5:709-18. [PMID: 27147196 PMCID: PMC4985603 DOI: 10.1002/mbo3.364] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 03/10/2016] [Accepted: 03/21/2016] [Indexed: 11/23/2022] Open
Abstract
Lentinula edodes, one of the most important edible mushrooms in China, is affected heavily by the infection of green mold that overgrows mushroom mycelia. We collected the diseased samples from main L. edodes cultivation regions in China to characterize the pathogen and to study the effect of Trichoderma spp. on L. edodes species. We identified six Trichoderma species, that is, T. harzianum, T. atroviride, T. viride, T. pleuroticola, T. longibrachiatum, and T. oblongisporum based on the internal transcribed spacer or tef1-α sequences and morphology characteristics. In confrontation cultures on Petri plates or in tubes, and in L. edodes cultures in a medium containing Trichoderma metabolites, L. edodes mycelia were not only distorted and swollen, but also inhibited by Trichoderma isolates. It is not possible that adjusting pH value or temperature is used for controlling L. edodes green disease, because the growth of most of Trichoderma isolates and L. edodes shared similar pH and temperature conditions.
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Affiliation(s)
- Gangzheng Wang
- Institute of Applied MycologyHuazhong Agricultural UniversityNo. 1 Shizishan RdWuhanHubei430070China
- Key Laboratory of Agro‐Microbial Resource and DevelopmentMinistry of AgricultureWuhanChina
| | - Xiantao Cao
- Institute of Applied MycologyHuazhong Agricultural UniversityNo. 1 Shizishan RdWuhanHubei430070China
- Key Laboratory of Agro‐Microbial Resource and DevelopmentMinistry of AgricultureWuhanChina
| | - Xiaolong Ma
- Institute of Applied MycologyHuazhong Agricultural UniversityNo. 1 Shizishan RdWuhanHubei430070China
- Key Laboratory of Agro‐Microbial Resource and DevelopmentMinistry of AgricultureWuhanChina
| | - Mengpei Guo
- Institute of Applied MycologyHuazhong Agricultural UniversityNo. 1 Shizishan RdWuhanHubei430070China
- Key Laboratory of Agro‐Microbial Resource and DevelopmentMinistry of AgricultureWuhanChina
| | - Changhao Liu
- Institute of Applied MycologyHuazhong Agricultural UniversityNo. 1 Shizishan RdWuhanHubei430070China
- Key Laboratory of Agro‐Microbial Resource and DevelopmentMinistry of AgricultureWuhanChina
| | - Lianlian Yan
- Institute of Applied MycologyHuazhong Agricultural UniversityNo. 1 Shizishan RdWuhanHubei430070China
- Key Laboratory of Agro‐Microbial Resource and DevelopmentMinistry of AgricultureWuhanChina
| | - Yinbing Bian
- Institute of Applied MycologyHuazhong Agricultural UniversityNo. 1 Shizishan RdWuhanHubei430070China
- Key Laboratory of Agro‐Microbial Resource and DevelopmentMinistry of AgricultureWuhanChina
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32
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Stefaniuk E, Baraniak A, Fortuna M, Hryniewicz W. Usefulness of CHROMagar Candida Medium, Biochemical Methods--API ID32C and VITEK 2 Compact and Two MALDI-TOF MS Systems for Candida spp. Identification. Pol J Microbiol 2016; 65:111-4. [PMID: 27282002 DOI: 10.5604/17331331.1197283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study was conducted to compare of the yeasts identification results obtained with two new systems using the MALDI-TOF MS technique with the ones obtained using the routine identification methods of Candida spp. in clinical microbiology laboratories. All 124 Candida spp. isolates were recovered from the routine examination of clinical specimens in microbiological laboratories and collected in the Centre of Quality Control in Microbiology in Warsaw (Poland). Our findings confirm the high agreement (98%) of fungal identification using the standard, biochemistry laboratory methods and mass spectrometry technique.
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Dulla EL, Kathera C, Gurijala HK, Mallakuntla TR, Srinivasan P, Prasad V, Mopati RD, Jasti PK. Highlights of DNA Barcoding in identification of salient microorganisms like fungi. J Mycol Med 2016; 26:291-297. [PMID: 27402509 DOI: 10.1016/j.mycmed.2016.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/22/2016] [Accepted: 05/25/2016] [Indexed: 11/19/2022]
Abstract
Fungi, the second largest kingdom of eukaryotic life, are diverse and widespread. Fungi play a distinctive role in the production of different products on industrial scale, like fungal enzymes, antibiotics, fermented foods, etc., to give storage stability and improved health to meet major global challenges. To utilize algae perfectly for human needs, and to pave the way for getting a healthy relationship with fungi, it is important to identify them in a quick and robust manner with molecular-based identification system. So, there is a technique that aims to provide a well-organized method for species level identifications and to contribute powerfully to taxonomic and biodiversity research is DNA Barcoding. DNA Barcoding is generally achieved by the retrieval of a short DNA sequence - the 'barcode' - from a standard part of the genome and that barcode is then compared with a library of reference barcode sequences derived from individuals of known identity for identification.
