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Saad-Hussein A, Soliman KM, Moubarz G. 18S rRNA gene sequencing for environmental aflatoxigenic fungi and risk of hepatic carcinoma among exposed workers. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2022; 57:174-182. [PMID: 35236253 DOI: 10.1080/10934529.2022.2046428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/11/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Aspergillus exposure causes an increase in aflatoxin (AF) levels among exposed workers thereby increasing their risk of developing hepatocellular carcinoma (HCC). This study attempted to determine the presence of airborne aflatoxigenic fungi in environment of waste water treatment plant (WWTP); and study the hepatic cancer risks among exposed workers, emphasizing the role of glutathione S-transferases (GST) gene polymorphism protecting against the risk of hepatic cancer development due to exposure to AFs. The study isolated and identified different Aspergillus species producing AFs in air samples from WWTP sites using 18S ribosomal ribonucleic acid (18S rRNA) gene sequencing technique. GST gene polymorphisms were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). A significant increase in blood AF levels was found among WWTP exposed workers. The occurrence of GSTT1& M1 gene polymorphism in 6% of the workers was accompanied by significant decrease in the levels of AFs and alpha fetoprotein (AFP). In conclusion, Aspergillus-producing AFs were found in air of WWTP. Continuous exposure to AF-producing fungi caused elevated AF-levels in exposed workers. However only workers with heterozygous GSTT1& M1 genotypes can detoxify AFs, thereby decreasing the risk of HCC development among exposed workers.
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Affiliation(s)
- Amal Saad-Hussein
- Environmental & Occupational Medicine Department, National Research Centre, Dokki, Cairo, Egypt
| | - Kawther M Soliman
- Food Toxicology and Contaminants Department, National Research Centre, Dokki, Cairo, Egypt
| | - Gehan Moubarz
- Environmental & Occupational Medicine Department, National Research Centre, Dokki, Cairo, Egypt
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The Fibrolytic Enzyme Profiles and the Composition of Fungal Communities in Donkey Cecum-Colon Ecosystem. Animals (Basel) 2022; 12:ani12040412. [PMID: 35203120 PMCID: PMC8868365 DOI: 10.3390/ani12040412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/08/2022] [Indexed: 11/22/2022] Open
Abstract
Simple Summary The donkey hindgut is a microbial-rich ecosystem in which caecum and colon fungi play an important role in dietary fiber degradation. In addition, the fibrolytic enzymes produced by hindgut microorganisms are key to the ability of equines to hydrolysis plant fiber. In the present study, the fibrolytic enzyme activities within donkey caecum and colon were firstly measured by spectrophotometry. The dorsal colon presented a higher fibrolytic enzyme activity in comparison with caecum. The fungal community composition along donkey caecum and colon was determined by sequencing an internal transcribed spacer region (ITS) using Illumina MiSeq. The predominant fungi at phylum level were Ascomycota, Basidiomycota, and Neocallimastigomycota. The Aspergillus, Wallemia, Phanerochaete, Fusarium, and Penicillium were detected as the dominant genera, but their metabolic and functional significance in donkey cecum-colon ecosystem need further investigation. In terms of the anaerobic fungi Neocallimastigomycota, its abundance was greater in donkey colon than in caecum. The relative abundance of enzymes related to plant cell wall breakdown were also predicted by PICRUSt, and they were also greater in donkey colon than in caecum. The present study provided new information about fibrolytic enzyme profiles and fungal communities in donkey hindgut. The findings could therefore contribute to the further understanding of the fungal taxa and their dietary fiber degradation mechanisms in donkey hindgut ecosystem. Abstract The fibrolytic enzymes and the hindgut fungi in donkey cecum-colon ecosystem play an important role in dietary fiber digestion. A better understanding of the fibrolytic enzyme profiles and the fungal community along donkey caecum and colon is key for optimizing hindgut function. In the present study, the fibrolytic enzyme activities within donkey caecum and colon were firstly measured by spectrophotometry. Activities of carboxymethyl cellulase, avicelase, xylanase, and acetyl esterase were greater in donkey dorsal colon than in caecum, indicating that the colon microorganisms may be more efficient in producing fibrolytic enzymes compared to caecum microbes. The fungal community composition along donkey hindgut was determined by sequencing ITS region using Illumina MiSeq. Three fungal phyla were identified by sequence comparison: Ascomycota (66.8%–74.4%), Basidiomycota (21.6%–30.9%), and Neocallimastigomycota (0.9%–3.3%). The Aspergillus, Wallemia, Phanerochaete, Fusarium, and Penicillium were detected as the dominant genera, but their metabolic and functional significance in donkey cecum-colon ecosystem need further investigation. In terms of the anaerobic fungi Neocallimastigomycota, its abundance was greater in donkey colon than in caecum (p < 0.05), indicating that the donkey hindgut region was associated with differences in fungal community composition. Moreover, the relative abundance of enzymes related to plant cell wall degradation were predicted by PICRUSt, and they were also lower in caecum than in colon. The present study provided new information about fibrolytic enzyme profiles and fungal composition in donkey hindgut ecosystem.
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Technical challenges for complete implementation of automated growth-based methods for microbiological examination of advanced therapy medicinal products. What's wrong with Candida albicans? Cytotherapy 2022; 24:320-333. [DOI: 10.1016/j.jcyt.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 11/22/2022]
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McLean SA, Cullen L, Gardam DJ, Schofield CJ, Laucirica DR, Sutanto EN, Ling KM, Stick SM, Peacock CS, Kicic A, Garratt LW. Cystic Fibrosis Clinical Isolates of Aspergillus fumigatus Induce Similar Muco-inflammatory Responses in Primary Airway Epithelial Cells. Pathogens 2021; 10:pathogens10081020. [PMID: 34451484 PMCID: PMC8399118 DOI: 10.3390/pathogens10081020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022] Open
Abstract
Aspergillus is increasingly associated with lung inflammation and mucus plugging in early cystic fibrosis (CF) disease during which conidia burden is low and strains appear to be highly diverse. It is unknown whether clinical Aspergillus strains vary in their capacity to induce epithelial inflammation and mucus production. We tested the hypothesis that individual colonising strains of Aspergillus fumigatus would induce different responses. Ten paediatric CF Aspergillus isolates were compared along with two systemically invasive clinical isolates and an ATCC reference strain. Isolates were first characterised by ITS gene sequencing and screened for antifungal susceptibility. Three clusters (A-C) of Aspergillus isolates were identified by ITS. Antifungal susceptibility was variable, particularly for itraconazole. Submerged CF and non-CF monolayers as well as differentiated primary airway epithelial cell cultures were incubated with conidia for 24 h to allow germination. None of the clinical isolates were found to significantly differ from one another in either IL-6 or IL-8 release or gene expression of secretory mucins. Clinical Aspergillus isolates appear to be largely homogenous in their mucostimulatory and immunostimulatory capacities and, therefore, only the antifungal resistance characteristics are likely to be clinically important.
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Affiliation(s)
- Samantha A. McLean
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
| | - Leilani Cullen
- Faculty of Health and Medical Sciences, University of Western Australia, Crawley 6009, Australia; (L.C.); (C.S.P.)
| | - Dianne J. Gardam
- PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch 6150, Australia;
| | - Craig J. Schofield
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
| | - Daniel R. Laucirica
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
- Faculty of Health and Medical Sciences, University of Western Australia, Crawley 6009, Australia; (L.C.); (C.S.P.)
| | - Erika N. Sutanto
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
| | - Kak-Ming Ling
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
- Faculty of Health and Medical Sciences, University of Western Australia, Crawley 6009, Australia; (L.C.); (C.S.P.)
| | - Stephen M. Stick
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
- Faculty of Health and Medical Sciences, University of Western Australia, Crawley 6009, Australia; (L.C.); (C.S.P.)
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Nedlands 6009, Australia
| | - Christopher S. Peacock
- Faculty of Health and Medical Sciences, University of Western Australia, Crawley 6009, Australia; (L.C.); (C.S.P.)
| | - Anthony Kicic
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
- Faculty of Health and Medical Sciences, University of Western Australia, Crawley 6009, Australia; (L.C.); (C.S.P.)
