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Almeida-Paes R, Teixeira MDM, Oliveira FAD, Almeida MDA, Almeida-Silva F, Geraldo KM, Nunes EP, Baker BM, Stajich JE, Grinsztejn B, Veloso VG, Freitas AD, Zancopé-Oliveira RM. A Cluster of Diutina catenulata Funguria in Patients with Coronavirus Disease 2019 (COVID-19) Hospitalized in a Tertiary Reference Hospital from Rio de Janeiro, Brazil. Curr Microbiol 2024; 81:338. [PMID: 39223407 DOI: 10.1007/s00284-024-03854-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 08/17/2024] [Indexed: 09/04/2024]
Abstract
During the COVID-19 pandemic, fungal infections, especially pulmonary aspergillosis, mucormycosis, and invasive candidiasis, have emerged as a significant health concern. Beyond Candida albicans, the most common cause of invasive candidiasis, other rare ascomycetous yeast species have been described in tertiary care units, potentially posing a broader health threat. We have isolated, from September 2020 to June 2021, nine Diutina catenulata strains from urine samples of six patients. This was intriguing as this fungus had not been previously identified in our institution, nor after June 2021. Therefore, we decided to outline the clinical features of the patients with this rare pathogen, to describe phenotypic characteristics, including antifungal susceptibility profiles, of this yeast species and to identify the genetic makeup through whole-genome sequencing analysis to evaluate if this was a cluster of genetically similar D. catenulata isolates in our institution. The strains were identified through MALDI-TOF MS analyses and Sanger sequencing of two rDNA regions. All patients yielding D. catenulata from urine samples needed ventilator support and used urinary catheters during hospitalization for treatment of COVID-19. None of them had received COVID-19 vaccines. Morphological and biochemical profiles of the nine strains were largely consistent, although fluconazole susceptibility varied, ranging from 4 to 32 μg/mL. Phylogenomic analysis revealed minimal genetic variation among the isolates, with low intrapopulation variation, supported by the identification of only 84 SNPs across all strains. Therefore, we propose that the yeast strains isolated were part of a cluster of D. catenulata funguria in the context of COVID-19.
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Affiliation(s)
- Rodrigo Almeida-Paes
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Fiocruz, Av. Brazil 4365 - Manguinhos, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Marcus de Melo Teixeira
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
- Faculdade de Medicina, Universidade de Brasília, Brasília, DF, Brazil
| | - Fernanda Alves de Oliveira
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Fiocruz, Av. Brazil 4365 - Manguinhos, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Marcos de Abreu Almeida
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Fiocruz, Av. Brazil 4365 - Manguinhos, Rio de Janeiro, RJ, 21045-900, Brazil
- Laboratório de Bioquímica e Imunologia das Micoses, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Fernando Almeida-Silva
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Fiocruz, Av. Brazil 4365 - Manguinhos, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Kim Mattos Geraldo
- Laboratório de Pesquisa Clínica em IST e Aids, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Estevão Portela Nunes
- Laboratório de Pesquisa Clínica em IST e Aids, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Bridget M Baker
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA, USA
| | - Beatriz Grinsztejn
- Laboratório de Pesquisa Clínica em IST e Aids, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Valdilea Gonçalves Veloso
- Laboratório de Pesquisa Clínica em IST e Aids, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Andrea d'Avila Freitas
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Fiocruz, Av. Brazil 4365 - Manguinhos, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Rosely Maria Zancopé-Oliveira
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Fiocruz, Av. Brazil 4365 - Manguinhos, Rio de Janeiro, RJ, 21045-900, Brazil.
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Platt AP, Bradley BT, Nasir N, Stein SR, Ramelli SC, Ramos-Benitez MJ, Dickey JM, Purcell M, Singireddy S, Hays N, Wu J, Raja K, Curto R, Salipante SJ, Chisholm C, Carnes S, Marshall DA, Cookson BT, Vannella KM, Madathil RJ, Soherwardi S, McCurdy MT, Saharia KK, Rabin J, Nih Covid-Autopsy Consortium, Grazioli A, Kleiner DE, Hewitt SM, Lieberman JA, Chertow DS. Pulmonary Co-Infections Detected Premortem Underestimate Postmortem Findings in a COVID-19 Autopsy Case Series. Pathogens 2023; 12:932. [PMID: 37513779 PMCID: PMC10383307 DOI: 10.3390/pathogens12070932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Bacterial and fungal co-infections are reported complications of coronavirus disease 2019 (COVID-19) in critically ill patients but may go unrecognized premortem due to diagnostic limitations. We compared the premortem with the postmortem detection of pulmonary co-infections in 55 fatal COVID-19 cases from March 2020 to March 2021. The concordance in the premortem versus the postmortem diagnoses and the pathogen identification were evaluated. Premortem pulmonary co-infections were extracted from medical charts while applying standard diagnostic definitions. Postmortem co-infection was defined by compatible lung histopathology with or without the detection of an organism in tissue by bacterial or fungal staining, or polymerase chain reaction (PCR) with broad-range bacterial and fungal primers. Pulmonary co-infection was detected premortem in significantly fewer cases (15/55, 27%) than were detected postmortem (36/55, 65%; p < 0.0001). Among cases in which co-infection was detected postmortem by histopathology, an organism was identified in 27/36 (75%) of cases. Pseudomonas, Enterobacterales, and Staphylococcus aureus were the most frequently identified bacteria both premortem and postmortem. Invasive pulmonary fungal infection was detected in five cases postmortem, but in no cases premortem. According to the univariate analyses, the patients with undiagnosed pulmonary co-infection had significantly shorter hospital (p = 0.0012) and intensive care unit (p = 0.0006) stays and significantly fewer extra-pulmonary infections (p = 0.0021). Bacterial and fungal pulmonary co-infection are under-recognized complications in critically ill patients with COVID-19.
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Affiliation(s)
- Andrew P Platt
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Benjamin T Bradley
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Nadia Nasir
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sydney R Stein
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Sabrina C Ramelli
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marcos J Ramos-Benitez
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
- Department of Basic Sciences, Division of Microbiology, Ponce Research Institute, School of Medicine, Ponce Health Sciences University, Ponce, PR 00716, USA
| | - James M Dickey
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | | | | | - Nicole Hays
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jocelyn Wu
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Katherine Raja
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ryan Curto
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Claire Chisholm
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA 98195, USA
| | | | - Desiree A Marshall
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Brad T Cookson
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Kevin M Vannella
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Ronson J Madathil
- Department of Surgery, Division of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | - Michael T McCurdy
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland St. Joseph Medical Center, Towson, MD 21204, USA
| | - Kapil K Saharia
- Institute of Human Virology, Division of Infectious Diseases, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Joseph Rabin
- R Adams Cowley Shock Trauma Center, Department of Surgery and Program in Trauma, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | - Alison Grazioli
- R Adams Cowley Shock Trauma Center, Department of Medicine and Program in Trauma, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - David E Kleiner
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joshua A Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Daniel S Chertow
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
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Liu C, Yao X, Liu C, You S, Qi W, Wang M. Development and evaluation of RPA-NFO-LFT and RPA-Cas12a-LFT systems for the detection of Candida albicans. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:2355-2365. [PMID: 37161551 DOI: 10.1039/d3ay00259d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Recently, the growing number of medical interventions has led to the risk of invasive candidiasis. Among them, Candida albicans (C. albicans) infection has the highest incidence, which has led to great demand for developing early diagnosis methods. In this study, two lateral flow device based molecular assay systems, RPA-NFO-LFT and RPA-Cas12a-LFT, were established and optimized to achieve the detection of C. albicans. Firstly, efficient and specific primers for C. albicans detection were designed and screened, and the purification of amplification products was also explored. Then, many important conditions and issues for each system were investigated and discussed to improve the performances of the test strip devices in C. albicans detection. An evaluation study revealed that both systems showed favorable specificity and sensitivity in the detection of C. albicans samples with a lower detection limit of 103 CFU ml-1, while RPA-Cas12a-LFT is more accurate for visual interpretation and more stable toward samples that exhibit serum nucleic acid interference. Finally, the performances of RPA-NFO-LFT and RPA-Cas12a-LFT were compared with that of the conventional qPCR method. This work might provide a reference for the development of molecular assay devices in practical candidiasis diagnosis.
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Affiliation(s)
- Chang Liu
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China.
- School of Life Sciences, Tianjin University, Tianjin 300072, P. R. China.
| | - Xuechun Yao
- Dynamiker Biotechnology Sub-Center, Beijing Key Laboratory for Mechanism Study and Precision Diagnosis of Invasive Fungal Diseases, Tianjin 300467, China
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Chunlong Liu
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China.
- Dynamiker Biotechnology Sub-Center, Beijing Key Laboratory for Mechanism Study and Precision Diagnosis of Invasive Fungal Diseases, Tianjin 300467, China
| | - Shengping You
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China.
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300350, P. R. China
| | - Wei Qi
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China.
- The Co-Innovation Centre of Chemistry and Chemical Engineering of Tianjin, Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300350, P. R. China
| | - Mengfan Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, P. R. China.
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300350, P. R. China
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Gonçalves CGE, Lourenço LDFH, Philippsen HK, Santos AS, Santos LND, Ferreira NR. Crude Enzyme Concentrate of Filamentous Fungus Hydrolyzed Chitosan to Obtain Oligomers of Different Sizes. Polymers (Basel) 2023; 15:polym15092079. [PMID: 37177223 PMCID: PMC10181246 DOI: 10.3390/polym15092079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 05/15/2023] Open
Abstract
Chitosan is a non-cytotoxic polysaccharide that, upon hydrolysis, releases oligomers of different sizes that may have antioxidant, antimicrobial activity and the inhibition of cancer cell growth, among other applications. It is, therefore, a hydrolysis process with great biotechnological relevance. Thus, this study aims to use a crude enzyme concentrate (CEC) produced by a filamentous fungus to obtain oligomers with different molecular weights. The microorganism was cultivated in a liquid medium (modified Czapeck-with carboxymethylcellulose as enzyme inducer). The enzymes present in the CEC were identified by LC-MS/MS, with an emphasis on cellobiohydrolase (E.C 3.2.1.91). The fungus of the Aspergillus genus was identified by amplifying the ITS1-5.8S-ITS2 rDNA region and metaproteomic analysis, where the excreted enzymes were identified with sequence coverage greater than 84% to A. nidulans. Chitosan hydrolysis assays compared the CEC with the commercial enzyme (Celluclast 1.5 L®). The ability to reduce the initial molecular mass of chitosan by 47.80, 75.24, and 93.26% after 2.0, 5.0, and 24 h of reaction, respectively, was observed. FTIR analyses revealed lower absorbance of chitosan oligomers' spectral signals, and their crystallinity was reduced after 3 h of hydrolysis. Based on these results, we can conclude that the crude enzyme concentrate showed a significant technological potential for obtaining chitosan oligomers of different sizes.