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Affiliation(s)
- E L Dulla
- Department of Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - C Kathera
- Jiangsu key laboratory for Molecular and Medicak Biotechnology, College of life sciences, Nanjing normal university, Nanjing, China
| | - H K Gurijala
- Department of Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India; Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - T R Mallakuntla
- Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - P Srinivasan
- Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - V Prasad
- Jiangsu key laboratory for Molecular and Medicak Biotechnology, College of life sciences, Nanjing normal university, Nanjing, China
| | - R D Mopati
- Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - P K Jasti
- Department of Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India.
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Tra Bi CY, N'guessan FK, Kouakou CA, Jacques N, Casaregola S, Djè MK. Identification of yeasts isolated from raffia wine (Raphia hookeri) produced in Côte d'Ivoire and genotyping of Saccharomyces cerevisiae strains by PCR inter-delta. World J Microbiol Biotechnol 2016; 32:125. [PMID: 27339306 DOI: 10.1007/s11274-016-2095-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/05/2016] [Indexed: 11/27/2022]
Abstract
Raffia wine is a traditional alcoholic beverage produced in several African countries where it plays a significant role in traditional customs and population diet. Alcoholic fermentation of this beverage is ensured by a complex natural yeast flora which plays a decisive role in the quality of the final product. This present study aims to evaluate the distribution and the diversity of the yeast strains isolated in raffia wine from four sampling areas (Abengourou, Alépé, Grand-Lahou and Adzopé) in Côte d'Ivoire. Based on the D1/D2 domain of the LSU rDNA sequence analysis, nine species belonging to six genera were distinguished. With a percentage of 69.5 % out of 171 yeast isolates, Saccharomyces cerevisiae was the predominant species in the raffia wine, followed by Kodamaea ohmeri (20.4 %). The other species isolated were Candida haemulonii (4.1 %), Candida phangngensis (1.8 %), Pichia kudriavzevii (1.2 %), Hanseniaspora jakobsenii (1.2 %), Candida silvae (0.6 %), Hanseniaspora guilliermondii (0.6 %) and Meyerozyma caribbica (0.6 %). The molecular characterization of S. cerevisiae isolates at the strain level using the PCR-interdelta method revealed the presence of 21 profiles (named I to XXI) within 115 isolates. Only four profiles (I, III, V and XI) were shared by the four areas under study. Phenotypic characterization of K. ohmeri strains showed two subgroups for sugar fermentation and no diversity for the nitrogen compound assimilations and the growth at different temperatures.
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Affiliation(s)
- Charles Y Tra Bi
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, 02 BP 801, Abidjan, 02, Côte d'Ivoire.
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Florent K N'guessan
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, 02 BP 801, Abidjan, 02, Côte d'Ivoire
| | - Clémentine A Kouakou
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, 02 BP 801, Abidjan, 02, Côte d'Ivoire
| | - Noemie Jacques
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Serge Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Marcellin K Djè
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, 02 BP 801, Abidjan, 02, Côte d'Ivoire
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Hou X, Xiao M, Chen SCA, Wang H, Zhang L, Fan X, Xu ZP, Cheng JW, Kong F, Zhao YP, Xu YC. Sequencer-Based Capillary Gel Electrophoresis (SCGE) Targeting the rDNA Internal Transcribed Spacer (ITS) Regions for Accurate Identification of Clinically Important Yeast Species. PLoS One 2016; 11:e0154385. [PMID: 27105313 PMCID: PMC4841527 DOI: 10.1371/journal.pone.0154385] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/12/2016] [Indexed: 12/30/2022] Open
Abstract
Accurate species identification of Candida, Cryptococcus, Trichosporon and other yeast pathogens is important for clinical management. In the present study, we developed and evaluated a yeast species identification scheme by determining the rDNA internal transcribed spacer (ITS) region length types (LTs) using a sequencer-based capillary gel electrophoresis (SCGE) approach. A total of 156 yeast isolates encompassing 32 species were first used to establish a reference SCGE ITS LT database. Evaluation of the ITS LT database was then performed on (i) a separate set of (n = 97) clinical isolates by SCGE, and (ii) 41 isolates of 41 additional yeast species from GenBank by in silico analysis. Of 156 isolates used to build the reference database, 41 ITS LTs were identified, which correctly identified 29 of the 32 (90.6%) species, with the exception of Trichosporon asahii, Trichosporon japonicum and Trichosporon asteroides. In addition, eight of the 32 species revealed different electropherograms and were subtyped into 2–3 different ITS LTs each. Of the 97 test isolates used to evaluate the ITS LT scheme, 96 (99.0%) were correctly identified to species level, with the remaining isolate having a novel ITS LT. Of the additional 41 isolates for in silico analysis, none was misidentified by the ITS LT database except for Trichosporon mucoides whose ITS LT profile was identical to that of Trichosporon dermatis. In conclusion, yeast identification by the present SCGE ITS LT assay is a fast, reproducible and accurate alternative for the identification of clinically important yeasts with the exception of Trichosporon species.