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Nedlands 6009, Australia
- Occupation and Environment, School of Public Health, Curtin University, Bentley 6102, Australia
| | - Luke W. Garratt
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
- Correspondence:
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Jiang D, Wei D, Li H, Wang L, Jiang N, Li Y, Wang M. Natural occurrence of Alternaria mycotoxins in wheat and potential of reducing associated risks using magnolol. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:3071-3077. [PMID: 33124688 DOI: 10.1002/jsfa.10901] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/13/2020] [Accepted: 10/30/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Wheat is one of three major food crops in China. Alternaria species can cause spoilage of wheat with consequent mycotoxin accumulation. Alternariol (AOH), alternariol monomethyl ether (AME), and tenuazonic acid (TeA) are the most common and frequently studied mycotoxins. There are limited regulations placed on Alternaria mycotoxin concentrations worldwide due to the lack of toxicity data available. More data on the levels of mycotoxin contamination are also needed. It is also important to reduce the risks of Alternaria mycotoxins. RESULTS One hundred and thirty-two wheat samples were collected from Hebei Province, China, and analyzed for AOH, AME, and TeA. Tenuazonic acid was found to be the predominant Alternaria mycotoxin, especially in flour samples. Studying Alternaria species that cause black-point disease of wheat indicated that Alternaria alternata and Alternaria tenuissima were the dominant species. Most of the Alternaria strains studied produced more than one mycotoxin and TeA was produced at the highest concentration, which may have resulted in the high level of TeA contamination in the wheat samples. Furthermore, magnolol displayed obvious antifungal and antimycotoxigenic activity against Alternaria. This is the first report on the antimycotoxigenic activity of magnolol against Alternaria species. CONCLUSION The Alternaria mycotoxin contamination levels in wheat and wheat products from Hebei Province, China, were correlated with the toxigenic capacity of the Alternaria strains colonizing the wheat. Considering its safety, magnolol could be developed as a natural fungicide in wheat, or as a natural alternative food preservative based on its strong antifungal and antimycotoxigenic activity against Alternaria strains. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Dongmei Jiang
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Risk Assessment Laboratory for Agro-Products, Ministry of Agriculture, Beijing, China
| | - Dizhe Wei
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Risk Assessment Laboratory for Agro-Products, Ministry of Agriculture, Beijing, China
| | - Hongtao Li
- Institute of Genetics and Physiology/Research Center for Agricultural Products Quality and Safety, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Liuqing Wang
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Risk Assessment Laboratory for Agro-Products, Ministry of Agriculture, Beijing, China
| | - Nan Jiang
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Risk Assessment Laboratory for Agro-Products, Ministry of Agriculture, Beijing, China
| | - Yunchao Li
- Institute of Genetics and Physiology/Research Center for Agricultural Products Quality and Safety, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Meng Wang
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Risk Assessment Laboratory for Agro-Products, Ministry of Agriculture, Beijing, China
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Kumar M, Singh P, Murugesan S, Vetizou M, McCulloch J, Badger JH, Trinchieri G, Al Khodor S. Microbiome as an Immunological Modifier. Methods Mol Biol 2020; 2055:595-638. [PMID: 31502171 PMCID: PMC8276114 DOI: 10.1007/978-1-4939-9773-2_27] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Humans are living ecosystems composed of human cells and microbes. The microbiome is the collection of microbes (microbiota) and their genes. Recent breakthroughs in the high-throughput sequencing technologies have made it possible for us to understand the composition of the human microbiome. Launched by the National Institutes of Health in USA, the human microbiome project indicated that our bodies harbor a wide array of microbes, specific to each body site with interpersonal and intrapersonal variabilities. Numerous studies have indicated that several factors influence the development of the microbiome including genetics, diet, use of antibiotics, and lifestyle, among others. The microbiome and its mediators are in a continuous cross talk with the host immune system; hence, any imbalance on one side is reflected on the other. Dysbiosis (microbiota imbalance) was shown in many diseases and pathological conditions such as inflammatory bowel disease, celiac disease, multiple sclerosis, rheumatoid arthritis, asthma, diabetes, and cancer. The microbial composition mirrors inflammation variations in certain disease conditions, within various stages of the same disease; hence, it has the potential to be used as a biomarker.
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Affiliation(s)
- Manoj Kumar
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Parul Singh
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Selvasankar Murugesan
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Marie Vetizou
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - John McCulloch
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Souhaila Al Khodor
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar.
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Wang H, Li P, Liu X, Zhang C, Lu Q, Xi D, Yang R, Wang S, Bai W, Yang Z, Zhou R, Cheng X, Leng J. The Composition of Fungal Communities in the Rumen of Gayals ( Bos frontalis), Yaks ( Bos grunniens), and Yunnan and Tibetan Yellow Cattle ( Bos taurs). Pol J Microbiol 2019; 68:505-514. [PMID: 31880894 PMCID: PMC7260705 DOI: 10.33073/pjm-2019-050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 11/14/2022] Open
Abstract
The rumen is a microbial-rich ecosystem in which rumen fungi play an important role in the feed digestion of ruminants. The composition of rumen fungi in free-range ruminants such as gayals, yaks, Tibetan yellow cattle, and the domesticated Yunnan yellow cattle was investigated by sequencing an internal transcribed spacer region 1 (ITS1) using Illumina MiSeq. A total of 285 092 optimized sequences and 904 operational taxonomic units (OTUs) were obtained from the four cattle breeds. The rumen fungi abundance and Chao and Simpson indexes were all higher in free-range ruminants than in domesticated ruminants. Three fungal phyla were identified by sequence comparison: Neocallimastigomycota, Basidiomycota, and Ascomycota. Basidiomycota and Ascomycota have very low abundance in the rumen of four breeds cattle but anaerobic fungi (AF) Neocallimastigomycota occurred in a high abundance. In Neocallimastigomycota, the dominant genera were Piromyces, Anaeromyces, Cyllamyces, Neocallimastix, and Orpionmyces in four cattle breeds. The composition of the major genera of Neocallimastigaceae varied greatly among the four cattle breeds. The unclassified genera were unequally distributed in gayals, yaks, Tibetan and Yunnan yellow cattle, accounting for 90.63%, 98.52%, 97.79%, and 27.01% respectively. It appears that free-range ruminants have more unknown rumen fungi than domesticated ruminants and the cattle breeds and animal diets had an impact on the diversity of rumen fungi.
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Affiliation(s)
- Houfu Wang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Pengfei Li
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Xuchuan Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Chunyong Zhang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China ; Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Qiongfen Lu
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China ; Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Renhui Yang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Shuling Wang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Wenshun Bai
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Zhen Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Rongkang Zhou
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Xiao Cheng
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Jing Leng
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China ; Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
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Miller S, Naccache SN, Samayoa E, Messacar K, Arevalo S, Federman S, Stryke D, Pham E, Fung B, Bolosky WJ, Ingebrigtsen D, Lorizio W, Paff SM, Leake JA, Pesano R, DeBiasi R, Dominguez S, Chiu CY. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Genome Res 2019; 29:831-842. [PMID: 30992304 PMCID: PMC6499319 DOI: 10.1101/gr.238170.118] [Citation(s) in RCA: 333] [Impact Index Per Article: 66.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 02/25/2019] [Indexed: 02/06/2023]
Abstract
Metagenomic next-generation sequencing (mNGS) for pan-pathogen detection has been successfully tested in proof-of-concept case studies in patients with acute illness of unknown etiology but to date has been largely confined to research settings. Here, we developed and validated a clinical mNGS assay for diagnosis of infectious causes of meningitis and encephalitis from cerebrospinal fluid (CSF) in a licensed microbiology laboratory. A customized bioinformatics pipeline, SURPI+, was developed to rapidly analyze mNGS data, generate an automated summary of detected pathogens, and provide a graphical user interface for evaluating and interpreting results. We established quality metrics, threshold values, and limits of detection of 0.2-313 genomic copies or colony forming units per milliliter for each representative organism type. Gross hemolysis and excess host nucleic acid reduced assay sensitivity; however, spiked phages used as internal controls were reliable indicators of sensitivity loss. Diagnostic test accuracy was evaluated by blinded mNGS testing of 95 patient samples, revealing 73% sensitivity and 99% specificity compared to original clinical test results, and 81% positive percent agreement and 99% negative percent agreement after discrepancy analysis. Subsequent mNGS challenge testing of 20 positive CSF samples prospectively collected from a cohort of pediatric patients hospitalized with meningitis, encephalitis, and/or myelitis showed 92% sensitivity and 96% specificity relative to conventional microbiological testing of CSF in identifying the causative pathogen. These results demonstrate the analytic performance of a laboratory-validated mNGS assay for pan-pathogen detection, to be used clinically for diagnosis of neurological infections from CSF.
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Affiliation(s)
- Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Samia N Naccache
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California 90027, USA
| | - Erik Samayoa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Kevin Messacar
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Shaun Arevalo
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Doug Stryke
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Elizabeth Pham
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Becky Fung
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | | | - Danielle Ingebrigtsen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Walter Lorizio
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Sandra M Paff
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - John A Leake
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California 92675, USA
| | - Rick Pesano
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California 92675, USA
| | - Roberta DeBiasi
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Children's National Health System, Washington, DC 20010, USA
- Department of Pediatrics, Microbiology, Immunology, and Tropical Medicine, The George Washington University School of Medicine, Washington, DC 20037, USA
| | - Samuel Dominguez
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, California 94143, USA
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Maubon D, Dard C, Garnaud C, Cornet M. Profile of GenMark's ePlex® blood culture identification fungal pathogen panel. Expert Rev Mol Diagn 2017; 18:119-132. [PMID: 29284316 DOI: 10.1080/14737159.2018.1420476] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Fungemia presents high morbi-mortality and thus rapid microbiological diagnosis may contribute to appropriate patient management. In the last decade, kits based on molecular technologies have become available and health care institutes are increasingly facing critical investment choices. Although all these tools aim to achieve rapid fungal detection and species identification, they display different inherent characteristics. Areas covered: Considering technologies allowing detection and identification of fungal species in a sepsis context, the market proposes either tests on positive blood culture or tests on patient's whole blood. In this review, the authors describe and compare the ePlex® Blood Culture Identification Fungal Pathogen (BCID-FP) test, a fully automated one-step single-use cartridge assay that has been designed to detect identify frequent or rare but emerging, fungal species, from positive blood culture. A comparison with the competing kits is provided. Expert commentaries: The ePlex BCID-FP test provides a diversified and rather relevant panel. Its easy-to-use cartridges allow flexible use around the clock. Nevertheless, prospective clinical studies assessing the time-to-result benefit on antifungal stewardship and on hospital length of stay are not available yet. New tools aim to benefit clinicians and patients, but they should be accompanied by supervision of result interpretation and adaptation of antifungal stewardship.