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Affiliation(s)
| | | | - Hellen Kempfer Philippsen
- Faculty of Biology, Socioenvironmental and Water Resources Institute, Federal Rural University of the Amazon, Campus Belém, Belem 66077-830, PA, Brazil
| | - Alberdan Silva Santos
- Faculty of Chemistry, Institute of Exact and Natural Sciences, Federal University of Pará, Belem 66075-110, PA, Brazil
| | - Lucely Nogueira Dos Santos
- Graduate Program in Food Science and Technology, Federal University of Pará, Belem 66075-110, PA, Brazil
| | - Nelson Rosa Ferreira
- Graduate Program in Food Science and Technology, Federal University of Pará, Belem 66075-110, PA, Brazil
- Faculty of Food Engineering, Technology Institute, Federal University of Pará, Belem 66075-110, PA, Brazil
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5
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Hilt EE, Ferrieri P. Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases. Genes (Basel) 2022; 13:genes13091566. [PMID: 36140733 PMCID: PMC9498426 DOI: 10.3390/genes13091566] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/03/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years.
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Yang Q, Rutherfurd-Markwick K, Mutukumira AN. Identification of dominant lactic acid bacteria and yeast in rice sourdough produced in New Zealand. Curr Res Food Sci 2021; 4:729-736. [PMID: 34729499 PMCID: PMC8546371 DOI: 10.1016/j.crfs.2021.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/07/2021] [Accepted: 10/06/2021] [Indexed: 11/21/2022] Open
Abstract
This study characterised a commercial New Zealand gluten free (GF) rice sourdough and its starter culture composition. Acidity of the mother sourdough, dough before proofing and dough after proofing was determined during the production of rice sourdough bread, and colour was measured for the baked bread. Yeast and lactic acid bacteria (LAB) were enumerated in the rice sourdough samples and representative colonies characterised using API kits and sequenced by the Internal Transcribed Spacer and 16 S rRNA region. Sourdough LAB isolates were identified as Lactobacillus (L.) papraplantarum DSM 10667 and L. fermentarum CIP 102980 and the yeast isolates as Saccharomyces (S.) cerevisiae CBS 1171. Dough acidity increased significantly (p < 0.05) during fermentation due to the metabolic activities of the sourdough cultures. After baking, the colour of the rice sourdough bread crust was similar to that of unleavened wheat bread (golden brown). The improved colour of the rice sourdough bread crust may be a result of combined use of sourdough technique and optimal baking conditions. The results of this study may allow bakers to improve the overall quality of GF rice sourdough baked bread by selecting suitable fermentation and baking parameters. Gluten-free rice sourdough bread. Rice sourdough fermentation of gluten-free bread improved bread crust colour Rice sourdough LAB identified as Lactobacillus paraplantarum CIP 102980 and Lactobacillus fermentarum DSM 10667 Yeast isolated from rice sourdough was identified as S. cerevisiae CBS 1171.
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Affiliation(s)
- Qiwei Yang
- School of Food and Advanced Technology, Massey University, Auckland, 0745, New Zealand
| | - Kay Rutherfurd-Markwick
- School of Health Sciences, College of Health, Massey University, Auckland, 0745, New Zealand
| | - Anthony N. Mutukumira
- School of Food and Advanced Technology, Massey University, Auckland, 0745, New Zealand
- Corresponding author.
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High Clinical Impact of Broad-Range Fungal PCR in Suspected Fungal Sinusitis. J Clin Microbiol 2021; 59:e0095521. [PMID: 34406798 DOI: 10.1128/jcm.00955-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Broad-range fungal PCR is a powerful tool for identifying pathogens directly from patient specimens; however, reported estimates of clinical utility vary and costs discourage universal testing. We investigated the diagnostic and clinical utility of broad-range fungal PCR by examining 9 years of results from sinonasal specimens, hypothesizing that this anatomic location would identify immunocompromised patients at high risk for invasive fungal disease. We retrospectively identified 644 PCRs and 1,446 fungal cultures from sinus sites. To determine the relative performance of each testing modality, we performed chart review on 52 patients having specimens submitted for culture and PCR on the same day. Positivity rates were significantly higher for PCR (37.1%) than culture (13.7%) but similar for formalin-fixed and fresh tissues (42.3% versus 34.6%). Relative to culture, PCR had significantly faster turnaround time to both preliminary (94.5 versus 108.8 h) and final positive (137.9 versus 278.5 h) results. Among chart-reviewed patients, 88% were immunocompromised, 65% had proven or probable fungal disease, and testing sensitivities for culture and PCR (67.5% and 85.0%) were not statistically different. Nevertheless, PCR identified pathogens not recovered by culture in 14.9% of cases and informed clinical decision-making in 16.7% of all reviewed cases, and sensitivity of PCR combined with culture (90.0%) was higher than that of culture alone. We conclude that broad-range fungal PCR is frequently informative for patients at risk of serious fungal disease and is complementary to and has faster turnaround time than culture. Formalin-fixed tissue does not adversely affect diagnostic yield, but anatomic site may impact assay positivity rates.
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8
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Regulatory roles of nucleolus organizer region-derived long non-coding RNAs. Mamm Genome 2021; 33:402-411. [PMID: 34436664 DOI: 10.1007/s00335-021-09906-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022]
Abstract
The nucleolus is the largest sub-nuclear domain, serving primarily as the place for ribosome biogenesis. A delicately regulated function of the nucleolus is vital to the cell not only for maintaining proper protein synthesis but is also tightly associated with responses to different types of cellular stresses. Recently, several long non-coding RNAs (lncRNAs) were found to be part of the regulatory network that modulate nucleolar functions. Several of these lncRNAs are encoded in the ribosomal DNA (rDNA) repeats or are transcribed from the genomic regions that are located near the nucleolus organizer regions (NORs). In this review, we first discuss the current understanding of the sequence of the NORs and variations between different NORs. We then focus on the NOR-derived lncRNAs in mammalian cells and their functions in rRNA transcription and the organization of nucleolar structure under different cellular conditions. The identification of these lncRNAs reveals great potential of the NORs in harboring novel genes involved in the regulation of nucleolar functions.
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9
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Gil-Cardoso K, Saldaña G, Luengo E, Pastor J, Virto R, Alcaide-Hidalgo JM, Del Bas JM, Arola L, Caimari A. Consumption of Sourdough Breads Improves Postprandial Glucose Response and Produces Sourdough-Specific Effects on Biochemical and Inflammatory Parameters and Mineral Absorption. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3044-3059. [PMID: 33656322 DOI: 10.1021/acs.jafc.0c07200] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
To evaluate responses to different sourdough breads, six groups of rats were fed a conventional refined wheat bread with no sourdough content (C_WhB); a leavened spelt bread baked with Rebola sourdough (Re_SpB); a durum wheat bread with Rebola sourdough (Re_DuB); or a multigrain bread leavened with Rebola (Re_MGB), Carla (Ca_MGB), or San Francisco sourdough (SF_MGB). Compared to C_WhB-fed rats, Re_SpB-, Re_DuB-, and Re_MGB-fed animals showed lower postprandial blood glucose levels, whereas SF_MGB-fed rats displayed a decreased postprandial blood insulin response and glucose and insulin products. The 3 week intake of Ca_MGB decreased blood triacylglycerols and the relative apparent absorption (RAA) of Fe2+, Cu2+, and Zn2+, whereas Re_MGB-fed animals showed lower serum levels of the MCP-1 inflammatory marker and decreased the Fe RAA. The 3 week consumption of the multigrain bread produced sourdough-specific effects. Thus, Re_MGB-fed animals displayed higher insulin concentrations than Ca_MGB- and SF_MGB-fed rats and decreased blood MCP-1 levels compared to those of Ca_MGB-fed animals. In addition, Ca_MGB-fed rats showed lower serum triacylglycerol concentrations than those of Re_MGB- and SF_MGB-fed animals, whereas SF_MGB-fed rats displayed higher RAA values of Ca2+, Cu2+, Fe2+, Mg2+, and Zn2+ than their Re_MGB and Ca_MGB counterparts. These sourdough-specific effects could be related to changes in the contents of sugars and organic acids, acidity, microbial composition, and proteolytic activity among sourdoughs. Hence, the consumption of sourdough breads improved postprandial blood glucose and insulin responses and produced sourdough-specific effects on RAA and serum insulin and triacylglycerol and MCP-1 levels in rats, showing that SF_MGB has the most promising beneficial effects.
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Affiliation(s)
- Katherine Gil-Cardoso
- Eurecat, Centre Tecnològic de Catalunya, Technological Unit of Nutrition and Health, Reus 43204, Spain
| | - Guillermo Saldaña
- NOVAPAN S.L, Research & Development Department, Zaragoza 50014, Spain
| | - Elisa Luengo
- NOVAPAN S.L, Research & Development Department, Zaragoza 50014, Spain
| | - Jorge Pastor
- NOVAPAN S.L, Research & Development Department, Zaragoza 50014, Spain
| | - Raquel Virto
- CNTA, National Centre for Food Technology and Safety, San Adrián 31570, Navarra, Spain
| | | | - Josep M Del Bas
- Eurecat, Centre Tecnològic de Catalunya, Technological Unit of Nutrition and Health, Reus 43204, Spain
| | - Lluís Arola
- Eurecat, Centre Tecnològic de Catalunya, Technological Unit of Nutrition and Health, Reus 43204, Spain
- Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, Nutrigenomics Research Group, Campus Sescelades, Tarragona 43001, Spain
| | - Antoni Caimari
- Eurecat, Centre Tecnològic de Catalunya, Biotechnology Area, Avinguda Universitat, Reus 43204, Spain
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10
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Isolation and identification of Candida tropicalis in sows with fatal infection: a case report. BMC Vet Res 2021; 17:108. [PMID: 33663504 PMCID: PMC7934564 DOI: 10.1186/s12917-021-02821-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/25/2021] [Indexed: 11/13/2022] Open
Abstract
Background Candida is the common conditionally pathogenic fungus that infected human and animal clinically. C. tropicalis had been isolated from the skin and hair of healthy pigs, but with no report of fatal infection in gastrointestinal diseases. Case presentation In a pig farm in Henan Province of China, about 20 % of pregnant and postpartum sows suffered from severe gastrointestinal diseases, with a mortality rate higher than 60 % in the diseased animals. The sows had gastrointestinal symptoms such as blood in stool and vomiting. Necropsy revealed obvious gastric ulcers, gastrointestinal perforation, and intestinal hemorrhage in the gastrointestinal tract, but no lesions in other organs. The microbial species in gastric samples collected from gastric ulcer of the diseased sows then was initially identified as Candida by using routine systems of microscopic examination, culture characteristics on the medium Sabouraud dextrose agar medium. The fungus was further identified as C. tropicalis by species-specific PCR and sequencing. This study revealed an infection of C. tropicalis in sows through gastrointestinal mucosa could cause fatal digestive system disease and septicemia. Conclusions For the first time, a strain of C. tropicalis was isolated and identified from the gastric tissue of sows with severe gastrointestinal diseases. PCR and sequencing of ITS-rDNA combined with morphology and histopathological assay were reliable for the identification of Candida clinically.