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Affiliation(s)
- Xin Hou
- 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
| | - Meng Xiao
- 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
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR– Pathology West, Westmead Hospital, University of Sydney, Darcy Road, Westmead, New South Wales, Australia
| | - He Wang
- 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
| | - Li Zhang
- 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
| | - Xin Fan
- 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
| | - Zhi-Peng 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
| | - 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
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR– Pathology West, Westmead Hospital, University of Sydney, Darcy Road, Westmead, New South Wales, Australia
| | - Yu-Pei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- * E-mail:
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Katiyar S, Shiffrin E, Shelton C, Healey K, Vermitsky JP, Edlind T. Evaluation of Polymorphic Locus Sequence Typing for Candida glabrata Epidemiology. J Clin Microbiol 2016; 54:1042-50. [PMID: 26842706 PMCID: PMC4809956 DOI: 10.1128/jcm.03106-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/29/2016] [Indexed: 11/20/2022] Open
Abstract
The opportunistic yeast Candida glabratais increasingly refractory to antifungal treatment or prophylaxis and relatedly is increasingly implicated in health care-associated infections. To elucidate the epidemiology of these infections, strain typing is required. Sequence-based typing provides multiple advantages over length-based methods, such as pulsed-field gel electrophoresis (PFGE); however, conventional multilocus sequence typing (targeting 6 conserved loci) and whole-genome sequencing are impractical for routine use. A commercial sequence-based typing service for C. glabratathat targets polymorphic tandem repeat-containing loci has recently been developed. These CgMT-J and CgMT-M services were evaluated with 56 epidemiologically unrelated isolates, 4 to 7 fluconazole-susceptible or fluconazole-resistant isolates from each of 5 center A patients, 5 matched pairs of fluconazole-susceptible/resistant isolates from center B patients, and 7 isolates from a center C patient who responded to then failed caspofungin therapy. CgMT-J and CgMT-M generated congruent results, resolving isolates into 24 and 20 alleles, respectively. Isolates from all but one of the center A patients shared the same otherwise rare alleles, suggesting nosocomial transmission. Unexpectedly, Pdr1 sequencing showed that resistance arose independently in each patient. Similarly, most isolates from center B also clustered together; however, this may reflect a dominant clone since their alleles were shared by multiple unrelated isolates. Although distinguishable by their echinocandin susceptibilities, all isolates from the center C patient shared alleles, in agreement with the previously reported relatedness of these isolates based on PFGE. Finally, we show how phylogenetic clusters can be used to provide surrogate parents to analyze the mutational basis for antifungal resistance.
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Affiliation(s)
- Santosh Katiyar
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Eric Shiffrin
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Celeste Shelton
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Kelley Healey
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - John-Paul Vermitsky
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Tom Edlind
- MicrobiType LLC, Plymouth Meeting, Pennsylvania, USA
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Canfora L, Malusà E, Tkaczuk C, Tartanus M, Łabanowska B, Pinzari F. Development of a method for detection and quantification of B. brongniartii and B. bassiana in soil. Sci Rep 2016; 6:22933. [PMID: 26975931 PMCID: PMC4791642 DOI: 10.1038/srep22933] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/25/2016] [Indexed: 11/30/2022] Open
Abstract
A culture independent method based on qPCR was developed for the detection and quantification of two fungal inoculants in soil. The aim was to adapt a genotyping approach based on SSR (Simple Sequence Repeat) marker to a discriminating tracing of two different species of bioinoculants in soil, after their in-field release. Two entomopathogenic fungi, Beauveria bassiana and B. brongniartii, were traced and quantified in soil samples obtained from field trials. These two fungal species were used as biological agents in Poland to control Melolontha melolontha (European cockchafer), whose larvae live in soil menacing horticultural crops. Specificity of SSR markers was verified using controls consisting of: i) soil samples containing fungal spores of B. bassiana and B. brongniartii in known dilutions; ii) the DNA of the fungal microorganisms; iii) soil samples singly inoculated with each fungus species. An initial evaluation of the protocol was performed with analyses of soil DNA and mycelial DNA. Further, the simultaneous detection and quantification of B. bassiana and B. brongniartii in soil was achieved in field samples after application of the bio-inoculants. The protocol can be considered as a relatively low cost solution for the detection, identification and traceability of fungal bio-inoculants in soil.