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Affiliation(s)
- Danièle Maubon
- a Univsité Grenoble Alpes, CNRS, Grenoble INP*, TIMC-IMAG , Grenoble , France.,b Parasitology-Mycology Laboratory, Infectious Agents Department , CHU Grenoble-Alpes , Grenoble , France
| | - Céline Dard
- b Parasitology-Mycology Laboratory, Infectious Agents Department , CHU Grenoble-Alpes , Grenoble , France
| | - Cécile Garnaud
- a Univsité Grenoble Alpes, CNRS, Grenoble INP*, TIMC-IMAG , Grenoble , France.,b Parasitology-Mycology Laboratory, Infectious Agents Department , CHU Grenoble-Alpes , Grenoble , France
| | - Muriel Cornet
- a Univsité Grenoble Alpes, CNRS, Grenoble INP*, TIMC-IMAG , Grenoble , France.,b Parasitology-Mycology Laboratory, Infectious Agents Department , CHU Grenoble-Alpes , Grenoble , France
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Barbedo LS, Figueiredo-Carvalho MHG, Muniz MDM, Zancopé-Oliveira RM. Comparison of four molecular approaches to identify Candida parapsilosis complex species. Mem Inst Oswaldo Cruz 2017; 112:214-219. [PMID: 28225905 PMCID: PMC5319372 DOI: 10.1590/0074-02760160412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/08/2016] [Indexed: 12/11/2022] Open
Abstract
Since the description of Candida orthopsilosis and C. metapsilosis in 2005, several methods have been proposed to identify and differentiate these species from C. parapsilosis sensu stricto. Species-specific uniplex polymerase chain reaction (PCR) was performed and compared with sequencing of the D1/D2 region of the LSU 28S rDNA gene, microsatellite typing of C. parapsilosis sensu stricto, and PCR-restriction fragment length polymorphism patterns in the ITS1-5.8S-ITS2 region of the rDNA gene. There was agreement between results of testing of 98 clinical isolates with the four PCR-based methods, with 59 isolates identified as C. parapsilosis sensu stricto, 37 as C. orthopsilosis, and two as C. metapsilosis.
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Affiliation(s)
- Leonardo Silva Barbedo
- Fundação Oswaldo Cruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Micologia, Rio de Janeiro, RJ, Brasil
| | | | - Mauro de Medeiros Muniz
- Fundação Oswaldo Cruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Micologia, Rio de Janeiro, RJ, Brasil
| | - Rosely Maria Zancopé-Oliveira
- Fundação Oswaldo Cruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Micologia, Rio de Janeiro, RJ, Brasil
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Ziccardi M, Souza LOP, Gandra RM, Galdino ACM, Baptista ARS, Nunes APF, Ribeiro MA, Branquinha MH, Santos ALS. Candida parapsilosis (sensu lato) isolated from hospitals located in the Southeast of Brazil: Species distribution, antifungal susceptibility and virulence attributes. Int J Med Microbiol 2015; 305:848-59. [PMID: 26319940 DOI: 10.1016/j.ijmm.2015.08.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/28/2015] [Accepted: 08/10/2015] [Indexed: 01/12/2023] Open
Abstract
Candida parapsilosis (sensu lato), which represents a fungal complex composed of three genetically related species - Candida parapsilosis sensu stricto, Candida orthopsilosis and Candida metapsilosis, has emerged as an important yeast causing fungemia worldwide. The goal of the present work was to assess the prevalence, antifungal susceptibility and production of virulence traits in 53 clinical isolates previously identified as C. parapsilosis (sensu lato) obtained from hospitals located in the Southeast of Brazil. Species forming this fungal complex are physiologically/morphologically indistinguishable; however, polymerase chain reaction followed by restriction fragment length polymorphism of FKS1 gene has solved the identification inaccuracy, revealing that 43 (81.1%) isolates were identified as C. parapsilosis sensu stricto and 10 (18.9%) as C. orthopsilosis. No C. metapsilosis was found. The geographic distribution of these Candida species was uniform among the studied Brazilian States (São Paulo, Rio de Janeiro and Espírito Santo). All C. orthopsilosis and almost all C. parapsilosis sensu stricto (95.3%) isolates were susceptible to amphotericin B, fluconazole, itraconazole, voriconazole and caspofungin. Nevertheless, one C. parapsilosis sensu stricto isolate was resistant to fluconazole and another one was resistant to caspofungin. C. parapsilosis sensu stricto isolates exhibited higher MIC mean values to amphotericin B, fluconazole and caspofungin than those of C. orthopsilosis, while C. orthopsilosis isolates displayed higher MIC mean to itraconazole compared to C. parapsilosis sensu stricto. Identical MIC mean values to voriconazole were measured for these Candida species. All the isolates of both species were able to form biofilm on polystyrene surface. Impressively, biofilm-growing cells of C. parapsilosis sensu stricto and C. orthopsilosis exhibited a considerable resistance to all antifungal agents tested. Pseudohyphae were observed in 67.4% and 80% of C. parapsilosis sensu stricto and C. orthopsilosis isolates, respectively. The secretion of phytase (93% versus 100%), aspartic protease (88.4% versus 90%), esterase (20.9% versus 50%) and hemolytic factors (25.6% versus 40%) was detected in C. parapsilosis sensu stricto and C. orthopsilosis isolates, respectively; however, no phospholipase activity was identified. An interesting fact was observed concerning the caseinolytic activity, for which all the producers (53.5%) belonged to C. parapsilosis sensu stricto. Collectively, our results add new data on the epidemiology, antifungal susceptibility and production of potential virulence attributes in clinical isolates of C. parapsilosis complex.
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Affiliation(s)
- Mariangela Ziccardi
- Laboratório de Investigação de Peptidases, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Lucieri O P Souza
- Laboratório de Investigação de Peptidases, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael M Gandra
- Laboratório de Investigação de Peptidases, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Programa de Pós-Graduação em Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anna Clara M Galdino
- Laboratório de Investigação de Peptidases, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Programa de Pós-Graduação em Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andréa R S Baptista
- Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Ana Paula F Nunes
- Departamento de Patologia, Programa de Pós-Graduação em Doenças Infecciosas, Universidade Federal do Espírito Santo, Brazil
| | - Mariceli A Ribeiro
- Departamento de Patologia, Programa de Pós-Graduação em Doenças Infecciosas, Universidade Federal do Espírito Santo, Brazil
| | - Marta H Branquinha
- Laboratório de Investigação de Peptidases, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - André L S Santos
- Laboratório de Investigação de Peptidases, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Programa de Pós-Graduação em Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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Layios N, Canivet JL, Baron F, Moutschen M, Hayette MP. Mortierella wolfii-associated invasive disease. Emerg Infect Dis 2015; 20:1591-2. [PMID: 25153198 PMCID: PMC4178392 DOI: 10.3201/eid2009.140469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Molecular and nonmolecular diagnostic methods for invasive fungal infections. Clin Microbiol Rev 2015; 27:490-526. [PMID: 24982319 DOI: 10.1128/cmr.00091-13] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Invasive fungal infections constitute a serious threat to an ever-growing population of immunocompromised individuals and other individuals at risk. Traditional diagnostic methods, such as histopathology and culture, which are still considered the gold standards, have low sensitivity, which underscores the need for the development of new means of detecting fungal infectious agents. Indeed, novel serologic and molecular techniques have been developed and are currently under clinical evaluation. Tests like the galactomannan antigen test for aspergillosis and the β-glucan test for invasive Candida spp. and molds, as well as other antigen and antibody tests, for Cryptococcus spp., Pneumocystis spp., and dimorphic fungi, have already been established as important diagnostic approaches and are implemented in routine clinical practice. On the other hand, PCR and other molecular approaches, such as matrix-assisted laser desorption ionization (MALDI) and fluorescence in situ hybridization (FISH), have proved promising in clinical trials but still need to undergo standardization before their clinical use can become widespread. The purpose of this review is to highlight the different diagnostic approaches that are currently utilized or under development for invasive fungal infections and to identify their performance characteristics and the challenges associated with their use.
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Kondori N, Erhard M, Welinder-Olsson C, Groenewald M, Verkley G, Moore ERB. Analyses of black fungi by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS): species-level identification of clinical isolates of Exophiala dermatitidis. FEMS Microbiol Lett 2014; 362:1-6. [PMID: 25790495 DOI: 10.1093/femsle/fnu016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Conventional mycological identifications based on the recognition of morphological characteristics can be problematic. A relatively new methodology applicable for the identification of microorganisms is based on the exploitation of taxon- specific mass patterns recorded from abundant cell proteins directly from whole-cell preparations, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This study reports the application of MALDI-TOF MS for the differentiation and identifications of black yeasts, isolated from the respiratory tracts of patients with cystic fibrosis (CF). Initial phenotypic and DNA sequence-based analyses identified these isolates to be Exophiala dermatitidis. The type strains of E. dermatitidis (CBS 207.35(T)) and other species of Exophiala were included in the MALDI-TOF MS analyses to establish the references for comparing the mass spectra of the clinical isolates of Exophiala. MALDI-TOF MS analyses exhibited extremely close relationships among the clinical isolates and with the spectra generated from the type strain of E. dermatitidis. The relationships observed between the E. dermatitidis strains from the MALDI-TOF MS profiling analyses were supported by DNA sequence-based analyses of the rRNA ITS1 and ITS2 regions. These data demonstrated the applicability of MALDI-TOF MS as a reliable, rapid and cost-effective method for the identification of isolates of E. dermatitidis and other clinically relevant fungi and yeasts that typically are difficult to identify by conventional methods.