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Unraveling microbial fermentation features in kimchi: from classical to meta-omics approaches. Appl Microbiol Biotechnol 2020; 104:7731-7744. [PMID: 32749526 DOI: 10.1007/s00253-020-10804-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/22/2020] [Accepted: 07/30/2020] [Indexed: 12/31/2022]
Abstract
Kimchi is a traditional Korean fermented food prepared via spontaneous fermentation by various microorganisms originating from vegetables such as kimchi cabbage, radishes, and garlic. Recent advances in meta-omics approaches that integrate metataxonomics, metagenomics, metatranscriptomics, and metabolomics have contributed to explaining and understanding food fermentation processes. Kimchi microbial communities are composed of majorly lactic acid bacteria such as Leuconostoc, Lactobacillus, and Weissella and fewer eukaryotic microorganisms and kimchi fermentation are accomplished by complex microbial metabolisms to produce diverse metabolites such as lactate, acetate, CO2, ethanol, mannitol, amino acids, formate, malate, diacetyl, acetoin, and 2, 3-butanediol, which determine taste, quality, health benefit, and safety of fermented kimchi products. Therefore, in the future, kimchi researches should be systematically performed using the meta-omics approaches to understand complex microbial metabolisms during kimchi fermentation. KEY POINTS: • Spontaneous fermentation by raw material microbes gives kimchi its unique flavor. • The kimchi microbiome is altered by environmental factors and raw materials. • Through the multi-omics approaches, it is possible to accurately analyze the diversity and metabolic characteristics of kimchi microbiome and discover potential functionalities.
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Sulaiman IM, Jacobs E, Simpson S. Application of Ribosomal Internal Transcribed Spacer 1, Internal Transcribed Spacer 2, and Large-Subunit D1-D2 Regions as the Genetic Markers to Identify Fungi Isolated from Different Environmental Samples: A Molecular Surveillance Study of Public Health Importance. J AOAC Int 2020; 103:843-850. [PMID: 33241369 DOI: 10.1093/jaocint/qsz012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/08/2019] [Accepted: 12/20/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND In September 2012, a multistate fungal meningitis outbreak started across 20 states in the United States. It affected 753 individuals and caused 64 deaths who received contaminated spinal injections. In a previous study, we analyzed 26 environmental samples collected from the manufacturing premises of a compounding company to determine the possible cause of an outbreak and identified 14 distinct fungal species. OBJECTIVES In this follow-up study, we have analyzed 198 environmental samples collected from three additional compounding company premises located in the United States for the presence of pathogenic fungi. METHODS Environmental swab samples were initially examined by standard microbiological methods. Subsequently, DNA sequencing was performed on all of the 25 recovered fungal isolates at the D1-D2 domain of the large subunit (LSU) ribosomal RNA (rRNA) and the internal transcribed spacer (ITS) regions. RESULTS Sequence analysis of the ITS1, ITS2, and LSU rRNA regions confirmed the presence of the following fungal species in the environmental samples analyzed: (i) Pestalotiopsis cocculi from the region Ia; (ii) Epicoccum nigrum and Trichaptum biforme from the region Ib; (iii) Nigrospora sphaerica and Fusarium sp. from the region II; and (iv) Curvularia sp., Fusarium sp., Penicillium sp., and Preussia sp. from the region III. Species identification of 25 recovered fungal isolates matched, in most cases, at 3 sequenced loci (ITS1, ITS2, and LSU). HIGHLIGHTS DNA sequencing of ITS1, ITS2, and LSU D1-D2 regions can be used to perform fungal typing and in implementing effective environmental monitoring programs of public health importance.
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Affiliation(s)
- Irshad M Sulaiman
- Microbiological Sciences Branch, Southeast Food and Feed Laboratory, Office of Regulatory Affairs, U. S. Food and Drug Administration, 60, Eighth Street NE, Atlanta, GA 30309, USA
| | - Emily Jacobs
- Microbiological Sciences Branch, Southeast Food and Feed Laboratory, Office of Regulatory Affairs, U. S. Food and Drug Administration, 60, Eighth Street NE, Atlanta, GA 30309, USA
| | - Steven Simpson
- Microbiological Sciences Branch, Southeast Food and Feed Laboratory, Office of Regulatory Affairs, U. S. Food and Drug Administration, 60, Eighth Street NE, Atlanta, GA 30309, USA
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Clinical Spectrum, Diagnosis and Outcome of Rare Fungal Infections in Patients with Hematological Malignancies: Experience of 15-Year Period from a Single Tertiary Medical Center. Mycopathologia 2020; 185:347-355. [PMID: 32100219 DOI: 10.1007/s11046-020-00436-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 02/11/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Patients with hematological malignancies and allogeneic hematopoietic stem-cell transplant recipients carry a high risk of rare (non-Aspergillus molds and non-Candida yeasts) invasive fungal infections (IFI). METHODS We retrospectively evaluated and described the patient profile, clinical manifestations, isolated species, treatment and outcome of patients with hematological malignancies diagnosed with these rare IFIs during 15 years in a large single hemato-oncology center. RESULTS Eighty-seven patients with hematological malignancies treated in our center had at least one positive culture or molecular identification of a rare fungus. Ninety-three isolates were considered the etiological agents of the infection. The most common underlying hematological malignancy was acute myeloid leukemia, 36 patients (41.4%). Eighty patients (91%) received chemotherapy less than 30 days prior to IFI diagnosis. The most frequent site of infection was the respiratory tract: 34 patients (39%) had pulmonary and 19 patients (22%) had a sinusal or nasopharyngeal infections. Disseminated infection, defined as positive blood cultures or parallel infection in multiple organ systems, was documented in 20 patients (23%). The most common fungal species were Fusarium (35%) and Zygomycetes (25%). Coinfection with more than one fungus was noted in 20 patients (23%). Forty-seven of 87 patients (54%) in this study died within 90 days of IFI diagnosis. CONCLUSIONS Rare IFIs in patients with hematological malignancy become increasingly frequent. Early identification with traditional and molecular methods is important in management of these patients.
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Vanegas J, Muñoz-García A, Pérez-Parra KA, Figueroa-Galvis I, Mestanza O, Polanía J. Effect of salinity on fungal diversity in the rhizosphere of the halophyte Avicennia germinans from a semi-arid mangrove. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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16
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Filamentous fungi diversity in the natural fermentation of Amazonian cocoa beans and the microbial enzyme activities. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01488-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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17
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Phong HX, Klanrit P, Dung NTP, Yamada M, Thanonkeo P. Isolation and characterization of thermotolerant yeasts for the production of second-generation bioethanol. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01468-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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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] [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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Sabz G, Gharaghani M, Mirhendi H, Ahmadi B, Gatee MA, Sisakht MT, Hemati A, Mohammadi R, Taghavi J, Nouripour-Sisakht S. Clinical and microbial epidemiology of otomycosis in the city of Yasuj, southwest Iran, revealing Aspergillus tubingensis as the dominant causative agent. J Med Microbiol 2019; 68:585-590. [PMID: 30801244 DOI: 10.1099/jmm.0.000948] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
PURPOSE Otomycosis is a mycotic infection of the external auditory canal and can be caused by a wide range of fungal species. In this study, we aimed to identify fungal isolates from patients suspected of otomycosis. METHODOLOGY External ear canal samples were taken from patients referred to the outpatient department of Shahid-Mofatteh Clinic in the city of Yasuj, Iran, and examined by direct microscopy and culture. DNA of the isolated fungi was tested by internal transcribed spacer PCR restriction fragment length polymorphism analysis for identification of yeasts and β-tubulin sequencing for identification of Aspergillus species. RESULTS Among 275 patients suspected of otomycosis, 144 cases (83 female and 61 male) were confirmed with otomycosis. For 89% (n=128) of positive cultures, microscopy was also positive, while there were no cases with a microscopy-positive and culture-negative result. The predominant predisposing factor was self-cleaning of the external ear using unhygienic tools, and the main risk occupation was 'housewife'. The most common isolated fungi were typically Aspergillus (n=120), including 73 isolates of Aspergillus section Nigri, 43 of section Flavi, 3 of section Terrei and 1 of section Fumigati. After sequencing, 44 out of 73 strains primarily identified as Aspergillus niger turned out to be Aspergillus tubingensis. Thirty-five isolates were identified as Candida, including Candida parapsilosis (n=22), Candida albicans (n=12) and Candida tropicalis (n=1). CONCLUSION Aspergillus tubingensis was the most common species involved in otomycosis. This work corroborates the difficulty of precise identification of species within the black Aspergilli by morphological characteristics.