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Affiliation(s)
- L. Canfora
- Council for Agricultural Research and Economics - Research Centre for the Soil-Plant System, Via della Navicella 2-4, 00184 Rome, Italy
| | - E. Malusà
- Council for Agricultural Research and Economics - Research Centre for the Soil-Plant System, Via della Navicella 2-4, 00184 Rome, Italy
- Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - C. Tkaczuk
- Department of Plant Protection and Breeding, Siedlce University of Natural Sciences and Humanities, Prusa 14 Street, 08-110 Siedlce, Poland
| | - M. Tartanus
- Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - B.H. Łabanowska
- Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - F. Pinzari
- Council for Agricultural Research and Economics - Research Centre for the Soil-Plant System, Via della Navicella 2-4, 00184 Rome, Italy
- Life Science Department, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
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Libert X, Chasseur C, Packeu A, Bureau F, Roosens NH, De Keersmaecker SJC. A molecular approach for the rapid, selective and sensitive detection of Exophiala jeanselmei in environmental samples: development and performance assessment of a real-time PCR assay. Appl Microbiol Biotechnol 2016; 100:1377-1392. [PMID: 26615400 PMCID: PMC4717172 DOI: 10.1007/s00253-015-7175-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/09/2015] [Accepted: 11/11/2015] [Indexed: 11/04/2022]
Abstract
Exophiala jeanselmei is an opportunistic pathogenic black yeast growing in humid environments such as water reservoirs of air-conditioning systems. Because this fungal contaminant could be vaporized into the air and subsequently cause health problems, its monitoring is recommended. Currently, this monitoring is based on culture and microscopic identification which are complex, sometimes ambiguous and time-demanding, i.e., up to 21 days. Therefore, molecular, culture-independent methods could be more advantageous for the monitoring of E. jeanselmei. In this study, we developed a SYBR®green real-time PCR assay based on the internal transcribed spacer 2 from the 18S ribosomal DNA complex for the specific detection of E. jeanselmei. The selectivity (100 %), PCR efficiency (95.5 %), dynamic range and repeatability of this qPCR assay were subsequently evaluated. The limit of detection for this qPCR assay was determined to be 1 copy of genomic DNA of E. jeanselmei. Finally, water samples collected from cooling reservoirs were analyzed using this qPCR assay to deliver a proof of concept for the molecular detection of E. jeanselmei in environmental samples. The results obtained by molecular analysis were compared with those of classical methods (i.e., culture and microscopic identification) used in routine analysis and were 100 % matching. This comparison demonstrated that this SYBR®green qPCR assay can be used as a molecular alternative for monitoring and routine investigation of samples contaminated by E. jeanselmei, while eliminating the need for culturing and thereby considerably decreasing the required analysis time to 2 days.
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Affiliation(s)
- X Libert
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050, Brussels, Belgium
- Cellular and Molecular Immunology, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA), Université de Liège (ULg), Liège, Wallonia, Belgium
| | - C Chasseur
- Health and Environment, Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - A Packeu
- Mycology and Aerobiology, Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - F Bureau
- Cellular and Molecular Immunology, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA), Université de Liège (ULg), Liège, Wallonia, Belgium
| | - N H Roosens
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - S J C De Keersmaecker
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050, Brussels, Belgium.
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Ergin Ç, Gök Y, Bayğu Y, Gümral R, Özhak-Baysan B, Döğen A, Öğünç D, Ilkit M, Seyedmousavi S. ATR-FTIR Spectroscopy Highlights the Problem of Distinguishing Between Exophiala dermatitidis and E. phaeomuriformis Using MALDI-TOF MS. Microb Ecol 2016; 71:339-346. [PMID: 26373644 DOI: 10.1007/s00248-015-0670-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/28/2015] [Indexed: 06/05/2023]
Abstract
The present study compared two chemical-based methods, namely, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, to understand the misidentification of Exophiala dermatitidis and Exophiala phaeomuriformis. The study utilized 44 E. dermatitidis and 26 E. phaeomuriformis strains, which were partially treated with strong acids and bases for further evaluation. MALDI-TOF MS and ATR-FTIR spectroscopy data of the two Exophiala species were compared. Data groupings were observed for the chromic acid- and nitric acid-treated species when the black yeast sources were categorized as creosoted-oak sleepers, concrete sleepers, or dishwasher isolates. The MALDI-TOF MS data for the metalloenzyme-containing regions were consistent with the ATR-FTIR spectroscopy data. These results indicated that environmental isolates might contain metals not found in human isolates and might interfere with chemical-based identification methods. Therefore, MALDI-TOF MS reference libraries should be created for clinical strains and should exclude petroleum-associated environmental isolates.
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Affiliation(s)
- Çağrı Ergin
- Department of Microbiology, Faculty of Medicine, Pamukkale University, Denizli, Turkey.