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Affiliation(s)
- Nahid Kondori
- Department of Infectious Diseases, Sahlgrenska Academy of the University of Gothenburg, SE-40234 Gothenburg, Sweden
| | | | - Christina Welinder-Olsson
- Department of Infectious Diseases, Sahlgrenska Academy of the University of Gothenburg, SE-40234 Gothenburg, Sweden
| | - Marizeth Groenewald
- Centraalbureau voor Schimmelcultures (CBS), CBS-KNAW Fungal Biodiversity Centre, 3584 CT Utrecht, Netherlands
| | - Gerard Verkley
- Centraalbureau voor Schimmelcultures (CBS), CBS-KNAW Fungal Biodiversity Centre, 3584 CT Utrecht, Netherlands
| | - Edward R B Moore
- Department of Infectious Diseases, Sahlgrenska Academy of the University of Gothenburg, SE-40234 Gothenburg, Sweden Culture Collection University of Gothenburg, Sahlgrenska Academy of the University of Gothenburg, SE-40234 Gothenburg, Sweden
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Ingram PR, Suthananthan AE, Rajan R, Pryce TM, Sieunarine K, Gardam DJ, Heath CH. Cutaneous mucormycosis and motor vehicle accidents: Findings from an Australian case series. Med Mycol 2014; 52:819-25. [PMID: 25288654 DOI: 10.1093/mmy/myu054] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Cutaneous disease is the third most frequent manifestation of mucormycosis. The clinical manifestations of and subsequent mortality due to cutaneous mucormycosis are dependent on the mode of acquisition and the host immune status. Here, we describe the epidemiology, clinical presentation, microbiology, and outcomes of 16 cutaneous mucormycosis infections managed in an Australian tertiary hospital over a 15-year period. The proportion with localized (56%), deep (38%), and disseminated (6%) cutaneous disease as well as the overall mortality (25%) were consistent with findings reported in the published literature. Two novel forms of hospital-acquired infection were reported following a sacral pressure sore and insertion of a foreign body during a bone graft procedure. The majority of patients were immunocompetent (75%) and/or suffered trauma (56%) with associated environmental contamination. A novel finding was that motor vehicle accidents (MVAs) accounted for 78% of all trauma-related cases, suggesting MVAs should receive greater recognition as a potential precipitant of cutaneous mucormycosis. Aggressive decontamination and debridement of devitalized tissue following trauma is therefore likely to play an important role in the prevention of this rare but potentially devastating infection.
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Affiliation(s)
- Paul R Ingram
- Department of Microbiology and Infectious Diseases, Royal Perth Hospital, Perth, Australia School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia
| | | | - Ruben Rajan
- Department of General Surgery, Royal Perth Hospital, Perth, Australia
| | - Todd M Pryce
- Department of Microbiology and Infectious Diseases, Royal Perth Hospital, Perth, Australia
| | | | - Dianne J Gardam
- Department of Microbiology and Infectious Diseases, Royal Perth Hospital, Perth, Australia
| | - Christopher H Heath
- Department of Microbiology and Infectious Diseases, Royal Perth Hospital, Perth, Australia School of Medicine and Pharmacology, University of Western Australia, Perth, Australia
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Layios N, Canivet JL, Baron F, Moutschen M, Hayette MP. Mortierella wolfii–Associated Invasive Disease. Emerg Infect Dis 2014. [DOI: 10.3201/2009.140469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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17
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Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control. BMC Infect Dis 2014; 14:15. [PMID: 24405747 PMCID: PMC3897990 DOI: 10.1186/1471-2334-14-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 12/20/2013] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Carefully conducted, community-based, longitudinal studies are required to gain further understanding of the nature and timing of respiratory viruses causing infections in the population. However, such studies pose unique challenges for field specimen collection, including as we have observed the appearance of mould in some nasal swab specimens. We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays. METHODS Anterior nasal swab samples were collected from infants participating in an ongoing community-based, longitudinal, dynamic birth cohort study. The samples were first collected from each infant shortly after birth and weekly thereafter. They were then mailed to the laboratory where they were catalogued, stored at -80°C and later screened by PCR for 17 respiratory viruses. The quality of specimen collection was assessed by screening for human deoxyribonucleic acid (DNA) using endogenous retrovirus 3 (ERV3). The impact of ERV3 load upon respiratory virus detection and the impact of visible mould observed in a subset of swabs reaching the laboratory upon both ERV3 loads and respiratory virus detection was determined. RESULTS In total, 4933 nasal swabs were received in the laboratory. ERV3 load in nasal swabs was associated with respiratory virus detection. Reduced respiratory virus detection (odds ratio 0.35; 95% confidence interval 0.27-0.44) was observed in samples where the ERV3 could not be identified. Mould was associated with increased time of samples reaching the laboratory and reduced ERV3 loads and respiratory virus detection. CONCLUSION Suboptimal sample collection and high levels of visible mould can impact negatively upon sample quality. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies.
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18
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Xafranski H, Melo ASA, Machado AM, Briones MRS, Colombo AL. A quick and low-cost PCR-based assay for Candida spp. identification in positive blood culture bottles. BMC Infect Dis 2013; 13:467. [PMID: 24099320 PMCID: PMC3851980 DOI: 10.1186/1471-2334-13-467] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 09/26/2013] [Indexed: 12/26/2022] Open
Abstract
Background Differences in the susceptibility of Candida species to antifungal drugs make identification to the species level important for clinical management of candidemia. Molecular tests are not yet standardized or available in most clinical laboratories, although such tests can reduce the time required for species identification, as compared to the conventional culture-based methods. To decrease laboratory costs and improve diagnostic accuracy, different molecular methods have been proposed, including DNA extraction protocols to produce pure DNA free of PCR inhibitors. The objective of this study was to validate a new format of molecular method, based on the internal transcribed spacer (ITS) of the rDNA gene amplification followed by sequencing, to identify common and cryptic Candida species causing candidemia by analyzing DNA in blood culture bottles positive for yeasts. Methods For DNA extraction, an “in-house” protocol based on organic solvent extraction was tested. Additional steps of liquid nitrogen incubation followed by mechanical disruption ensured complete cell lysis, and highly pure DNA. One hundred sixty blood culture bottles positive for yeasts were processed. PCR assays amplified the ITS region. The DNA fragments of 152 samples were sequenced and these sequences were identified using the GenBank database (NCBI). Molecular yeast identification was compared to results attained by conventional method. Results The organic solvent extraction protocol showed high reproducibility in regards to DNA quantity, as well as high PCR sensitivity (10 pg of C. albicans DNA and 95% amplification on PCR). The identification of species at the molecular level showed 97% concordance with the conventional culturing method. The molecular method tested in the present study also allowed identification of species not commonly implicated in human infections. Conclusions This study demonstrated that our molecular method presents significant advantages over the conventional yeast culture identification method by providing accurate results within 24 hours, in contrast to at least 72 hours required by the automated conventional culture method. Additionally, our molecular method allowed the identification of mixed infections, as well as infections due to emergent fungal pathogens. This economical DNA extraction method developed in our laboratory provided high-quality DNA and 60% cost savings compared to commercial methods.
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Affiliation(s)
- Hemílio Xafranski
- Laboratório Especial de Micologia, Departamento de Medicina, Universidade Federal de São Paulo, Rua Pedro de Toledo 669 5 andar, São Paulo, SP, Brazil.
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Lin D, Qurat-Ul-Ain K, Lai S, Musher DM, Hamill R. Cerebral Scedosporium apiospermum infection presenting with intestinal manifestations. Infection 2013; 41:723-6. [DOI: 10.1007/s15010-013-0429-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 02/12/2013] [Indexed: 10/27/2022]
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Bonfietti LX, Martins MDA, Szeszs MW, Pukiskas SBS, Purisco SU, Pimentel FC, Pereira GH, Silva DC, Oliveira L, Melhem MDSC. Prevalence, distribution and antifungal susceptibility profiles of Candida parapsilosis, Candida orthopsilosis and Candida metapsilosis bloodstream isolates. J Med Microbiol 2012; 61:1003-1008. [DOI: 10.1099/jmm.0.037812-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lucas Xavier Bonfietti
- Instituto Adolfo Lutz, Nucleo de Micologia, Centro de Parasitologia e Micologia, Av. Dr Arnaldo 351, São Paulo, Brazil
| | - Marilena dos Anjos Martins
- Instituto Adolfo Lutz, Nucleo de Micologia, Centro de Parasitologia e Micologia, Av. Dr Arnaldo 351, São Paulo, Brazil
| | - Maria Walderez Szeszs
- Instituto Adolfo Lutz, Nucleo de Micologia, Centro de Parasitologia e Micologia, Av. Dr Arnaldo 351, São Paulo, Brazil
| | - Sandra Brasil Stolf Pukiskas
- Instituto Adolfo Lutz, Nucleo de Micologia, Centro de Parasitologia e Micologia, Av. Dr Arnaldo 351, São Paulo, Brazil
| | - Sonia Ueda Purisco
- Instituto Adolfo Lutz, Nucleo de Micologia, Centro de Parasitologia e Micologia, Av. Dr Arnaldo 351, São Paulo, Brazil
| | - Fabiana Cortez Pimentel
- Instituto Adolfo Lutz, Nucleo de Micologia, Centro de Parasitologia e Micologia, Av. Dr Arnaldo 351, São Paulo, Brazil
| | - Graziella Hanna Pereira
- Instituto Adolfo Lutz, Nucleo de Micologia, Centro de Parasitologia e Micologia, Av. Dr Arnaldo 351, São Paulo, Brazil
| | - Dayane Cristina Silva
- Instituto Adolfo Lutz, Nucleo de Micologia, Centro de Parasitologia e Micologia, Av. Dr Arnaldo 351, São Paulo, Brazil
| | - Lidiane Oliveira
- Instituto Adolfo Lutz, Nucleo de Micologia, Centro de Parasitologia e Micologia, Av. Dr Arnaldo 351, São Paulo, Brazil
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Frickmann H, Lakner A, Essig A, Poppert S. Rapid identification of yeast by fluorescencein situhybridisation from broth and blood cultures. Mycoses 2012; 55:521-31. [DOI: 10.1111/j.1439-0507.2012.02214.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Abstract
In the last 15 years, the genus Malassezia has been a topic of intense basic research on taxonomy, physiology, biochemistry, ecology, immunology, and metabolomics. Currently, the genus encompasses 14 species. The 1996 revision of the genus resulted in seven accepted taxa: M. furfur, M. pachydermatis, M. sympodialis, M. globosa, M. obtusa, M. restricta, and M. slooffiae. In the last decade, seven new taxa isolated from healthy and lesional human and animal skin have been accepted: M. dermatis, M. japonica, M. yamatoensis, M. nana, M. caprae, M. equina, and M. cuniculi. However, forthcoming multidisciplinary research is expected to show the etiopathological relationships between these new species and skin diseases. Hitherto, basic and clinical research has established etiological links between Malassezia yeasts, pityriasis versicolor, and sepsis of neonates and immunocompromised individuals. Their role in aggravating seborrheic dermatitis, dandruff, folliculitis, and onychomycosis, though often supported by histopathological evidence and favorable antifungal therapeutic outcomes, remains under investigation. A close association between skin and Malassezia IgE binding allergens in atopic eczema has been shown, while laboratory data support a role in psoriasis exacerbations. Finally, metabolomic research resulted in the proposal of a hypothesis on the contribution of Malassezia-synthesized aryl hydrocarbon receptor (AhR) ligands to basal cell carcinoma through UV radiation-induced carcinogenesis.