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Affiliation(s)
- Gholamabbas Sabz
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Maral Gharaghani
- Department of Medical Mycology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hossein Mirhendi
- Departments of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bahram Ahmadi
- Department of Medical Laboratory Sciences, Faculty of Paramedical, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohamad Amin Gatee
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran.,Student Research Committee, Yasuj University of Medical Sciences, Yasuj, Iran
| | | | - Alireza Hemati
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Reza Mohammadi
- Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Jabar Taghavi
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Sadegh Nouripour-Sisakht
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran.,Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
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Abdel-Aziz MS, Ghareeb MA, Saad AM, Refahy LA, Hamed AA. Chromatographic isolation and structural elucidation of secondary metabolites from the soil-inhabiting fungus Aspergillus fumigatus 3T-EGY. ACTA CHROMATOGR 2018. [DOI: 10.1556/1326.2017.00329] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Mohamed S. Abdel-Aziz
- Microbial Chemistry Department, Genetic Engineering and Biotechnology Division, National Research Center, El-Bohouth Street 33, Dokki-Giza 12622, Egypt
| | - Mosad A. Ghareeb
- Medicinal Chemistry Department, Theodor Bilharz Research Institute, Kornaish El-Nile, Warrak El-Hadar 12411, Imbaba, Giza, Egypt
| | - Amal M. Saad
- Medicinal Chemistry Department, Theodor Bilharz Research Institute, Kornaish El-Nile, Warrak El-Hadar 12411, Imbaba, Giza, Egypt
| | - Laila A. Refahy
- Medicinal Chemistry Department, Theodor Bilharz Research Institute, Kornaish El-Nile, Warrak El-Hadar 12411, Imbaba, Giza, Egypt
| | - Ahmed A. Hamed
- Microbial Chemistry Department, Genetic Engineering and Biotechnology Division, National Research Center, El-Bohouth Street 33, Dokki-Giza 12622, Egypt
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Multilocus sequence typing of Candida albicans isolates from the oral cavities of patients undergoing haemodialysis. Sci Rep 2018; 8:16413. [PMID: 30401875 PMCID: PMC6219599 DOI: 10.1038/s41598-018-34565-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 10/17/2018] [Indexed: 12/15/2022] Open
Abstract
This study evaluates the prevalence, diversity, and genetic profiles of Candida albicans isolates recovered from the oral cavities of haemodialysis patients. Oral swab samples were obtained from haemodialysis patients (n = 126) and healthy control subjects (n = 233) and Candida species were characterised. There was no significant difference between the haemodialysis and control groups in the prevalence of yeast carriers (23.6% vs. 31.0%, respectively) or C. albicans carriers (19.8% vs. 21.0%, respectively). C. albicans was the most populous species in both cohorts, followed by C. parapsilosis. C. parapsilosis and C. glabrata were more prevalent in the haemodialysis group than in the control group (C. parapsilosis 5.6% vs. 0.9% and C. glabrata 3.2% vs. 0.4%, respectively; P < 0.05). C. albicans isolates were analysed by multilocus sequence typing and the results were used to construct a phylogenetic tree. Most haemodialysis isolates were placed into Clade 4 (20.0%) and Clade 19 (16.0%) and most control isolates into Clade 8 (17%) and Clade 4 (14.9%). Differences in the strain abundance in each clade were not statistically significant between the two groups. Moreover, there was no significant association between the health status or diagnosis and either the sequence types or clades.
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Basein T, Gardiner BJ, Andujar Vazquez GM, Joel Chandranesan AS, Rabson AR, Doron S, Snydman DR. Microbial Identification Using DNA Target Amplification and Sequencing: Clinical Utility and Impact on Patient Management. Open Forum Infect Dis 2018; 5:ofy257. [PMID: 30539032 PMCID: PMC6284463 DOI: 10.1093/ofid/ofy257] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/04/2018] [Indexed: 12/21/2022] Open
Abstract
Broad-range polymerase chain reaction (PCR) is increasingly used in patients with culture-negative infections; however, few studies have assessed the diagnostic utility of this test in this context. We performed a retrospective cohort study of patients who had clinical specimens sent for broad-range PCR, aiming to evaluate performance and determine impact on patient management. Organisms were identified in 21/71 samples. High numbers of polymorphonuclear leukocytes on Gram stain (odds ratio [OR], 4.17; P = .04) and acute inflammation on histopathology (OR, 5.69; P = .02) were significantly associated with a positive result. Management was altered in 18 patients, 11 with positive and 7 with negative results. Overall, broad-range PCR assay had the highest impact in patients with microscopic evidence of inflammation. Physicians ordering this complex, difficult to interpret, and expensive test should carefully consider all available clinical information on an individualized basis to optimize its performance.
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Affiliation(s)
- Tinzar Basein
- Division of Geographic Medicine and Infectious Diseases
| | | | | | | | - Arthur R Rabson
- Department of Pathology, Tufts Medical Center and Tufts University School of Medicine, Boston, Massachusetts
| | - Shira Doron
- Division of Geographic Medicine and Infectious Diseases
| | - David R Snydman
- Division of Geographic Medicine and Infectious Diseases.,Tufts Clinical and Translational Science Institute, Tufts University, Boston, Massachusetts
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In Vitro Antidrug Susceptibility Testing of Candida Species Isolated from Aseptic Body Fluids. Jundishapur J Microbiol 2018. [DOI: 10.5812/jjm.55547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Park JH, Kim YH, Ham CS, Shin SE, Lee HJ, Ko KS, Choi J, Son GH, Park SH. Molecular identification of forensically important calliphoridae and sarcophagidae species using ITS2 nucleotide sequences. Forensic Sci Int 2018; 284:1-4. [DOI: 10.1016/j.forsciint.2017.12.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 10/18/2022]
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Elias A, Saleh KA, Faranesh N, Dalal R, Geffen Y, Fisher Y, Neuberger A, Zaaroura S. Case Report: Histoplasmosis: First Autochthonous Case from Israel. Am J Trop Med Hyg 2018; 98:278-280. [PMID: 29165228 DOI: 10.4269/ajtmh.17-0603] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
We present an autochthonous Histoplasma infection in Israel. The patient presented with hoarseness and weight loss. Pathology findings and molecular tests confirmed the diagnosis, and the patient responded to antifungal therapy. Because the patient had an atypical presentation of histoplasmosis, it is likely that other more typical cases have gone unreported. To our knowledge, no other cases have been previously reported from Israel or the Middle East region.
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Affiliation(s)
- Adi Elias
- Department of Internal Medicine B, Rambam Healthcare Campus, Haifa, Israel
| | - Khaldun Abu Saleh
- Otorhinolaryngology (ENT) Department Head and Neck Surgery, French Hospital Nazareth, Faculty of Medicine of Bar Ilan University, Galilee, Israel
| | - Nabil Faranesh
- Otorhinolaryngology (ENT) Department Head and Neck Surgery, French Hospital Nazareth, Faculty of Medicine of Bar Ilan University, Galilee, Israel
| | - Raid Dalal
- Otorhinolaryngology (ENT) Department Head and Neck Surgery, French Hospital Nazareth, Faculty of Medicine of Bar Ilan University, Galilee, Israel
| | - Yuval Geffen
- Microbiology Laboratory, Rambam Healthcare Campus, Haifa, Israel
| | - Yael Fisher
- Department of Pathology, Rambam Healthcare Campus, Haifa, Israel
| | - Ami Neuberger
- Bruce Rappaport Faculty of Medicine, Technion Institute of Technology, Haifa, Israel.,Unit of Infectious Diseases, Department of Internal Medicine B, Rambam Healthcare Campus, Haifa, Israel.,Department of Internal Medicine B, Rambam Healthcare Campus, Haifa, Israel
| | - Suleiman Zaaroura
- Otorhinolaryngology (ENT) Department Head and Neck Surgery, French Hospital Nazareth, Faculty of Medicine of Bar Ilan University, Galilee, Israel
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Characterization of the Same Mutations in FCA1 Gene Associated With 5-FC Resistance of Candida albicans. Jundishapur J Microbiol 2017. [DOI: 10.5812/jjm.12952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Molecular Characterization and Phytochemical Studies of Pleurotus sp to Unveil Species Diversity and Pharmacological Activities. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2017. [DOI: 10.22207/jpam.11.2.28] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Methods of Candida dubliniensis identification and its occurrence in human clinical material. Folia Microbiol (Praha) 2017; 62:401-408. [DOI: 10.1007/s12223-017-0510-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 02/21/2017] [Indexed: 01/30/2023]
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Techaparin A, Thanonkeo P, Klanrit P. High-temperature ethanol production using thermotolerant yeast newly isolated from Greater Mekong Subregion. Braz J Microbiol 2017; 48:461-475. [PMID: 28365094 PMCID: PMC5498443 DOI: 10.1016/j.bjm.2017.01.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 01/04/2017] [Accepted: 01/05/2017] [Indexed: 11/24/2022] Open
Abstract
The application of high-potential thermotolerant yeasts is a key factor for successful ethanol production at high temperatures. Two hundred and thirty-four yeast isolates from Greater Mekong Subregion (GMS) countries, i.e., Thailand, The Lao People's Democratic Republic (Lao PDR) and Vietnam were obtained. Five thermotolerant yeasts, designated Saccharomyces cerevisiae KKU-VN8, KKU-VN20, and KKU-VN27, Pichia kudriavzevii KKU-TH33 and P. kudriavzevii KKU-TH43, demonstrated high temperature and ethanol tolerance levels up to 45 °C and 13% (v/v), respectively. All five strains produced higher ethanol concentrations and exhibited greater productivities and yields than the industrial strain S. cerevisiae TISTR5606 during high-temperature fermentation at 40 °C and 43 °C. S. cerevisiae KKU-VN8 demonstrated the best performance for ethanol production from glucose at 37 °C with an ethanol concentration of 72.69 g/L, a productivity of 1.59 g/L/h and a theoretical ethanol yield of 86.27%. The optimal conditions for ethanol production of S. cerevisiae KKU-VN8 from sweet sorghum juice (SSJ) at 40 °C were achieved using the Box–Behnken experimental design (BBD). The maximal ethanol concentration obtained during fermentation was 89.32 g/L, with a productivity of 2.48 g/L/h and a theoretical ethanol yield of 96.32%. Thus, the newly isolated thermotolerant S. cerevisiae KKU-VN8 exhibits a great potential for commercial-scale ethanol production in the future.
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Affiliation(s)
- Atiya Techaparin
- Graduate School, Khon Kaen University, Khon Kaen 40002, Thailand; Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Pornthap Thanonkeo
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen 40002, Thailand; Fermentation Research Center for Value Added Agricultural Products (FerVAAP), Khon Kaen University, Khon Kaen 40002, Thailand
| | - Preekamol Klanrit
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen 40002, Thailand; Fermentation Research Center for Value Added Agricultural Products (FerVAAP), Khon Kaen University, Khon Kaen 40002, Thailand.