| | - Yaşar Gök
- Chemistry Department, Faculty of Science and Arts, Pamukkale University, Denizli, Turkey
| | - Yasemin Bayğu
- Chemistry Department, Faculty of Science and Arts, Pamukkale University, Denizli, Turkey
| | - Ramazan Gümral
- Department of Microbiology, Gülhane Military Medical Academy, Ankara, Turkey
| | - Betil Özhak-Baysan
- Department of Microbiology, Faculty of Medicine, University of Akdeniz, Antalya, Turkey
| | - Aylin Döğen
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Mersin, Mersin, Turkey
| | - Dilara Öğünç
- Department of Microbiology, Faculty of Medicine, University of Akdeniz, Antalya, Turkey
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - Seyedmojtaba Seyedmousavi
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
- Invasive Fungi Research Center, Mazandaran University Medical Center, Sari, Iran
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Sariguzel FM, Berk E, Koc AN, Sav H, Aydemir G. Evaluation of chromogenic agar, [corrected] VITEK2 YST and VITEK® MS for identification of Candida strains isolated from blood cultures. Infez Med 2015; 23:318-322. [PMID: 26700081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The aim of this study is to compare conventional methods, chromogenic agar, [corrected] VITEK2 YST card and VITEK®MS system for the identification of Candida strains isolated from blood cultures. Fifty-four strains were identified according to conventional methods, chromogenic agar, [corrected] VITEK2 YST card and VITEK®MS. Sequencing was used as the reference method. The 54 strains included 32 Candida parapsilosis, 19 Candida albicans, 1 Candida glabrata and 2 Candida tropicalis according to the reference method. One C. albicans and one C. glabrata isolate were misidentified as C. parapsilosis by chromogenic agar. [corrected]. Two C. parapsilosis and three C. albicans isolates were misidentified by VITEK2 YST card. Chromogenic agar, [corrected] VITEK2 YST card and VITEK®MS identified correctly 96.2%, 90.7% and 100% of all strains, respectively. We found that the chromogenic agar, [corrected] VITEK2 YST card and VITEK®MS system are easy, rapid and accurate alternative methods for the identification of yeast species in the clinical microbiology laboratory.
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Affiliation(s)
- Fatma Mutlu Sariguzel
- Department of Microbiology, Kayseri Education and Research Hospital, Kayseri, Turkey
| | - Elife Berk
- Department of Microbiology, Erciyes University Medical School, Kayseri, Turkey
| | - Ayse Nedret Koc
- Department of Microbiology, Erciyes University Medical School, Kayseri, Turkey
| | - Hafize Sav
- Department of Microbiology, Erciyes University Medical School, Kayseri, Turkey
| | - Gonca Aydemir
- Department of Microbiology, Erciyes University Medical School, Kayseri, Turkey
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Affiliation(s)
- Marçal Mariné
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Neil Andrew Brown
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | | | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol—CTBE, Campinas, São Paulo, Brazil
- * E-mail:
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Stewart JE, Brooks K, Brannen PM, Cline WO, Brewer MT. Elevated Genetic Diversity in the Emerging Blueberry Pathogen Exobasidium maculosum. PLoS One 2015; 10:e0132545. [PMID: 26207812 PMCID: PMC4514876 DOI: 10.1371/journal.pone.0132545] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 06/17/2015] [Indexed: 01/26/2023] Open
Abstract
Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus Exobasidium maculosum, is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA, severely reducing fruit quality in some plantings. The objectives of this study were to determine the genetic diversity of E. maculosum in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of E. maculosum are structured by geography, host species, or tissue type. We sequenced three conserved loci from 82 isolates collected from leaves and fruit of rabbiteye blueberry (Vaccinium virgatum), highbush blueberry (V. corymbosum), and southern highbush blueberry (V. corymbosum hybrids) from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry (V. angustifolium) from Maine, USA, and Nova Scotia, Canada. Populations of E. maculosum from the southeastern USA and from lowbush blueberry in Maine and Nova Scotia are distinct, but do not represent unique species. No difference in genetic structure was detected between different host tissues or among different host species within the southeastern USA; however, differentiation was detected between populations in Georgia and North Carolina. Overall, E. maculosum showed extreme genetic diversity within the conserved loci with 286 segregating sites among the 1,775 sequenced nucleotides and each isolate representing a unique multilocus haplotype. However, 94% of the nucleotide substitutions were silent, so despite the high number of mutations, selective constraints have limited changes to the amino acid sequences of the housekeeping genes. Overall, these results suggest that the emergence of Exobasidium leaf and fruit spot is not due to a recent introduction or host shift, or the recent evolution of aggressive genotypes of E. maculosum, but more likely as a result of an increasing host population or an environmental change.
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Affiliation(s)
- Jane E. Stewart
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Kyle Brooks
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Phillip M. Brannen
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
| | - William O. Cline
- Department of Plant Pathology, North Carolina State University, Horticultural Crops Research Station, Castle Hayne, North Carolina, United States of America
| | - Marin T. Brewer
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
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Liu L, Yuan Y, Zhang J, Lei H, Wang Q, Liu J, Du X, Ni G, Liu Y. Automatic identification of fungi under complex microscopic fecal images. J Biomed Opt 2015; 20:76004. [PMID: 26169791 DOI: 10.1117/1.jbo.20.7.076004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/12/2015] [Indexed: 05/13/2023]
Abstract
Automatic identification of fungi in microscopic fecal images provides important information for evaluating digestive diseases. To date, disease diagnosis is primarily performed by manual techniques. However, the accuracy of this approach depends on the operator's expertise and subjective factors. The proposed system automatically identifies fungi in microscopic fecal images that contain other cells and impurities under complex environments. We segment images twice to obtain the correct area of interest, and select ten features, including the circle number, concavity point, and other basic features, to filter fungi. An artificial neural network (ANN) system is used to identify the fungi. The first stage (ANN-1) processes features from five images in differing focal lengths; the second stage (ANN-2) identifies the fungi using the ANN-1 output values. Images in differing focal lengths can be used to improve the identification result. The system output accurately detects the image, whether or not it has fungi. If the image does have fungi, the system output counts the number of different fungi types.