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Kubesová A, Šalplachta J, Horká M, Růžička F, Šlais K. Candida “Psilosis” – electromigration techniques and MALDI-TOF mass spectrometry for phenotypical discrimination. Analyst 2012; 137:1937-43. [DOI: 10.1039/c2an15931g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Prospective multicenter study of the epidemiology, molecular identification, and antifungal susceptibility of Candida parapsilosis, Candida orthopsilosis, and Candida metapsilosis isolated from patients with candidemia. Antimicrob Agents Chemother 2011; 55:5590-6. [PMID: 21930869 DOI: 10.1128/aac.00466-11] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A 13-month prospective multicenter study including 44 hospitals was carried out to evaluate the epidemiology of Candida parapsilosis complex candidemia in Spain. Susceptibility to amphotericin B, flucytosine, fluconazole, itraconazole, voriconazole, posaconazole, anidulafungin, caspofungin, and micafungin was tested by the microdilution colorimetric method. A total of 364 C. parapsilosis complex isolates were identified by molecular methods: C. parapsilosis (90.7%), Candida orthopsilosis (8.2%), and Candida metapsilosis (1.1%). Most candidemias (C. parapsilosis, 76.4%; C. orthopsilosis, 70.0%; C. metapsilosis, 100%) were observed in adults. No C. orthopsilosis or C. metapsilosis candidemias occurred in neonates. C. parapsilosis was most frequent in adult intensive care unit (28.8%), surgery (20.9%), and internal medicine (19.7%) departments; and C. orthopsilosis was most frequent in hematology (28.6%), pediatrics (12.0%), and neonatology (11.5%) departments. The geographic distribution of C. orthopsilosis and C. metapsilosis was not uniform. According to CLSI clinical breakpoints, all C. orthopsilosis and C. metapsilosis isolates were susceptible to the nine agents tested. Resistance (MICs > 1 mg/liter) was observed only in C. parapsilosis: amphotericin B, posaconazole, itraconazole, and caspofungin (0.3% each), anidulafungin (1.9%), and micafungin (2.5%). Applying the new species-specific fluconazole and echinocandin breakpoints, the rates of resistance to fluconazole for C. parapsilosis and C. orthopsilosis increased to 4.8% and 0.3%, respectively; conversely, for C. parapsilosis they shifted from 1.9 to 0.6% (anidulafungin) and from 2.5 to 0.6% (micafungin). Our study confirms the different prevalence of C. parapsilosis complex candidemia among age groups: neither C. orthopsilosis nor C. metapsilosis was isolated from neonates; interestingly, C. metapsilosis was isolated only from adults and the elderly. The disparity in antifungal susceptibility among species could be important for therapy.
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Madhavan P, Jamal F, Chong PP. Laboratory Isolation and Identification of Candida Species. ACTA ACUST UNITED AC 2011. [DOI: 10.3923/jas.2011.2870.2877] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Miranda-Zapico I, Eraso E, Hernandez-Almaraz JL, Lopez-Soria LM, Carrillo-Munoz AJ, Hernandez-Molina JM, Quindos G. Prevalence and antifungal susceptibility patterns of new cryptic species inside the species complexes Candida parapsilosis and Candida glabrata among blood isolates from a Spanish tertiary hospital. J Antimicrob Chemother 2011; 66:2315-22. [DOI: 10.1093/jac/dkr298] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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A novel ascosporogenous yeast species, Zygosaccharomyces siamensis, and the sugar tolerant yeasts associated with raw honey collected in Thailand. FUNGAL DIVERS 2011. [DOI: 10.1007/s13225-011-0115-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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del Pilar Vercher M, García Martínez JM, Cantón E, Pemán J, Gómez García MM, Gómez EV, del Castillo Agudo L. Differentiation of Candida parapsilosis, C. orthopsilosis, and C. metapsilosis by specific PCR amplification of the RPS0 intron. Int J Med Microbiol 2011; 301:531-5. [PMID: 21570908 DOI: 10.1016/j.ijmm.2011.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2010] [Revised: 01/12/2011] [Accepted: 02/17/2011] [Indexed: 11/15/2022] Open
Abstract
Although Candida parapsilosis is the most prevalent among the 3 species of the *psilosis group, studies applying DNA-based diagnostic techniques with isolates previously identified as C. parapsilosis have revealed that both C. orthopsilosis and C. metapsilosis account for 0-10% of all these isolates, depending on the geographical area. Differences in the degrees of antifungal susceptibility and virulence have been found, so a more precise identification is required. In a first approach, we reidentified 38 randomly chosen clinical isolates, previously identified as C. parapsilosis, using the RPO2 (CA2) RAPD marker. Among them, we reclassified 4 as C. metapsilosis and 5 as C. orthopsilosis. We previously developed a method to identify different pathogen yeast species, including C. parapsilosis, based on the amplification of the RPS0 gene intron. In this work, we extend this approach to the new *psilosis species by partially sequencing their RPS0 gene, including the intron sequence. Based on intron sequences, we designed specific primers capable of identifying C. orthopsilosis and C. metapsilosis species, and we reidentified species among the initial isolates. These new primers have allowed a specific and rapid identification of C. orthopsilosis and C. metapsilosis.
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Affiliation(s)
- M del Pilar Vercher
- GMCA Research Unit, Departamento de Microbiología y Ecología, Universidad de Valencia, Avda. Vicente Andrés Estellés s/n, 46100-Burjassot, Valencia, Spain
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Hsi SC, Sun JR, Chiueh TS. Evaluation of the alkaline wash/lysis procedure for the molecular diagnosis of a positive bacterial blood culture in clinical routine practice. J Clin Lab Anal 2011; 24:139-44. [PMID: 20486192 DOI: 10.1002/jcla.20396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Blood culture is commonly used to detect microorganisms in patients with a suspected blood infection. This study evaluated the alkaline wash/lysis procedure to extract DNA of microorganisms in a clinical blood culture. A multiplex polymerase chain reaction (PCR) targeting the 16S rDNA (ribosomal DNA) gene and the fungal ITS (internal transcribed spacer) gene was used as a reliable indicator for the presence of microorganism DNA in the extracts. A total of 535 BacT/ALERT positive blood culture bottles were evaluated. Multiplex PCR showed positive results in 530 DNA extracts, but 5 DNA extracts gave negative results. We conclude that the alkaline wash/lysis procedure in combination with the multiplex PCR is a simple and sensitive method, which can be used in a standard diagnostic laboratory to detect microorganisms in blood culture material.
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Affiliation(s)
- Sheng-Chuan Hsi
- Hsin Sheng College of Medical Care and Management, Taoyuan, Taiwan
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Sidrim JJC, Costa AKF, Cordeiro RA, Brilhante RSN, Moura FEA, Castelo-Branco DSCM, Neto MPDA, Rocha MFG. Molecular methods for the diagnosis and characterization of Cryptococcus: a review. Can J Microbiol 2010; 56:445-58. [PMID: 20657615 DOI: 10.1139/w10-030] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cryptococcosis is a fungal infection caused by yeasts of the genus Cryptococcus, with Cryptococcus neoformans and Cryptococcus gattii as the primary pathogenic species. This disease is a threat to immunocompromised patients, especially those who have AIDS. However, the disease has also been described in healthy individuals. The tests used to identify these microorganisms have limitations that make final diagnosis difficult. However, currently there are specific gene sequences that can be used to detect C. neoformans and C. gattii from clinical specimens and cultures. These sequences can be used for identification, typing, and the study of population genetics. Among the main identification techniques are hybridization, which was the pioneer in molecular identification and development of specific probes for pathogen detection; PCR and other PCR-based methods, particularly nested PCR and multiplex PCR; and sequencing of specific genomic regions that are amplified through PCR, which is especially useful for diagnosis of cryptococcosis caused by unconventional Cryptococcus sp. Concerning microorganism typing, the following techniques have shown the best ability to differentiate between fungal serotypes and molecular types: PCR fingerprinting, PCR-RFLP, AFLP, and MLST. Thus, the accumulation of data generated by molecular methods can have a positive impact on monitoring resistant strains and treating diseases.