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Isolation of aquatic yeasts with the ability to neutralize acidic media, from an extremely acidic river near Japan's Kusatsu-Shirane Volcano. J Biosci Bioeng 2017; 124:43-46. [PMID: 28258908 DOI: 10.1016/j.jbiosc.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 01/19/2017] [Accepted: 02/06/2017] [Indexed: 11/23/2022]
Abstract
The Yukawa River is an extremely acidic river whose waters on the east foot of the Kusatu-Shirane Volcano (in Gunma Prefecture, Japan) contain sulfate ions. Here we isolated many acid-tolerant yeasts from the Yukawa River, and some of them neutralized an acidic R2A medium containing casamino acid. Candida fluviatilis strain CeA16 had the strongest acid tolerance and neutralizing activity against the acidic medium. To clarify these phenomena, we performed neutralization tests with strain CeA16 using casamino acid, a mixture of amino acids, and 17 single amino acid solutions adjusted to pH 3.0, respectively. Strain CeA16 neutralized not only acidic casamino acid and the mixture of amino acids but also some of the acidic single amino acid solutions. Seven amino acids were strongly decomposed by strain CeA16 and simultaneously released ammonium ions. These results suggest strain CeA16 is a potential yeast as a new tool to neutralize acidic environments.
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de Gannes V, Bekele I, Dipchansingh D, Wuddivira MN, De Cairies S, Boman M, Hickey WJ. Microbial Community Structure and Function of Soil Following Ecosystem Conversion from Native Forests to Teak Plantation Forests. Front Microbiol 2016; 7:1976. [PMID: 28018311 PMCID: PMC5145857 DOI: 10.3389/fmicb.2016.01976] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/25/2016] [Indexed: 11/28/2022] Open
Abstract
Soil microbial communities can form links between forest trees and functioning of forest soils, yet the impacts of converting diverse native forests to monoculture plantations on soil microbial communities are limited. This study tested the hypothesis that conversion from a diverse native to monoculture ecosystem would be paralleled by a reduction in the diversity of the soil microbial communities. Soils from Teak (Tectona grandis) plantations and adjacent native forest were examined at two locations in Trinidad. Microbial community structure was determined via Illumina sequencing of bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) regions, and by phospholipid fatty acid (PLFA) analysis. Functional characteristics of microbial communities were assessed by extracellular enzyme activity (EEA). Conversion to Teak plantation had no effect on species richness or evenness of bacterial or fungal communities, and no significant effect on EEA. However, multivariate analyses (nested and two-way crossed analysis of similarity) revealed significant effects (p < 0.05) of forest type (Teak vs. native) upon the composition of the microbial communities as reflected in all three assays of community structure. Univariate analysis of variance identified two bacterial phyla that were significantly more abundant in the native forest soils than in Teak soils (Cyanobacteria, p = 0.0180; Nitrospirae, p = 0.0100) and two more abundant in Teak soils than in native forest (candidate phyla TM7, p = 0.0004; WS6, p = 0.044). Abundance of an unidentified class of arbuscular mycorrhizal fungi (AMF) was significantly greater in Teak soils, notable because Teak is colonized by AMF rather than by ectomycorrihzal fungi that are symbionts of the native forest tree species. In conclusion, microbial diversity indices were not affected in the conversion of native forest to teak plantation, but examination of specific bacterial taxa showed that there were significant differences in community composition.
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Affiliation(s)
- Vidya de Gannes
- Faculty of Food and Agriculture, The University of the West Indies at St. Augustine Trinidad and Tobago
| | - Isaac Bekele
- Faculty of Food and Agriculture, The University of the West Indies at St. Augustine Trinidad and Tobago
| | - Denny Dipchansingh
- Ministry of Agriculture, Land and Fisheries, The University of the West Indies at St. Augustine Trinidad and Tobago
| | - Mark N Wuddivira
- Faculty of Food and Agriculture, The University of the West Indies at St. Augustine Trinidad and Tobago
| | - Sunshine De Cairies
- Faculty of Food and Agriculture, The University of the West Indies at St. Augustine Trinidad and Tobago
| | - Mattias Boman
- Faculty of Food and Agriculture, The University of the West Indies at St. Augustine Trinidad and Tobago
| | - William J Hickey
- O. N. Allen Laboratory for Soil Microbiology, Department Soil Science, University of Wisconsin-Madison Madison, WI, USA
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Mongkolrattanothai K, Dien Bard J. The utility of direct specimen detection by Sanger sequencing in hospitalized pediatric patients. Diagn Microbiol Infect Dis 2016; 87:100-102. [PMID: 27889254 DOI: 10.1016/j.diagmicrobio.2016.10.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 10/26/2016] [Accepted: 10/28/2016] [Indexed: 11/28/2022]
Abstract
Direct microbial DNA detection from clinical specimens by polymerase chain reaction and Sanger sequencing has been developed to address the innate limitations of traditional culture-based work-up. We report our institution's experience with direct specimen sequencing, its clinical utility, and barriers to effective clinical implementation.
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Affiliation(s)
- Kanokporn Mongkolrattanothai
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Keck School of Medicine at the University of Southern California, Los Angeles, CA 90033, USA.
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Keck School of Medicine at the University of Southern California, Los Angeles, CA 90033, USA
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Ramanjaneyulu G, Rajasekhar Reddy B. Optimization of Xylanase Production through Response Surface Methodology by Fusarium sp. BVKT R2 Isolated from Forest Soil and Its Application in Saccharification. Front Microbiol 2016; 7:1450. [PMID: 27713726 PMCID: PMC5032753 DOI: 10.3389/fmicb.2016.01450] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 08/30/2016] [Indexed: 11/13/2022] Open
Abstract
Xylanses are hydrolytic enzymes with wide applications in several industries like biofuels, paper and pulp, deinking, food, and feed. The present study was aimed at hitting at high yield xylanase producing fungi from natural resources. Two highest xylanase producing fungal isolates-Q12 and L1 were picked from collection of 450 fungal cultures for the utilization of xylan. These fungal isolates-Q12 and L1 were identified basing on ITS gene sequencing analysis as Fusarium sp. BVKT R2 (KT119615) and Fusarium strain BRR R6 (KT119619), respectively with construction of phylogenetic trees. Fusarium sp. BVKT R2 was further optimized for maximum xylanase production and the interaction effects between variables on production of xylanase were studied through response surface methodology. The optimal conditions for maximal production of xylanase were sorbitol 1.5%, yeast extract 1.5%, pH of 5.0, Temperature of 32.5°C, and agitation of 175 rpm. Under optimal conditions, the yields of xylanase production by Fusarium sp. BVKT R2 was as high as 4560 U/ml in SmF. Incubation of different lignocellulosic biomasses with crude enzyme of Fusarium sp. BVKT R2 at 37°C for 72 h could achieve about 45% saccharification. The results suggest that Fusarium sp. BVKT R2 has potential applications in saccharification process of biomass.
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Affiliation(s)
- Golla Ramanjaneyulu
- Department of Microbiology, Sri Krishnadevaraya UniversityAnantapuramu, India
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Lydia Rajakumari M, Saravana Kumari P. Prevalence of Candida species in the buccal cavity of diabetic and non-diabetic individuals in and around Pondicherry. J Mycol Med 2016; 26:359-367. [PMID: 27601306 DOI: 10.1016/j.mycmed.2016.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/29/2016] [Accepted: 08/02/2016] [Indexed: 10/21/2022]
Abstract
OBJECTIVES The aim of the present study was to determine the prevalence of Candida in the buccal cavity of diabetic and non-diabetic individuals in and around Pondicherry, India and to analyse the antifungal susceptibility profile of the selected isolates. MATERIALS AND METHODS A total of 400 buccal samples, 200 each from diabetic and non-diabetic healthy individuals were included in the study. Sabouraud's dextrose agar was used for isolation of Candida species. Identification was performed through microscopy, germ tube test, sugar fermentation test, sugar assimilation test and by using Hichrome agar. Distinct and phenotypically representative colonies were selected and subjected to ITS analysis. In vitro antifungal susceptibility testing for the isolated Candida species was performed using E-test. RESULTS Results revealed that the prevalence of Candida species in diabetic individuals was higher when compared with non-diabetic healthy individuals. The most predominantly isolated species in diabetic and non-diabetic individuals from buccal cavity was Candida albicans. C. tropicalis was predominant among the non-albicans Candida isolated from both diabetic and non-diabetic individuals. Among denture wearers C. glabrata was predominant. In vitro antifungal susceptibility testing shows that ketoconazole, fluconazole and itraconazole were effective against the isolated Candida species. CONCLUSIONS The rate of candidal carriage in diabetic individuals is higher. Different species of Candida are present in the oral cavity of diabetic individuals. There may be a positive correlation between glycemic control and candidal colonization. In vitro antifungal susceptibility testing of Candia species are required for proper management and treatment of candidal infections.
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Affiliation(s)
- M Lydia Rajakumari
- Research and Development Centre, Bharathiar University, Coimbatore, Tamil Nadu, India; Department of Microbiology, Indira Gandhi College of Arts and Science, Kathirkamam, Pondicherry 605009, India.
| | - P Saravana Kumari
- Department of Microbiology, Sree Narayana Guru College, Coimbatore, Tamil Nadu, India
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Oren I, Hardak E, Zuckerman T, Geffen Y, Hoffman R, Yigla M, Avivi I. Does molecular analysis increase the efficacy of bronchoalveolar lavage in the diagnosis and management of respiratory infections in hemato-oncological patients? Int J Infect Dis 2016; 50:48-53. [PMID: 27484225 DOI: 10.1016/j.ijid.2016.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 07/17/2016] [Accepted: 07/18/2016] [Indexed: 10/21/2022] Open
Abstract
OBJECTIVES The identification of the specific pathogen responsible for a respiratory infection in patients with hematological malignancies (HM) would ensure relevant treatment and prevent toxicity associated with anti-infective therapy. This large-scale study aimed to explore the clinical impact of fiberoptic bronchoscopy with bronchoalveolar lavage (FOB-BAL) in conjunction with molecular analysis on the diagnosis and management of respiratory infections in hemato-oncological patients. METHODS All consecutive patients with HM and pulmonary infiltrates, who underwent FOB-BAL between January 2008 and January 2013, were included in the analysis. Clinical characteristics, FOB-BAL results, and treatment adjustments were recorded, and factors predicting a positive BAL were assessed. RESULTS Four hundred and twenty-five FOB-BAL procedures were analyzed. BAL revealed a specific diagnosis in 219 (51.5%) patients, 208 of them with a pulmonary infection. Infectious etiological agents found were mainly Aspergillus spp (n=142), bacterial species (n=44), and Pneumocystis jirovecii (n=34). Multivariate analysis showed that a lymphoproliferative disease, ≥2 symptoms (dyspnea/cough/hemoptysis/pleuritic pain), and less than 4 days between symptom appearance and FOB-BAL, predicted a positive FOB-BAL result. BAL results prompted a treatment modification in 48% of subjects. CONCLUSIONS FOB-BAL in conjunction with molecular assays is efficient in the rapid detection of life-threatening infections, allowing for adjustment of anti-infective therapy, which may result in better outcomes and reduce treatment-related toxicity.