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Terrell E, Cliff MA, Van Vuuren HJJ. Functional characterization of individual- and mixed-Burgundian Saccharomyces cerevisiae isolates for fermentation of Pinot noir. Molecules 2015; 20:5112-36. [PMID: 25808154 PMCID: PMC6272465 DOI: 10.3390/molecules20035112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 02/25/2015] [Accepted: 03/09/2015] [Indexed: 12/04/2022] Open
Abstract
Pinot noir has traditionally been fermented by native flora of multiple yeasts producing a complex combination of aromas and flavors. With the use of industrial dry yeasts, winemakers gained enological reliability and consistency in their wines, but lost diversity and complexity. This research evaluated the use of co-culturing yeasts to fulfill this dual role. Fermentations of Burgundian Saccharomyces cerevisiae isolates and their mixtures were evaluated for their enological characteristics and production of volatile compounds, at 22 °C and 27 °C. The novel isolates were genetically unique and enologically equivalent to the industrial strains. Analysis of variance and principal component analysis of 25 headspace volatiles revealed differences among the yeasts and between the fermentation temperatures. Wines from the mixed-Burgundian isolates were most similar to one another and could be differentiated from the industrial strains at both 22 °C and 27 °C. Mixed-Burgundian wines at both temperatures had higher concentrations of ethyl esters and acetate esters, compared to the industrial strains which had higher concentrations of higher alcohols at 27 °C and higher concentration of other ethyl esters at 22 °C. Given the unique profiles of the co-cultured wines, this research offers winemakers a strategy for producing wines with unique and more complex characters without the risk of spontaneous fermentations.
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Affiliation(s)
- Emily Terrell
- Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Margaret A Cliff
- Pacific Agri-Food Research Centre, Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada.
| | - Hennie J J Van Vuuren
- Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Oumeraci T, Jensen V, Talbot SR, Hofmann W, Kostrzewa M, Schlegelberger B, von Neuhoff N, Häussler S. Comprehensive MALDI-TOF biotyping of the non-redundant Harvard Pseudomonas aeruginosa PA14 transposon insertion mutant library. PLoS One 2015; 10:e0117144. [PMID: 25665154 PMCID: PMC4321832 DOI: 10.1371/journal.pone.0117144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 12/19/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is a gram-negative bacterium that is ubiquitously present in the aerobic biosphere. As an antibiotic-resistant facultative pathogen, it is a major cause of hospital-acquired infections. Its rapid and accurate identification is crucial in clinical and therapeutic environments. METHODS In a large-scale MALDI-TOF mass spectrometry-based screen of the Harvard transposon insertion mutant library of P. aeruginosa strain PA14, intact-cell proteome profile spectra of 5547 PA14 transposon mutants exhibiting a plethora of different phenotypes were acquired and analyzed. RESULTS Of all P. aeruginosa PA14 mutant profiles 99.7% were correctly identified as P. aeruginosa with the Biotyper software on the species level. On the strain level, 99.99% of the profiles were mapped to five different individual P. aeruginosa Biotyper database entries. A principal component analysis-based approach was used to determine the most important discriminatory mass features between these Biotyper groups. Although technical replicas were consistently categorized to specific Biotyper groups in 94.2% of the mutant profiles, biological replicas were not, indicating that the distinct proteotypes are affected by growth conditions. CONCLUSIONS The PA14 mutant profile collection presented here constitutes the largest coherent P. aeruginosa MALDI-TOF spectral dataset publicly available today. Transposon insertions in thousands of different P. aeruginosa genes did not affect species identification from MALDI-TOF mass spectra, clearly demonstrating the robustness of the approach. However, the assignment of the individual spectra to sub-groups proved to be non-consistent in biological replicas, indicating that the differentiation between biotyper groups in this nosocomial pathogen is unassured.