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Affiliation(s)
- José Júlio Costa Sidrim
- Specialized Medical Mycology Center, Federal University of Ceará, Rua Coronel Nunes de Melo, Rodolfo Teófilo, Fortaleza, Ceará, Brazil
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Mirhendi H, Bruun B, Schønheyder HC, Christensen JJ, Fuursted K, Gahrn-Hansen B, Johansen HK, Nielsen L, Knudsen JD, Arendrup MC. Molecular screening for Candida orthopsilosis and Candida metapsilosis among Danish Candida parapsilosis group blood culture isolates: proposal of a new RFLP profile for differentiation. J Med Microbiol 2010; 59:414-420. [PMID: 20056771 DOI: 10.1099/jmm.0.017293-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Candida orthopsilosis and Candida metapsilosis are recently described species phenotypically indistinguishable from Candida parapsilosis . We evaluated phenotyping and molecular methods for the detection of these species among 79 unique blood culture isolates of the C. parapsilosis group obtained during the years 2004-2008. The isolates were screened by PCR amplification of the secondary alcohol dehydrogenase-encoding gene ( SADH) followed by digestion with the restriction enzyme Ban I, using C. parapsilosis ATCC 22019, C. orthopsilosis ATCC 96139 and C. metapsilosis ATCC 96144 as controls. Isolates with RFLP patterns distinct from C. parapsilosis were characterized by sequence analysis of the ITS1-ITS2, 26S rRNA (D1/D2) and SADH regions. Restriction patterns for the 3 species with each of 610 restriction enzymes were predicted in silico using 12 available sequences. By PCR-RFLP of the SADH gene alone, four isolates (5.1 %) had a pattern identical to the C. orthopsilosis reference strain. Sequence analysis of SADH and ITS (internal transcribed spacer) regions identified two of these isolates as C. metapsilosis. These results were confirmed by creating a phylogenetic tree based on concatenated sequences of SADH, ITS and 26S rRNA gene sequence regions. Optimal differentiation between C. parapsilosis, C. metapsilosis and C. orthopsilosis was predicted using digestion with NlaIII, producing discriminatory band sizes of: 131 and 505 bp; 74, 288 and 348 bp; and 131, 217 and 288 bp, respectively. This was confirmed using the reference strains and 79 clinical isolates. In conclusion, reliable discrimination was obtained by PCR-RFLP profile analysis of the SADH gene after digestion with NlaIII but not with BanI. C. metapsilosis and C. orthopsilosis are involved in a small but significant number of invasive infections in Denmark.
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Affiliation(s)
- Hossein Mirhendi
- Mycology and Parasitology Unit, Statens Serum Institut,Copenhagen, Denmark
- Department of Medical Mycology and Parasitology,Faculty of Public Health and National Institute of Health Research, TehranUniversity of Medical Sciences, Tehran, Iran
| | - Brita Bruun
- Department of Clinical Microbiology, HillerødHospital, Hillerød, Denmark
| | - Henrik Carl Schønheyder
- Department of Clinical Microbiology, Aalborg Hospital,Aarhus University Hospital, Aalborg, Denmark
| | | | - Kurt Fuursted
- Department of Clinical Microbiology, Skejby Hospital,Aarhus University Hospital, Aarhus, Denmark
| | - Bente Gahrn-Hansen
- Department of Clinical Microbiology, Odense UniversityHospital, Odense, Denmark
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet,Copenhagen University Hospital, Copenhagen, Denmark
| | - Lene Nielsen
- Department of Clinical Microbiology, Herlev UniversityHospital, Herlev, Denmark
| | - Jenny Dahl Knudsen
- Department of Clinical Microbiology, Hvidovre UniversityHospital, Hvidovre, Denmark
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Harvey JBJ, Goff LJ. Genetic covariation of the marine fungal symbiont Haloguignardia irritans (Ascomycota, Pezizomycotina) with its algal hosts Cystoseira and Halidrys (Phaeophyceae, Fucales) along the west coast of North America. Fungal Biol 2010; 114:82-95. [PMID: 20965065 DOI: 10.1016/j.mycres.2009.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 10/26/2009] [Accepted: 10/28/2009] [Indexed: 11/24/2022]
Abstract
The fungal endophyte Haloguignardia irritans induces gall formation on the brown algal genera Cystoseira and Halidrys occurring from Oregon to Baja California, Mexico. Here we examine genetic covariation and compare rDNA phylogenies to investigate the coevolutionary histories of H. irritans and its algal hosts. Despite recognition of H. irritans as a single morphological species, internal transcribed spacer rDNA sequences representative of its geographic range are characterized by sequence variation at the intraspecific to intrageneric levels. An assessment of parallel cladogenesis between endophyte and host phylogenies provides evidence for a combination of independent fungal divergence and host jumping, similar to that observed in terrestrial lichens. Our results suggest that reduced gene flow due to geographic isolation is a major contributing factor to more concerted covariation observed at one island site, rather than to differences among algal host species alone. Because geography and its effects on gene flow can create heterogeneous mosaics of coevolution for symbioses in terrestrial environments, our results support the notion that conservation efforts toward the maintenance of genetic diversity in marine environments should likewise consider geographic complexity and its effects on coevolving marine species.
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Affiliation(s)
- J B J Harvey
- University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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Lau A, Chen S, Sleiman S, Sorrell T. Current status and future perspectives on molecular and serological methods in diagnostic mycology. Future Microbiol 2009; 4:1185-222. [DOI: 10.2217/fmb.09.70] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Invasive fungal infections are an important cause of infectious morbidity. Nonculture-based methods are increasingly used for rapid, accurate diagnosis to improve patient outcomes. New and existing DNA amplification platforms have high sensitivity and specificity for direct detection and identification of fungi in clinical specimens. Since laboratories are increasingly reliant on DNA sequencing for fungal identification, measures to improve sequence interpretation should support validation of reference isolates and quality control in public gene repositories. Novel technologies (e.g., isothermal and PNA FISH methods), platforms enabling high-throughput analyses (e.g., DNA microarrays and Luminex® xMAP™) and/or commercial PCR assays warrant further evaluation for routine diagnostic use. Notwithstanding the advantages of molecular tests, serological assays remain clinically useful for patient management. The serum Aspergillus galactomannan test has been incorporated into diagnostic algorithms of invasive aspergillosis. Both the galactomannan and the serum β-D-glucan test have value for diagnosing infection and monitoring therapeutic response.
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Affiliation(s)
- Anna Lau
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia
| | - Sharon Chen
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia and Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Sue Sleiman
- Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Tania Sorrell
- Centre for Infectious Diseases & Microbiology, Westmead Hospital, Darcy and Hawkesbury Roads, Westmead, NSW 2145, Australia
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Martínez JMG, Gómez EV, Pemán J, Cantón E, García MG, del Castillo Agudo L. Identification of pathogenic yeast species by polymerase chain reaction amplification of the RPS0 gene intron fragment. J Appl Microbiol 2009; 108:1917-27. [PMID: 19968730 DOI: 10.1111/j.1365-2672.2009.04595.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
AIMS This work focuses on the development of a method for the identification of pathogenic yeast. With this aim, we target the nucleotide sequence of the RPS0 gene of pathogenic yeast species with specific PCR primers. PCR analysis was performed with both the genomic DNA, whole cells of clinical isolates of Candida species and clinical samples. METHODS AND RESULTS A single pairs of primers, deduced from the nucleotide sequence of the RPS0 gene from pathogenic yeast, were used in PCR analysis performed with both the genomic DNA and whole cells of clinical isolates of Candida species and clinical samples. The primers designed are highly specific for their respective species and produce amplicons of the expected sizes and fail to amplify any DNA fragment from the other species tested. The set of primers was tested successfully for the identification of yeast from colonies, blood cultures and clinical samples. These results indicate that genes containing intron sequences may be useful for designing species-specific primers for the identification of fungal strains by PCR. The sensitivity of the method with genomic DNA was evaluated with decreasing DNA concentrations (200 ng to 1 pg) and different cell amounts (10(7)-10(5) cells). CONCLUSION The results obtained show that the amplification of RPS0 sequences may be suitable for the identification of pathogenic and other yeast species. SIGNIFICANCE AND IMPACT OF THE STUDY Identification of Candida species using molecular approaches with high discriminatory power is important in determining adequate measures for the interruption of transmission of this yeast. The approach described in this work is based on standard technology, and it is specific, sensitive and does not involve complex and expensive equipment. Furthermore, the method developed in this work not only can be used in eight yeast species, but also provides the basis to design primers for other fungi species of clinical, industrial or environmental interest.