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Affiliation(s)
- Ilana Oren
- Unit of Infectious Diseases, Rambam Health Care Campus, Haifa, Israel; The Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Emilia Hardak
- The Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel; Division of Pulmonary Medicine, Rambam Health Care Campus, 8 Ha'Aliya Street, Haifa 31096, Israel.
| | - Tsila Zuckerman
- The Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel; Department of Hematology and Bone Marrow Transplantation, Rambam Health Care Campus, Haifa, Israel
| | - Yuval Geffen
- Clinical Microbiology Laboratory, Rambam Health Care Campus, Haifa, Israel
| | - Ron Hoffman
- The Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel; Department of Hematology and Bone Marrow Transplantation, Rambam Health Care Campus, Haifa, Israel
| | - Mordechai Yigla
- The Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel; Division of Pulmonary Medicine, Rambam Health Care Campus, 8 Ha'Aliya Street, Haifa 31096, Israel
| | - Irit Avivi
- Department of Hematology and Bone Marrow Transplantation, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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Kim GY, Jeon JS, Kim JK. Isolation Frequency Characteristics of Candida Species from Clinical Specimens. MYCOBIOLOGY 2016; 44:99-104. [PMID: 27433120 PMCID: PMC4945544 DOI: 10.5941/myco.2016.44.2.99] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 05/31/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Candida spp. is an invasive infectious fungus, a major risk factor that can increase morbidity and mortality in hospitalized patients. In this study, 2,508 Candida spp. were isolated from various clinical specimens collected from university hospitals from July 2011 to October 2014. They were identified in order to determine isolation frequencies and characteristics by specimen, gender, age group, year, season, and month. The strain-specific isolation rate of Candida spp. is in the order of Candida albicans (1,218 strains, 48.56%), Candida glabrata (416 strains, 16.59%), Candida utilis (305 strains, 12.16%), Candida tropicalis (304 strains, 12.12%), and Candida parapsilosis (116 strains, 4.63%) and these five species accounted for more than 94% of the total strains. Of the specimens, Candida spp. were most frequently isolated from urine-catheter, followed by urine-voided, blood, sputum, other, open pus, vaginal discharge, Tip, ear discharge, bronchial aspiration and bile, in that order. Looking at the age distribution, the detection rate of patients in their 60s and older was significantly higher at 75.8% (1,900/2,508). The detection rate of patients in their 20s and younger was shown to be very low at 2.55% (64/2,508). By year, the detection rate of non-albicans Candida spp. showed a tendency to gradually increase each year compared with C. albicans. As isolation of Candida spp. from clinical samples at the specie level can vary depending on characteristics of the patient, sample, season, etc., continual studies are required.
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Affiliation(s)
- Ga-Yeon Kim
- Department of Dental Hygiene, College of Health Sciences, Dankook University, Cheonan 31116, Korea
| | - Jae-Sik Jeon
- Department of Laboratory Medicine, College of Medicine, Dankook University, Cheonan 31116, Korea
| | - Jae Kyung Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Dankook University, Cheonan 31116, Korea
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Sipiczki M, Pfliegler WP, Safar SVB, Morais PB, Rosa CA. Metahyphopichia laotica gen. nov., sp. nov., a polymorphic yeast related to Hyphopichia. Int J Syst Evol Microbiol 2016; 66:2550-2557. [PMID: 27088571 DOI: 10.1099/ijsem.0.001091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Four strains alternating between yeast and filamentous growth morphologies were isolated from flowers in two regions of Laos. In liquid environment the isolates propagated by budding and developed irregularly shaped pseudohyphae. On solid media, their yeast cells switched to hyphal growth which could return to the yeast phase by developing lateral blastoconidia. The sequences of the D1/D2 domains of the large subunit (LSU) 26S rRNA genes, the internal transcribed spacer (ITS) regions and the small subunit (SSU) 18S rRNA genes were identical in the four strains and differed from the corresponding sequences of other yeast species available in databases by at least 11 % (D1/D2), 13 % (ITS) and 7 % (SSU). In an independent project, two strains with D1/D2 and ITS sequences very similar to those of the Laotian strains were found in bark samples collected in Brazil. The six strains also differed from the closest yeast species in physiological properties, indicating that they represented a hitherto undescribed species. Phylogenetic analysis of the D1/D2 sequences, and the concatenated sequences of the SSU rRNA genes, D1/D2 domains of LSU rRNA genes as well as the protein-encoding genes ACT1 and TEF1 placed thestrains close to Hyphopichia. To reflect this position, the novel genus name Metahyphopichia gen. nov. and the novel species name Metahyphopichia laotica gen. nov., sp. nov. are proposed for them. The type strain of the type species is 11-1006T(=CBS 13022T=CCY 092-001-001T=NCAIM Y.02126T) and was isolated in Luang Prabang (Laos). MycoBank registration numbers are MB 808253 (Metahyphopichia) and MB 808254 (Metahyphopichia laotica).
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Affiliation(s)
- Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, 4032 Debrecen, Hungary
| | - Walter P Pfliegler
- Department of Genetics and Applied Microbiology, University of Debrecen, 4032 Debrecen, Hungary
| | - Silvana V B Safar
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais Belo Horizonte, MG 31270-901, Brazil
| | - Paula B Morais
- Laboratorio de Microbiologia Ambiental e Biotecnologia, Universidade Federal do Tocantins, Palmas, TO 77020-220, Brazil
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais Belo Horizonte, MG 31270-901, Brazil
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Genetic diversity and molecular evolution of Naga King Chili inferred from internal transcribed spacer sequence of nuclear ribosomal DNA. Meta Gene 2015; 7:56-63. [PMID: 26862481 PMCID: PMC4707246 DOI: 10.1016/j.mgene.2015.11.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/17/2015] [Accepted: 11/30/2015] [Indexed: 11/29/2022] Open
Abstract
Sequences of the Internal Transcribed Spacer (ITS1-5.8S-ITS2) of nuclear ribosomal DNAs were explored to study the genetic diversity and molecular evolution of Naga King Chili. Our study indicated the occurrence of nucleotide polymorphism and haplotypic diversity in the ITS regions. The present study demonstrated that the variability of ITS1 with respect to nucleotide diversity and sequence polymorphism exceeded that of ITS2. Sequence analysis of 5.8S gene revealed a much conserved region in all the accessions of Naga King Chili. However, strong phylogenetic information of this species is the distinct 13 bp deletion in the 5.8S gene which discriminated Naga King Chili from the rest of the Capsicum sp. Neutrality test results implied a neutral variation, and population seems to be evolving at drift–mutation equilibrium and free from directed selection pressure. Furthermore, mismatch analysis showed multimodal curve indicating a demographic equilibrium. Phylogenetic relationships revealed by Median Joining Network (MJN) analysis denoted a clear discrimination of Naga King Chili from its closest sister species (Capsicumchinense and Capsicumfrutescens). The absence of star-like network of haplotypes suggested an ancient population expansion of this chili. The phylogenetic relationship of Naga King Chili showed a clear grouping from C. chinense and C. frutescens. Naga King Chili population seems to be evolving at drift-mutation equilibrium and free from directed selection pressure. Our findings revealed an ancient evolutionary history of this species.
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Kiraz N, Oz Y, Aslan H, Erturan Z, Ener B, Akdagli SA, Muslumanoglu H, Cetinkaya Z. Is the extraction by Whatman FTA filter matrix technology and sequencing of large ribosomal subunit D1-D2 region sufficient for identification of clinical fungi? Mycoses 2015; 58:588-97. [PMID: 26293550 DOI: 10.1111/myc.12365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/05/2015] [Accepted: 07/07/2015] [Indexed: 11/30/2022]
Abstract
Although conventional identification of pathogenic fungi is based on the combination of tests evaluating their morphological and biochemical characteristics, they can fail to identify the less common species or the differentiation of closely related species. In addition these tests are time consuming, labour-intensive and require experienced personnel. We evaluated the feasibility and sufficiency of DNA extraction by Whatman FTA filter matrix technology and DNA sequencing of D1-D2 region of the large ribosomal subunit gene for identification of clinical isolates of 21 yeast and 160 moulds in our clinical mycology laboratory. While the yeast isolates were identified at species level with 100% homology, 102 (63.75%) clinically important mould isolates were identified at species level, 56 (35%) isolates at genus level against fungal sequences existing in DNA databases and two (1.25%) isolates could not be identified. Consequently, Whatman FTA filter matrix technology was a useful method for extraction of fungal DNA; extremely rapid, practical and successful. Sequence analysis strategy of D1-D2 region of the large ribosomal subunit gene was found considerably sufficient in identification to genus level for the most clinical fungi. However, the identification to species level and especially discrimination of closely related species may require additional analysis.