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Affiliation(s)
- Tonio Oumeraci
- Institute of Cell and Molecular Pathology, Hannover Medical School (MHH), Hannover, Germany
| | - Vanessa Jensen
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany
- Institute of Molecular Bacteriology, Twincore, Center for Experimental and Clinical Infection Research, A joint venture of the Helmholtz Center for Infection Research Braunschweig and the MHH, Hannover, Germany
| | - Steven R. Talbot
- Institute of Molecular and Cell Physiology, MHH, Hannover, Germany
| | - Winfried Hofmann
- Institute of Cell and Molecular Pathology, Hannover Medical School (MHH), Hannover, Germany
| | | | | | - Nils von Neuhoff
- Institute of Cell and Molecular Pathology, Hannover Medical School (MHH), Hannover, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany
- Institute of Molecular Bacteriology, Twincore, Center for Experimental and Clinical Infection Research, A joint venture of the Helmholtz Center for Infection Research Braunschweig and the MHH, Hannover, Germany
- * E-mail:
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Didehdar M, Gokanian A, Sofian M, Mohammadi S, Mohammadi R, Aslani N, Haghani I, Badali H. First fatal cerebral phaeohyphomycosis due to Rhinocladiella mackenziei in Iran, based on ITS rDNA. J Mycol Med 2015; 25:81-6. [PMID: 25637429 DOI: 10.1016/j.mycmed.2014.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 11/05/2014] [Accepted: 11/19/2014] [Indexed: 11/30/2022]
Abstract
Black yeast-like fungi and relatives as agents of cerebral phaeohyphomycosis are often encountered in human fatal brain abscesses and lead to almost 100% mortality despite the application of antifungal and surgical therapy. We report to our knowledge the first case of brain infection due to Rhinocladiella mackenziei in a 54-year-old immunocompetent male in Iran where R. mackenziei has not been reported previously. The initial diagnosis was brain fungal infection because of pigmented, irregular, branched, septated hyphae based on histopathological staining. The patient was treated with intravenous amphotericin B deoxycholate (0.5mg/kg/day) combined with oral itraconazole (200mg twice daily), nevertheless, his neurological function deteriorated rapidly and ultimately the patient died due to respiratory failure later two weeks. R. mackenziei was identified based on the sequencing of internal transcribed spacer (ITS rDNA region) (KJ140287). Therefore, considerable attention for this life-threatening infection is highly recommended.
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Affiliation(s)
- M Didehdar
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran; Department of Medical Mycology and Parasitology, Arak University of Medical Sciences, Arak, Iran
| | - A Gokanian
- Department of Surgery and cerebral, Arak University of Medical Sciences, Arak, Iran
| | - M Sofian
- Tuberculosis and pediatric infectious Research Center, Arak University of Medical Sciences, Arak, Iran
| | - S Mohammadi
- Laboratory of Valiaasr Hospital, Arak University of Medical Sciences, Arak, Iran
| | - R Mohammadi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - N Aslani
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
| | - I Haghani
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
| | - H Badali
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran.
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Ferrara G, Mercedes Panizol M, Mazzone M, Delia Pequeneze M, Reviakina V. [A comparative study between the Vitek YBC and Microscan Walk Away RYID automated systems with conventional phenotypic methods for the identification of yeasts of clinical interest]. Invest Clin 2014; 55:297-310. [PMID: 25558750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The aim of this study was to compare the identification of clin- ically relevant yeasts by the Vitek YBC and Microscan Walk Away RYID automated methods with conventional phenotypic methods. One hundred and ninety three yeast strains isolated from clinical samples and five controls strains were used. All the yeasts were identified by the automated methods previously mentioned and conventional phenotypic methods such as carbohydrate assimilation, visualization of microscopic morphology on corn meal agar and the use of chromogenic agar. Variables were assessed by 2 x 2 contingency tables, McNemar's Chi square, the Kappa index, and concordance values were calculated, as well as major and minor errors for the automated methods. Yeasts were divided into two groups: (1) frequent isolation and (2) rare isolation. The Vitek YBC and Microscan Walk Away RYID systems were concordant in 88.4 and 85.9% respectively, when compared to conventional phenotypic methods. Although both automated systems can be used for yeasts identification, the presence of major and minor errors indicates the possibility of misidentifications; therefore, the operator of this equipment must use in parallel, phenotypic tests such as visualization of microscopic morphology on corn meal agar and chromogenic agar, especially against infrequently isolated yeasts. Automated systems are a valuable tool; however, the expertise and judgment of the microbiologist are an important strength to ensure the quality of the results.
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Affiliation(s)
- Giuseppe Ferrara
- Departamento de MicologiáInstituto Nacional de Higíene Rafael Rangel, Caracas, Venezuela
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48
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Helmel M, Marchetti-Deschmann M, Allmaier G. Improved sample preparation for intact cell mass spectrometry (biotyping) of mycelium samples taken from a batch fermentation process of Penicillium chrysogenum. Rapid Commun Mass Spectrom 2014; 28:957-964. [PMID: 24623701 DOI: 10.1002/rcm.6849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 01/21/2014] [Accepted: 01/21/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE Penicillium chrysogenum is an important species in biotechnology and an improved production rate for penicillin drug variants is of utmost interest. Intact cell mass spectrometry (ICMS) or biotyping can be a novel and time-saving tool to monitor a fermentation process of Penicillium strains for fast intervention during penicillin production. METHODS Fermentation broth was collected directly from a fermenter at specific time points known to show significantly different penicillin production rates. The mycelium was purified by washing multiple times with water and recovered by centrifugation. The mycelium was further mixed with matrix-assisted laser desorption/ionization (MALDI) MS matrix and immediately spotted on different types of targets. ICMS spectra were obtained by MALDI time-of-flight (TOF) MS in the positive ion linear mode in the m/z range 3000 to 16 000. RESULTS An ICMS method for culture broth samples of P. chrysogenum was developed. It was shown that ferulic acid mixed with sinapinic acid (2.5 mg and 22.5 mg/mL) is the most appropriate matrix combination. The matrices were dissolved in acetonitrile/0.1% trifluoroacetic acid (70/30, v/v) and spotted together with the sample on various target types. Sample preparation was thoroughly studied for homogeneity and reproducibility. CONCLUSIONS Culture broth directly collected from a bioreactor could be analyzed applying the optimized approach. The ideal choice of matrix, the adequate preparation technique and the type of target were the focus of this work showing that samples collected at different times during fermentation exhibit a characteristic pattern using the developed method.