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Affiliation(s)
- J M García Martínez
- Departamento de Microbiología y Ecología, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
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Haas B, Nathens AB. Future diagnostic and therapeutic approaches in surgical infections. Surg Clin North Am 2009; 89:539-54, xi. [PMID: 19281899 DOI: 10.1016/j.suc.2008.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Despite ongoing efforts to standardize therapy and improve management, the morbidity and mortality associated with surgical infections remain high. Continued innovation is required to improve outcomes further, particularly in the face of the increasing prevalence of multidrug resistant organisms. Although they remain in the experimental stages, a number of recent advances have the potential to have significant impact on the management and outcomes of surgical infections. These include novel diagnostic strategies, antimicrobials targeting microbial virulence factors, novel vaccines, and risk stratification based on genetic profiling.
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Affiliation(s)
- Barbara Haas
- Department of Surgery, University of Toronto, Toronto, Ontario, M5G 1L5, Canada.
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Tay ST, Na SL, Chong J. Molecular differentiation and antifungal susceptibilities of Candida parapsilosis isolated from patients with bloodstream infections. J Med Microbiol 2009; 58:185-191. [PMID: 19141735 DOI: 10.1099/jmm.0.004242-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The genetic heterogeneity and antifungal susceptibility patterns of Candida parapsilosis isolated from blood cultures of patients were investigated in this study. Randomly amplified polymorphic DNA (RAPD) analysis generated 5 unique profiles from 42 isolates. Based on the major DNA fragments of the RAPD profiles, the isolates were identified as RAPD type P1 (29 isolates), P2 (6 isolates), P3 (4 isolates), P4 (2 isolates) and P5 (1 isolate). Sequence analysis of the internal transcribed spacer (ITS) gene of the isolates identified RAPD type P1 as C. parapsilosis, P2 and P3 as Candida orthopsilosis, P4 as Candida metapsilosis, and P5 as Lodderomyces elongisporus. Nucleotide variations in ITS gene sequences of C. orthopsilosis and C. metapsilosis were detected. Antifungal susceptibility testing using Etests showed that all isolates tested in this study were susceptible to amphotericin B, fluconazole, ketoconazole, itraconazole and voriconazole. C. parapsilosis isolates exhibited higher MIC(50) values than those of C. orthopsilosis for all of the drugs tested in this study; however, no significant difference in the MICs for these two Candida species was observed. The fact that C. orthopsilosis and C. metapsilosis were responsible for 23.8 and 4.8 % of the cases attributed to C. parapsilosis bloodstream infections, respectively, indicates the clinical relevance of these newly described yeasts. Further investigations of the ecological niche, mode of transmission and virulence of these species are thus essential.
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Affiliation(s)
- Sun Tee Tay
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Shiang Ling Na
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jennifer Chong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
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Multiplex tandem PCR: a novel platform for rapid detection and identification of fungal pathogens from blood culture specimens. J Clin Microbiol 2008; 46:3021-7. [PMID: 18632914 DOI: 10.1128/jcm.00689-08] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe the first development and evaluation of a rapid multiplex tandem PCR (MT-PCR) assay for the detection and identification of fungi directly from blood culture specimens that have been flagged as positive. The assay uses a short-cycle multiplex amplification, followed by 12 simultaneous PCRs which target the fungal internal transcribed spacer 1 (ITS1) and ITS2 region, elongation factor 1-alpha (EF1-alpha), and beta-tubulin genes to identify 11 fungal pathogens: Candida albicans, Candida dubliniensis, Candida glabrata, Candida guilliermondii, Candida krusei, Candida parapsilosis complex, Candida tropicalis, Cryptococcus neoformans complex, Fusarium solani, Fusarium species, and Scedosporium prolificans. The presence or absence of a fungal target was confirmed by melting curve analysis. Identification by MT-PCR correlated with culture-based identification for 44 (100%) patients. No cross-reactivity was detected in 200 blood culture specimens that contained bacteria or in 30 blood cultures without microorganisms. Fungi were correctly identified in five specimens with bacterial coinfection and in blood culture samples that were seeded with a mixture of yeast cells. The MT-PCR assay was able to provide rapid (<2 h), sensitive, and specific simultaneous detection and identification of fungal pathogens directly from blood culture specimens.
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Pastores SM, Dulu A, Voigt L, Raoof N, Alicea M, Halpern NA. Premortem clinical diagnoses and postmortem autopsy findings: discrepancies in critically ill cancer patients. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2008; 11:R48. [PMID: 17448238 PMCID: PMC2206477 DOI: 10.1186/cc5782] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Revised: 03/20/2007] [Accepted: 04/20/2007] [Indexed: 11/10/2022]
Abstract
Introduction Limited data are available regarding the relationship of premortem clinical diagnoses and postmortem autopsy findings in cancer patients who die in an oncologic intensive care unit (ICU). The purposes of this study were to compare the premortem clinical and postmortem diagnoses of cancer patients who died in the ICU and to analyze any discrepancies between them. Methods This is a retrospective review of medical records and autopsy reports of all cancer patients who died in a medical-surgical ICU and had an autopsy performed between 1 January 1999 and 30 September 2005 at a tertiary care cancer center. Premortem clinical diagnoses were compared with the postmortem findings. Major missed diagnoses were identified and classified, according to the Goldman criteria, into class I and class II discrepancies. Results Of 658 deaths in the ICU during the study period, 86 (13%) autopsies were performed. Of the 86 patients, 22 (26%) had 25 major missed diagnoses, 12 (54%) patients had class I discrepancies, 7 (32%) had class II discrepancies, and 3 (14%) had both class I and class II discrepancies. Class I discrepancies were due to opportunistic infections (67%) and cardiac complications (33%), whereas class II discrepancies were due to cardiopulmonary complications (70%) and opportunistic infections (30%). Conclusion There was a discrepancy rate of 26% between premortem clinical diagnoses and postmortem findings in cancer patients who died in a medical-surgical ICU at a tertiary care cancer center. Our findings underscore the need for enhanced surveillance, monitoring, and treatment of infections and cardiopulmonary disorders in critically ill cancer patients.
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Affiliation(s)
- Stephen M Pastores
- Critical Care Medicine Service, Department of Anesthesiology and Critical Care Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
| | - Alina Dulu
- Critical Care Medicine Service, Department of Anesthesiology and Critical Care Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
| | - Louis Voigt
- Critical Care Medicine Service, Department of Anesthesiology and Critical Care Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
| | - Nina Raoof
- Critical Care Medicine Service, Department of Anesthesiology and Critical Care Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
| | - Margarita Alicea
- Critical Care Medicine Service, Department of Anesthesiology and Critical Care Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
| | - Neil A Halpern
- Critical Care Medicine Service, Department of Anesthesiology and Critical Care Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
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Blanco MT, Sacristán B, Beteta A, Fernández-Calderón MC, Hurtado C, Pérez-Giraldo C, Gómez-García AC. Cellular surface hydrophobicity as an additional phenotypic criterion applied to differentiate strains of Candida albicans and Candida dubliniensis. Diagn Microbiol Infect Dis 2008; 60:129-31. [PMID: 17900846 DOI: 10.1016/j.diagmicrobio.2007.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 07/19/2007] [Accepted: 07/23/2007] [Indexed: 10/22/2022]
Abstract
We have evaluated the cellular surface hydrophobicity (CSH) determination as an additional criterion to differentiate Candida albicans from Candida dubliniensis. Our results show that C. albicans when grown at 37 degrees C in Sabouraud is always hydrophilic, and C. dubliniensis presents high CSH levels.
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Affiliation(s)
- María-Teresa Blanco
- Area of Microbiology, Faculty of Medicine, Department of Biomedical Sciences, University of Extremadura, 06071 Badajoz, Spain.
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DNA microarray based on arrayed-primer extension technique for identification of pathogenic fungi responsible for invasive and superficial mycoses. J Clin Microbiol 2007; 46:909-15. [PMID: 18160452 DOI: 10.1128/jcm.01406-07] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An oligonucleotide microarray based on the arrayed-primer extension (APEX) technique has been developed to simultaneously identify pathogenic fungi frequently isolated from invasive and superficial infections. Species-specific oligonucleotide probes complementary to the internal transcribed spacer 1 and 2 (ITS1 and ITS2) region were designed for 24 species belonging to 10 genera, including Candida species (Candida albicans, Candida dubliniensis, Candida famata, Candida glabrata, Candida tropicalis, Candida kefyr, Candida krusei, Candida guilliermondii, Candida lusitaniae, Candida metapsilosis, Candida orthopsilosis, Candida parapsilosis, and Candida pulcherrima), Cryptococcus neoformans, Aspergillus species (Aspergillus fumigatus and Aspergillus terreus), Trichophyton species (Trichophyton rubrum and Trichophyton tonsurans), Trichosporon cutaneum, Epidermophyton floccosum, Fusarium solani, Microsporum canis, Penicillium marneffei, and Saccharomyces cerevisiae. The microarray was tested for its specificity with a panel of reference and blinded clinical isolates. The APEX technique was proven to be highly discriminative, leading to unequivocal identification of each species, including the highly related ones C. parapsilosis, C. orthopsilosis, and C. metapsilosis. Because of the satisfactory basic performance traits obtained, such as reproducibility, specificity, and unambiguous interpretation of the results, this new system represents a reliable method of potential use in clinical laboratories for parallel one-shot detection and identification of the most common pathogenic fungi.