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Affiliation(s)
- Nuri Kiraz
- Cerrahpasa Medical Faculty, Department of Microbiology, Division of Mycology, Istanbul University, Istanbul, Turkey
| | - Yasemin Oz
- Faculty of Medicine, Department of Microbiology, Division of Mycology, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Huseyin Aslan
- Faculty of Medicine, Department of Medical Genetics, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Zayre Erturan
- Faculty of Medicine, Department of Microbiology, Division of Mycology, Istanbul University, Istanbul, Turkey
| | - Beyza Ener
- Faculty of Medicine, Department of Microbiology, Uludag University, Bursa, Turkey
| | - Sevtap Arikan Akdagli
- Faculty of Medicine, Department of Microbiology, Hacettepe University, Ankara, Turkey
| | - Hamza Muslumanoglu
- Faculty of Science and Arts, Department of Molecular Biology, Yildiz Technical University, Istanbul, Turkey
| | - Zafer Cetinkaya
- Department of Microbiology, Goztepe Research and Education Hospital, Istanbul, Turkey
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Cohort Study of Airway Mycobiome in Adult Cystic Fibrosis Patients: Differences in Community Structure between Fungi and Bacteria Reveal Predominance of Transient Fungal Elements. J Clin Microbiol 2015; 53:2900-7. [PMID: 26135861 DOI: 10.1128/jcm.01094-15] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 06/22/2015] [Indexed: 12/28/2022] Open
Abstract
The respiratory mycobiome is an important but understudied component of the human microbiota. Like bacteria, fungi can cause severe lung diseases, but their infection rates are much lower. This study compared the bacterial and fungal communities of sputum samples from a large cohort of 56 adult patients with cystic fibrosis (CF) during nonexacerbation periods and under continuous antibiotic treatment. Molecular fingerprinting based on single-strand conformation polymorphism (SSCP) analysis revealed fundamental differences between bacterial and fungal communities. Both groups of microorganisms were taxonomically classified by identification of gene sequences (16S rRNA and internal transcript spacer), and prevalences of single taxa were determined for the entire cohort. Major bacterial pathogens were frequently observed, whereas fungi of known pathogenicity in CF were detected only in low numbers. Fungal species richness increased without reaching a constant level (saturation), whereas bacterial richness showed saturation after 50 patients were analyzed. In contrast to bacteria, a large number of fungal species were observed together with high fluctuations over time and among patients. These findings demonstrated that the mycobiome was dominated by transient species, which strongly suggested that the main driving force was their presence in inhaled air rather than colonization. Considering the high exposure of human airways to fungal spores, we concluded that fungi have low colonization abilities in CF, and colonization by pathogenic fungal species may be considered a rare event. A comprehensive understanding of the conditions promoting fungal colonization may offer the opportunity to prevent colonization and substantially reduce or even eliminate fungus-related disease progression in CF.
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Abstract
Understanding of the taxonomy and phylogeny of Cryptococcus gattii has been advanced by modern molecular techniques. C. gattii probably diverged from Cryptococcus neoformans between 16 million and 160 million years ago, depending on the dating methods applied, and maintains diversity by recombining in nature. South America is the likely source of the virulent C. gattii VGII molecular types that have emerged in North America. C. gattii shares major virulence determinants with C. neoformans, although genomic and transcriptomic studies revealed that despite similar genomes, the VGIIa and VGIIb subtypes employ very different transcriptional circuits and manifest differences in virulence phenotypes. Preliminary evidence suggests that C. gattii VGII causes severe lung disease and death without dissemination, whereas C. neoformans disseminates readily to the central nervous system (CNS) and causes death from meningoencephalitis. Overall, currently available data indicate that the C. gattii VGI, VGII, and VGIII molecular types more commonly affect nonimmunocompromised hosts, in contrast to VGIV. New, rapid, cheap diagnostic tests and imaging modalities are assisting early diagnosis and enabling better outcomes of cerebral cryptococcosis. Complications of CNS infection include increased intracranial pressure, severe neurological sequelae, and development of immune reconstitution syndrome, although the mortality rate is low. C. gattii VGII isolates may exhibit higher fluconazole MICs than other genotypes. Optimal therapeutic regimens are yet to be determined; in most cases, initial therapy with amphotericin B and 5-flucytosine is recommended.
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Durney BC, Bachert BA, Sloane HS, Lukomski S, Landers JP, Holland LA. Reversible phospholipid nanogels for deoxyribonucleic acid fragment size determinations up to 1500 base pairs and integrated sample stacking. Anal Chim Acta 2015; 880:136-44. [PMID: 26092346 DOI: 10.1016/j.aca.2015.03.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/02/2015] [Accepted: 03/04/2015] [Indexed: 01/13/2023]
Abstract
Phospholipid additives are a cost-effective medium to separate deoxyribonucleic acid (DNA) fragments and possess a thermally-responsive viscosity. This provides a mechanism to easily create and replace a highly viscous nanogel in a narrow bore capillary with only a 10°C change in temperature. Preparations composed of dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) self-assemble, forming structures such as nanodisks and wormlike micelles. Factors that influence the morphology of a particular DMPC-DHPC preparation include the concentration of lipid in solution, the temperature, and the ratio of DMPC and DHPC. It has previously been established that an aqueous solution containing 10% phospholipid with a ratio of [DMPC]/[DHPC]=2.5 separates DNA fragments with nearly single base resolution for DNA fragments up to 500 base pairs in length, but beyond this size the resolution decreases dramatically. A new DMPC-DHPC medium is developed to effectively separate and size DNA fragments up to 1500 base pairs by decreasing the total lipid concentration to 2.5%. A 2.5% phospholipid nanogel generates a resolution of 1% of the DNA fragment size up to 1500 base pairs. This increase in the upper size limit is accomplished using commercially available phospholipids at an even lower material cost than is achieved with the 10% preparation. The separation additive is used to evaluate size markers ranging between 200 and 1500 base pairs in order to distinguish invasive strains of Streptococcus pyogenes and Aspergillus species by harnessing differences in gene sequences of collagen-like proteins in these organisms. For the first time, a reversible stacking gel is integrated in a capillary sieving separation by utilizing the thermally-responsive viscosity of these self-assembled phospholipid preparations. A discontinuous matrix is created that is composed of a cartridge of highly viscous phospholipid assimilated into a separation matrix of low viscosity. DNA sample stacking is facilitated with longer injection times without sacrificing separation efficiency.
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Affiliation(s)
- Brandon C Durney
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
| | - Beth A Bachert
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, United States
| | - Hillary S Sloane
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Slawomir Lukomski
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, United States
| | - James P Landers
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States; Department of Mechanical Engineering, University of Virginia, Charlottesville, VA 22904, United States; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22904, United States
| | - Lisa A Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States.
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Ng BLN, Omarzuki M, Lau GSK, Pannell CM, Yeo TC. A nucleotide signature for identification of Aglaia stellatopilosa Pannell. Mol Biotechnol 2015; 56:671-9. [PMID: 24623047 DOI: 10.1007/s12033-014-9746-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Members of the genus Aglaia have been reported to contain bioactive phytochemicals. The genus, belonging to the Meliaceae family, is represented by at least 120 known species of woody trees or shrubs in the tropical rain forest. As some of these species are very similar in their morphology, taxonomic identification can be difficult. A reliable and definitive molecular method which can identify Aglaia to the level of the species will hence be useful in comparing the content of specific bioactive compounds between the species of this genus. Here, we report the analysis of DNA sequences in the internal transcribed spacer (ITS) of the nuclear ribosomal DNA and the observation of a unique nucleotide signature in the ITS that can be used for the identification of Aglaia stellatopilosa. The nucleotide signature consists of nine bases over the length of the ITS sequence (654 bp). This uniqueness was validated in 37 samples identified as Aglaia stellatopilosa by an expert taxonomist, whereas the nucleotide signature was lacking in a selection of other Aglaia species and non-Aglaia genera. This finding suggests that molecular typing could be utilized in the identification of Aglaia stellatopilosa.
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Affiliation(s)
- Belinda Ling Nah Ng
- Sarawak Biodiversity Centre, KM20, Jalan Borneo Heights, Semengoh, Locked Bag No. 3032, 93990, Kuching, Sarawak, Malaysia
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Santos JRA, Holanda RA, Frases S, Bravim M, Araujo GDS, Santos PC, Costa MC, Ribeiro MJA, Ferreira GF, Baltazar LM, Miranda AS, Oliveira DB, Santos CMA, Fontes ACL, Gouveia LF, Resende-Stoianoff MA, Abrahão JS, Teixeira AL, Paixão TA, Souza DG, Santos DA. Fluconazole alters the polysaccharide capsule of Cryptococcus gattii and leads to distinct behaviors in murine Cryptococcosis. PLoS One 2014; 9:e112669. [PMID: 25392951 PMCID: PMC4231059 DOI: 10.1371/journal.pone.0112669] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/10/2014] [Indexed: 11/30/2022] Open
Abstract
Cryptococcus gattii is an emergent human pathogen. Fluconazole is commonly used for treatment of cryptococcosis, but the emergence of less susceptible strains to this azole is a global problem and also the data regarding fluconazole-resistant cryptococcosis are scarce. We evaluate the influence of fluconazole on murine cryptococcosis and whether this azole alters the polysaccharide (PS) from cryptococcal cells. L27/01 strain of C. gattii was cultivated in high fluconazole concentrations and developed decreased drug susceptibility. This phenotype was named L27/01F, that was less virulent than L27/01 in mice. The physical, structural and electrophoretic properties of the PS capsule of L27/01F were altered by fluconazole. L27/01F presented lower antiphagocytic properties and reduced survival inside macrophages. The L27/01F did not affect the central nervous system, while the effect in brain caused by L27/01 strain began after only 12 hours. Mice infected with L27/01F presented lower production of the pro-inflammatory cytokines, with increased cellular recruitment in the lungs and severe pulmonary disease. The behavioral alterations were affected by L27/01, but no effects were detected after infection with L27/01F. Our results suggest that stress to fluconazole alters the capsule of C. gattii and influences the clinical manifestations of cryptococcosis.
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Affiliation(s)
- Julliana Ribeiro Alves Santos
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Rodrigo Assunção Holanda
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Susana Frases
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Biotecnologia (LABIO), Instituto Nacional de Metrologia, Normalização e Qualidade Industrial (INMETRO), Rio de Janeiro, Brazil
| | - Mayara Bravim
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Glauber de S. Araujo
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Biotecnologia (LABIO), Instituto Nacional de Metrologia, Normalização e Qualidade Industrial (INMETRO), Rio de Janeiro, Brazil
| | - Patrícia Campi Santos
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Marliete Carvalho Costa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Maira Juliana Andrade Ribeiro
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Gabriella Freitas Ferreira
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Ludmila Matos Baltazar
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Aline Silva Miranda
- Laboratório Interdisciplinar de Investigação Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Danilo Bretas Oliveira
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Carolina Maria Araújo Santos
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Alide Caroline Lima Fontes
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Ludmila Ferreira Gouveia
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | | | - Jonatas Santos Abrahão
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Antônio Lúcio Teixeira
- Laboratório Interdisciplinar de Investigação Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Tatiane Alves Paixão
- Departamento de Patologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Danielle G. Souza
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Daniel Assis Santos
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
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de la Bastide PY, Leung WL, Hintz WE. Species composition of the genus Saprolegnia in fin fish aquaculture environments, as determined by nucleotide sequence analysis of the nuclear rDNA ITS regions. Fungal Biol 2014; 119:27-43. [PMID: 25601147 DOI: 10.1016/j.funbio.2014.10.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 09/29/2014] [Accepted: 10/22/2014] [Indexed: 11/26/2022]
Abstract
The ITS region of the rDNA gene was compared for Saprolegnia spp. in order to improve our understanding of nucleotide sequence variability within and between species of this genus, determine species composition in Canadian fin fish aquaculture facilities, and to assess the utility of ITS sequence variability in genetic marker development. From a collection of more than 400 field isolates, ITS region nucleotide sequences were studied and it was determined that there was sufficient consistent inter-specific variation to support the designation of species identity based on ITS sequence data. This non-subjective approach to species identification does not rely upon transient morphological features. Phylogenetic analyses comparing our ITS sequences and species designations with data from previous studies generally supported the clade scheme of Diéguez-Uribeondo et al. (2007) and found agreement with the molecular taxonomic cluster system of Sandoval-Sierra et al. (2014). Our Canadian ITS sequence collection will thus contribute to the public database and assist the clarification of Saprolegnia spp. taxonomy. The analysis of ITS region sequence variability facilitated genus- and species-level identification of unknown samples from aquaculture facilities and provided useful information on species composition. A unique ITS-RFLP for the identification of S. parasitica was also described.