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Affiliation(s)
- Michaela Helmel
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164, A-1060, Vienna, Austria
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49
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Gallardo G, Ruiz-Moyano S, Hernández A, Benito MJ, Córdoba MG, Pérez-Nevado F, Martín A. Application of ISSR-PCR for rapid strain typing of Debaryomyces hansenii isolated from dry-cured Iberian ham. Food Microbiol 2014; 42:205-11. [PMID: 24929738 DOI: 10.1016/j.fm.2014.03.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/14/2014] [Accepted: 03/17/2014] [Indexed: 11/17/2022]
Abstract
Yeast populations of dry-cured Iberian ham isolated from seven industries in the province of Badajoz were characterized by ISSR-PCR using the (CAG)4 primer and PCR-RFLP of the ITS1-5.8S rRNA-ITS2 fragment, and identified by DNA sequencing. A total of 242 isolates were analyzed, indicating the primary species present was Debaryomyces hansenii at 80.9% of the isolates followed by Candida zeylanoides at 10.3% of the isolates. The remainders of isolates were identified as Yamadazyma triangularis, Sporobolomyces roseus, Meyerozyma guilliermondii, Rhodotorula slooffiae, and Cryptococcus victoriae. The ISSR-PCR method was a fast and reliable method which was able to discriminate species at a level comparable to restriction analyses of the ITS1-5.8S rRNA-ITS2 region. This method allowed for strain typing of D. hansenii, yielding 29 different PCR patterns within 196 isolates. Moreover, ISSR-PCR using the (CAG)4 primer indicated that this technique could be a promising tool for rapid discrimination of yeast starter cultures and spoilage species in dry-cured Iberian ham.
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Affiliation(s)
- G Gallardo
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Av. Adolfo Suarez, 06007 Badajoz, Spain
| | - S Ruiz-Moyano
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Av. Adolfo Suarez, 06007 Badajoz, Spain
| | - A Hernández
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Av. Adolfo Suarez, 06007 Badajoz, Spain.
| | - M J Benito
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Av. Adolfo Suarez, 06007 Badajoz, Spain
| | - M G Córdoba
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Av. Adolfo Suarez, 06007 Badajoz, Spain
| | - F Pérez-Nevado
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Av. Adolfo Suarez, 06007 Badajoz, Spain
| | - A Martín
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Av. Adolfo Suarez, 06007 Badajoz, Spain
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50
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Katiraee F, Khalaj V, Khosravi AR, Hajiabdolbaghi M. Sequences type analysis of Candida albicans isolates from Iranian human immunodeficiency virus infected patients with oral candidiasis. Acta Med Iran 2014; 52:187-191. [PMID: 24901719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Accepted: 04/30/2013] [Indexed: 06/03/2023] Open
Abstract
The growing number of immunocompromised individuals has increased the incidence of infections caused by Candida species during the recent decades. Typing of C. albicans on the basis of DNA sequences at multiple loci has greatly advanced our knowledge about the epidemiology and phylogeny of candidiasis. The aim of this study was to evaluate the diversity, and genetic relationships among C. albicans isolates obtained from HIV patients in Iran. using multilocus sequence typing (MLST) method. We analyzed 25 C. albicans isolates obtained from HIV positive patients referred to Iranian Research Center for HIV/AIDS. After diagnostic test and DNA extraction C. albicans isolates were typed using the original MLST scheme explained previously include of six loci: ACC1, VPS13, GLN4, ADP1, RPN2, and SYA1. Fifty one (2.17%) nucleotide sites were found to be polymorphic; all were found to be heterozygous in at least one isolate. For the 25 clinical isolates, 22 diploid sequence types were defined by the genotypes identified from the six loci. The MLST data suggest a relatively high level of divergence in the population structure of C. albicans isolated from HIV infected patients. These findings indicate that in these patients there is a favorable context for the growth of potential pathogenic C. albicans. We found no association between fluconazole resistance, highly active antiretroviral therapy (HAART) receiving and either sequence type or group.
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Affiliation(s)
- Farzad Katiraee
- Department of Pathobiology, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran.
| | - Vahid Khalaj
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Ali Reza Khosravi
- Department of Mycology, Mycology Research Center, University of Tehran, Tehran, Iran.
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