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Gupta V, Cobb RR, Brown L, Fleming L, Mukherjee N. A quantitative polymerase chain reaction assay for detecting and identifying fungal contamination in human allograft tissue. Cell Tissue Bank 2007; 9:75-82. [DOI: 10.1007/s10561-007-9059-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 11/06/2007] [Indexed: 10/22/2022]
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Paterson RRM. Internal amplification controls have not been employed in fungal PCR hence potential false negative results. J Appl Microbiol 2007; 102:1-10. [PMID: 17184314 DOI: 10.1111/j.1365-2672.2006.03220.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polymerase chain reaction (PCR) is subject to false negative results. Samples of fungi with the genes of interest (e.g. a disease or mycotoxin) may be categorized as negative and safe as a consequence. Fungi are eukaryotic organisms that are involved in many fields of human activity such as antibiotic, toxin and food production. Certain taxa are implicated in human, animal and plant diseases. However, fungi are difficult to identify and PCR techniques have been proposed increasingly for this purpose. Internal amplification controls (IACs) will ameliorate the situation and need to become mandatory. These are nucleic acids that posses a sequence which will provide a PCR product (i) using the same primers employed for the target gene, and (ii) that will not coincide on the gel with the product of the target gene. Only one group of workers employed an IAC, to respond to potential inhibition, which was reported in 1995 from this present assessment of numerous reports. Inhibitors in cultures need to be minimized, and secondary metabolites are an obvious source. The fields reviewed herein include medical mycology, mycotoxicology, environmental mycology and plant mycology. The conclusion is that previous reports are compromised because IACs have not been employed in fungal PCR; future research must include this control at an early stage.
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Affiliation(s)
- R R M Paterson
- Centro de Engenharia Biológica, Micoteca da Universidade do Minho, Braga, Portugal.
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Leaw SN, Chang HC, Barton R, Bouchara JP, Chang TC. Identification of medically important Candida and non-Candida yeast species by an oligonucleotide array. J Clin Microbiol 2007; 45:2220-9. [PMID: 17507521 PMCID: PMC1933000 DOI: 10.1128/jcm.00543-07] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The incidence of yeast infections has increased in the recent decades, with Candida albicans still being the most common cause of infections. However, infections caused by less common yeasts have been widely reported in recent years. Based on the internal transcribed spacer 1 (ITS 1) and ITS 2 sequences of the rRNA genes, an oligonucleotide array was developed to identify 77 species of clinically relevant yeasts belonging to 16 genera. The ITS regions were amplified by PCR with a pair of fungus-specific primers, followed by hybridization of the digoxigenin-labeled PCR product to a panel of oligonucleotide probes immobilized on a nylon membrane for species identification. A collection of 452 yeast strains (419 target and 33 nontarget strains) was tested, and a sensitivity of 100% and a specificity of 97% were obtained by the array. The detection limit of the array was 10 pg of yeast genomic DNA per assay. In conclusion, yeast identification by the present method is highly reliable and can be used as an alternative to the conventional identification methods. The whole procedure can be finished within 24 h, starting from isolated colonies.
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Affiliation(s)
- Shiang Ning Leaw
- Institute of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan, Republic of China
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Kocsubé S, Tóth M, Vágvölgyi C, Dóczi I, Pesti M, Pócsi I, Szabó J, Varga J. Occurrence and genetic variability of Candida parapsilosis sensu lato in Hungary. J Med Microbiol 2007; 56:190-195. [PMID: 17244799 DOI: 10.1099/jmm.0.46838-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The occurrence and genetic variability of Candida parapsilosis isolates in two Hungarian hospitals, located in Debrecen and Pécs, were examined. Among the 209 Candida isolates examined, 20 were found to belong to C. parapsilosis sensu lato, based on morphological, physiological and molecular data. The frequency of occurrence of C. parapsilosis isolates (9.6%) was lower than that observed in Europe but higher than that observed previously in Hungary. The genetic variability of C. parapsilosis sensu lato isolates was also examined using random amplified polymorphic DNA (RAPD) analysis and sequence analysis of the intergenic transcribed spacer (ITS) region of the rRNA gene cluster. The genetic variability of the isolates was relatively high, as revealed by RAPD analysis. Two isolates were found to belong to the recently described Candida metapsilosis species (C. parapsilosis group III), based on ITS sequence data, RAPD analysis and phenotypic data. These two isolates could also be distinguished from C. parapsilosis sensu stricto isolates using a primer pair developed for the detection of C. parapsilosis group I isolates. To the best of the authors' knowledge, this is the first report on the identification of C. metapsilosis from bloodstream infection.
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Affiliation(s)
- Sándor Kocsubé
- Department of Microbiology, Faculty of Sciences, University of Szeged, PO Box 533, H-6701 Szeged, Hungary
| | - Mónika Tóth
- Department of Microbiology, Faculty of Sciences, University of Szeged, PO Box 533, H-6701 Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Sciences, University of Szeged, PO Box 533, H-6701 Szeged, Hungary
| | - Ilona Dóczi
- Department of Clinical Microbiology, Faculty of Medicine, University of Szeged, PO Box 427, H-6701 Szeged, Hungary
| | - Miklós Pesti
- Department of General and Environmental Microbiology, University of Pécs, H-7601 Pécs, Hungary
| | - István Pócsi
- Department of Microbiology and Biotechnology, Medical and Health Science Center, University of Debrecen, PO Box 63, H-4010, Debrecen, Hungary
| | - Judit Szabó
- Institute of Medical Microbiology, Faculty of Sciences, University of Debrecen, PO Box 63, H-4010, Debrecen, Hungary
| | - János Varga
- CBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Department of Microbiology, Faculty of Sciences, University of Szeged, PO Box 533, H-6701 Szeged, Hungary
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de Andrade TS, Cury AE, de Castro LGM, Hirata MH, Hirata RDC. Rapid identification of Fonsecaea by duplex polymerase chain reaction in isolates from patients with chromoblastomycosis. Diagn Microbiol Infect Dis 2007; 57:267-72. [PMID: 17338941 DOI: 10.1016/j.diagmicrobio.2006.08.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 08/06/2006] [Accepted: 08/29/2006] [Indexed: 11/26/2022]
Abstract
Fonsecaea pedrosoi is the most common etiologic agent of chromoblastomycosis. F. pedrosoi and other dematiaceous fungi are usually identified by morphologic studies. We have developed a duplex polymerase chain reaction (PCR) targeting the ribosomal DNA for rapid and more specific identification of the genus Fonsecaea. DNA samples from 103 isolates of Fonsecaea species and other dematiaceous fungi were amplified by PCR using universal and specific primers targeting ITS1-5.8S-ITS2 region of the ribosomal DNA. Universal primers were used for detection of non-Fonsecaea DNA. Fonsecaea-specific PCR product was found in 70 (68.0%) isolates including 4 strains that did not develop conidiogenesis. Thirty non-Fonsecaea and 3 Fonsecaea compacta isolates were negative by duplex PCR. These results were confirmed by DNA sequencing analysis indicating the high specificity of the duplex PCR assay. In conclusion, the duplex PCR is a rapid and specific assay for identification of Fonsecaea isolates mainly for the strains that are difficult to identify by morphologic methods.
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Affiliation(s)
- Tânia Sueli de Andrade
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brasil.
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Tavanti A, Hensgens LAM, Ghelardi E, Campa M, Senesi S. Genotyping of Candida orthopsilosis clinical isolates by amplification fragment length polymorphism reveals genetic diversity among independent isolates and strain maintenance within patients. J Clin Microbiol 2007; 45:1455-62. [PMID: 17329454 PMCID: PMC1865889 DOI: 10.1128/jcm.00243-07] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Candida parapsilosis former groups II and III have recently been established as independent species named C. orthopsilosis and C. metapsilosis, respectively. In this report, 400 isolates (290 patients) previously classified as C. parapsilosis by conventional laboratory tests were screened by BanI digestion profile analysis of the secondary alcohol dehydrogenase gene fragment and by amplification fragment length polymorphism (AFLP). Thirty-three strains collected from 13 patients were identified as C. orthopsilosis, thus giving the first retrospective evidence that C. orthopsilosis was responsible for 4.5% of the infections/colonization attributed to C. parapsilosis. AFLP was proven to unambiguously identify C. orthopsilosis at the species level and efficiently delineate intraspecific genetic relatedness. A high percentage of polymorphic AFLP bands was observed for independent isolates collected from each patient. Statistical analysis of the pairwise genetic distances and bootstrapping revealed that clonal reproduction and recombination both contribute to C. orthopsilosis genetic population structure. AFLP patterns of sequential isolates obtained from two patients demonstrated that a successful strain colonization within the same patient occurred, as revealed by strain maintenance in various body sites. No association between AFLP markers and drug resistance was observed, and none of the clinical C. orthopsilosis isolates were found to produce biofilm in vitro.
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Balajee SA, Marr KA. Phenotypic and genotypic identification of human pathogenic aspergilli. Future Microbiol 2006; 1:435-45. [PMID: 17661634 DOI: 10.2217/17460913.1.4.435] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Human pathogenic aspergilli are identified in the clinical diagnostic laboratory predominantly by macro- and micro-morphology. Such phenotypic characteristics are largely subjective and unstable, as they are influenced by environmental factors, including media and temperature of incubation. Recent advances in molecular biology have impacted the field of mycology; multiple studies have noted new genetically distinct species that are not easily distinguished by phenotypic characteristics. Strengths of molecular typing methods include objectivity and the ability to identify nonsporulating or slowly growing fungi. As such, molecular methods provide powerful tools for the study of the epidemiology, evolution and population biology of fungal pathogens. This review focuses on current and future methods of identifying aspergilli, and implications regarding Aspergillus species/strain identification.
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Affiliation(s)
- S Arunmozhi Balajee
- Centers for Disease Control and Prevention, Mycotic Diseases Branch, Atlanta, GA 30333, USA.
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