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Affiliation(s)
- Paul Y de la Bastide
- Biology Department, Centre for Forest Biology, University of Victoria, P.O. Box 3020 STN CSC, Victoria, B.C. V8W 3N5, Canada.
| | - Wai Lam Leung
- Biology Department, Centre for Forest Biology, University of Victoria, P.O. Box 3020 STN CSC, Victoria, B.C. V8W 3N5, Canada.
| | - William E Hintz
- Biology Department, Centre for Forest Biology, University of Victoria, P.O. Box 3020 STN CSC, Victoria, B.C. V8W 3N5, Canada.
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Massive fungal biodiversity data re-annotation with multi-level clustering. Sci Rep 2014; 4:6837. [PMID: 25355642 PMCID: PMC4213798 DOI: 10.1038/srep06837] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 10/10/2014] [Indexed: 11/08/2022] Open
Abstract
With the availability of newer and cheaper sequencing methods, genomic data are being generated at an increasingly fast pace. In spite of the high degree of complexity of currently available search routines, the massive number of sequences available virtually prohibits quick and correct identification of large groups of sequences sharing common traits. Hence, there is a need for clustering tools for automatic knowledge extraction enabling the curation of large-scale databases. Current sophisticated approaches on sequence clustering are based on pairwise similarity matrices. This is impractical for databases of hundreds of thousands of sequences as such a similarity matrix alone would exceed the available memory. In this paper, a new approach called MultiLevel Clustering (MLC) is proposed which avoids a majority of sequence comparisons, and therefore, significantly reduces the total runtime for clustering. An implementation of the algorithm allowed clustering of all 344,239 ITS (Internal Transcribed Spacer) fungal sequences from GenBank utilizing only a normal desktop computer within 22 CPU-hours whereas the greedy clustering method took up to 242 CPU-hours.
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Genetic Characterization of Fungi Isolated from the Environmental Swabs collected from a Compounding Center Known to Cause Multistate Meningitis Outbreak in United States Using ITS Sequencing. Pathogens 2014; 3:732-42. [PMID: 25438021 PMCID: PMC4243438 DOI: 10.3390/pathogens3030732] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/31/2014] [Accepted: 08/19/2014] [Indexed: 02/06/2023] Open
Abstract
A multistate fungal meningitis outbreak started in September of 2012 which spread in 20 states of the United States. The outbreak has been fatal so far, and has affected 751 individuals with 64 deaths among those who received contaminated spinal injections manufactured by a Compounding Center located in Massachusetts. In a preliminary study, Food and Drug Administration (FDA) investigated the outbreak in collaboration with Centers for Disease Control and Prevention (CDC), state and local health departments, and identified four fungal and several bacterial contaminations in the recalled unopened injection vials. This follow-up study was carried out to assess DNA sequencing of the ITS1 region of rRNA gene for rapid identification of fungal pathogens during public health outbreak investigations. A total of 26 environmental swabs were collected from several locations at the manufacturing premises of the Compounding Center known to have caused the outbreak. The swab samples were initially examined by conventional microbiologic protocols and a wide range of fungal species were recovered. Species-identification of these microorganisms was accomplished by nucleotide sequencing of ITS1 region of rRNA gene. Analysis of data confirmed 14 additional fungal species in the swabs analyzed.
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Park MS, Lee H, Oh SY, Jung PE, Seok SJ, Fong JJ, Lim YW. Species delimitation of three species within the Russula subgenus Compacta in Korea: R. eccentrica, R. nigricans, and R. subnigricans. J Microbiol 2014; 52:631-8. [PMID: 24994012 DOI: 10.1007/s12275-014-4168-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 04/20/2014] [Accepted: 04/21/2014] [Indexed: 11/29/2022]
Abstract
Distinguishing individual Russula species can be very difficult due to extensive phenotypic plasticity and obscure morphological and anatomical discontinuities. In this study, we use the internal transcribed spacer (ITS) and 28S nuclear ribosomal large subunit (LSU) markers to identify and study the genetic diversity of species in the Russula subgenus Compacta in Korea. We focus on two morphologically similar species that are often misidentified for each other: R. nigricans and R. subnigricans. Based on molecular phylogenetic analyses, we identify three subgroups of R. nigricans, with two from Asia and one from Europe/North America. Surprisingly, we find Korean R. subnigricans are more closely related to R. eccentrica from North America than the type specimen of R. subnigricans from Japan. These molecular data, along with habitat data, reveal that Korean R. subnigricans had previously been misclassified and should now be recognized as R. eccentrica. Both ITS and LSU exhibit high interspecific and low intraspecific variation for R. eccentrica, R. nigricans, and R. subnigricans. These markers provide enough resolutional power to differentiate these species and uncover phylogeographic structure, and will be powerful tools for future ecological studies of Russula.
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Affiliation(s)
- Myung Soo Park
- School of Biological Sciences, Seoul National University, Seoul, 151-747, Republic of Korea
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Molecular identification of isolated fungi from unopened containers of greek yogurt by DNA sequencing of internal transcribed spacer region. Pathogens 2014; 3:499-509. [PMID: 25438008 PMCID: PMC4243425 DOI: 10.3390/pathogens3030499] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/11/2014] [Accepted: 06/19/2014] [Indexed: 12/12/2022] Open
Abstract
In our previous study, we described the development of an internal transcribed spacer (ITS)1 sequencing method, and used this protocol in species-identification of isolated fungi collected from the manufacturing areas of a compounding company known to have caused the multistate fungal meningitis outbreak in the United States. In this follow-up study, we have analyzed the unopened vials of Greek yogurt from the recalled batch to determine the possible cause of microbial contamination in the product. A total of 15 unopened vials of Greek yogurt belonging to the recalled batch were examined for the detection of fungi in these samples known to cause foodborne illness following conventional microbiological protocols. Fungi were isolated from all of the 15 Greek yogurt samples analyzed. The isolated fungi were genetically typed by DNA sequencing of PCR-amplified ITS1 region of rRNA gene. Analysis of data confirmed all of the isolated fungal isolates from the Greek yogurt to be Rhizomucor variabilis. The generated ITS1 sequences matched 100% with the published sequences available in GenBank. In addition, these yogurt samples were also tested for the presence of five types of bacteria (Salmonella, Listeria, Staphylococcus, Bacillus and Escherichia coli) causing foodborne disease in humans, and found negative for all of them.
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Szweda P, Gucwa K, Naumiuk L, Romanowska E, Dzierzanowska-Fangrat K, Brillowska-Dabrowska A, Wojciechowska-Koszko I, Milewski S. Evaluation of possibilities in identification and susceptibility testing for Candida glabrata clinical isolates with the Integral System Yeast Plus (ISYP). Acta Microbiol Immunol Hung 2014; 61:161-72. [PMID: 24939684 DOI: 10.1556/amicr.61.2014.2.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The aim of this study was to evaluate possibilities of correct identification and susceptibility testing of C. glabrata clinical isolates with Integral System Yeast Plus (ISYP). For species identification, as the reference method, API Candida test and species-specific PCR reactions were used. The potential of antifungal susceptibility testing by the ISYP test was compared with the Sensititre Yeast One. Whilst the reference methods confirmed that the received population (n = 65 isolates) represented only C. glabrata, identification with the ISYP system showed correct data only in the case of 18 strains tested (27.7%). Species identification of the other 47 strains with the ISYP test was not possible at all. Significant differences were also observed for drug susceptibility testing carried out by the ISYP and the Sensititre Yeast One. The highest level of disagreement in classifying strains as resistant or susceptible estimated, as 73.9% and 40.0%, was observed for itraconazole and amphotericin B, respectively. Satisfactory results were only obtained for 5-fluorocytosine with 93.8% agreement between both methods. In our opinion the idea of the ISYP system is certainly good. The combination of identification ability and drug susceptibility testing in one test is very important, especially from a clinical point of view. However, the current version of the ISYP has many disadvantages. We would like to encourage the manufacturer to make an effort and develop a new, more accurate version of the test.
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Affiliation(s)
- Piotr Szweda
- 1 Gdansk University of Technology Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry ul. G. Narutowicza 11/12 80-233 Gdansk Poland
| | - Katarzyna Gucwa
- 1 Gdansk University of Technology Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry ul. G. Narutowicza 11/12 80-233 Gdansk Poland
| | - Lukasz Naumiuk
- 2 Hospital of the Medical University of Gdansk Department of Clinical Microbiology ul. Debinki 7 80-954 Gdansk Poland
| | - Ewa Romanowska
- 3 The Children’s Memorial Health Institute Department of Clinical Microbiology and Immunology Aleja Dzieci Polskich 20 04-730 Warsaw Poland
| | - Katarzyna Dzierzanowska-Fangrat
- 3 The Children’s Memorial Health Institute Department of Clinical Microbiology and Immunology Aleja Dzieci Polskich 20 04-730 Warsaw Poland
| | - Anna Brillowska-Dabrowska
- 4 Gdansk University of Technology Department of Microbiology, Faculty of Chemistry ul. Debinki 7 80-954 Gdansk Poland
| | - Iwona Wojciechowska-Koszko
- 5 Pomeranian Medical University Department of Microbiology and Immunology Powstancow Wielkopolskich 72 70-111 Szczecin Poland
| | - Slawomir Milewski
- 1 Gdansk University of Technology Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry ul. G. Narutowicza 11/12 80-233 Gdansk Poland
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