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Layouni S, Remadi L, Chaâbane-Banaoues R, Haouas N, Babba H. Identification of cuticle and midgut fungal microflora of phlebotomine sandflies collected in Tunisia. Arch Microbiol 2023; 205:64. [PMID: 36633698 DOI: 10.1007/s00203-022-03386-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023]
Abstract
Phlebotomine sand flies (Diptera: Psychodidae) are the proven vectors of Leishmaniases which are widespread parasitosis in many tropical and subtropical countries. The development of infective metacyclic Leishmania (Kinetoplastida: Trypanosomatidae) promastigotes stage is restricted to the vector midgut. Recently, several studies have assessed the influence of the sand fly midgut fungal microflora on the development of invective Leishmania stage. The aim of this study was to identify the fungal microflora from the cuticle and midgut of wild caught sandflies. A total of 50 sandflies were caught in two different leishmaniasis foci of center Tunisia and analyzed using an in vitro isolation of fungi followed by a morphological and molecular identification of fungal isolates. The morphological identification of sandflies specimens revealed five Species: Phlebotomus (P.) papatasi (n = 25), P. perniciosus (n = 15) P. riouxi (n = 6), P. longicuspis (n = 3) and P. sergenti (n = 1). Forty positive fungal cultures were isolated from 34 sand flies (19 males and 15 females) distributed as following: P. papatasi (n = 16), P. perniciosus (n = 11), P. riouxi (n = 4), P. longicuspis (n = 2) and P. sergenti (n = 1). Thirty-five cultures were isolated from the cuticles and five from the guts. A total of 15 fungi genera belonging to 8 families were identified with the predominance of Aspergillus genus followed by Penicillium genus. Among the 15 fungi genera, five were common between males and females specimens. Lecytophora canina and Leishmania major co-infection was detected in the gut of a female P. papatasi. Our preliminary findings highlight the high diversity of fungal microflora from the sand flies midguts.
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Affiliation(s)
- Samia Layouni
- Laboratory of Medical and Molecular Parasitology-Mycology LP3M (Code LR12ES08), Department of Clinical Biology B, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia. .,Department of Nutrition and Environmental Sciences, Higher Institute of Applied Sciences and Technology of Mahdia, University of Monastir, Monastir, Tunisia.
| | - Latifa Remadi
- Laboratory of Medical and Molecular Parasitology-Mycology LP3M (Code LR12ES08), Department of Clinical Biology B, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Raja Chaâbane-Banaoues
- Laboratory of Medical and Molecular Parasitology-Mycology LP3M (Code LR12ES08), Department of Clinical Biology B, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Najoua Haouas
- Laboratory of Medical and Molecular Parasitology-Mycology LP3M (Code LR12ES08), Department of Clinical Biology B, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Hamouda Babba
- Laboratory of Medical and Molecular Parasitology-Mycology LP3M (Code LR12ES08), Department of Clinical Biology B, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
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A culture-free biphasic approach for sensitive and rapid detection of pathogens in dried whole-blood matrix. Proc Natl Acad Sci U S A 2022; 119:e2209607119. [PMID: 36161889 DOI: 10.1073/pnas.2209607119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Blood stream infections (BSIs) cause high mortality, and their rapid detection remains a significant diagnostic challenge. Timely and informed administration of antibiotics can significantly improve patient outcomes. However, blood culture, which takes up to 5 d for a negative result, followed by PCR remains the gold standard in diagnosing BSI. Here, we introduce a new approach to blood-based diagnostics where large blood volumes can be rapidly dried, resulting in inactivation of the inhibitory components in blood. Further thermal treatments then generate a physical microscale and nanoscale fluidic network inside the dried matrix to allow access to target nucleic acid. The amplification enzymes and primers initiate the reaction within the dried blood matrix through these networks, precluding any need for conventional nucleic acid purification. High heme background is confined to the solid phase, while amplicons are enriched in the clear supernatant (liquid phase), giving fluorescence change comparable to purified DNA reactions. We demonstrate single-molecule sensitivity using a loop-mediated isothermal amplification reaction in our platform and detect a broad spectrum of pathogens, including gram-positive methicillin-resistant and methicillin-susceptible Staphylococcus aureus bacteria, gram-negative Escherichia coli bacteria, and Candida albicans (fungus) from whole blood with a limit of detection (LOD) of 1.2 colony-forming units (CFU)/mL from 0.8 to 1 mL of starting blood volume. We validated our assay using 63 clinical samples (100% sensitivity and specificity) and significantly reduced sample-to-result time from over 20 h to <2.5 h. The reduction in instrumentation complexity and costs compared to blood culture and alternate molecular diagnostic platforms can have broad applications in healthcare systems in developed world and resource-limited settings.
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New insights on mucormycosis and its association with the COVID-19 pandemic. Future Sci OA 2022; 8:FSO772. [PMID: 35059222 PMCID: PMC8686842 DOI: 10.2144/fsoa-2021-0122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/10/2021] [Indexed: 11/23/2022] Open
Abstract
COVID-19 continues to cause significant fatality worldwide. Glucocorticoids prove to play essential roles in COVID-19 management; however, the extensive use of steroids together with the virus immune dysregulation may increase the danger of secondary infections with mucormycosis, an angioinvasive fungal infection. Unfortunately, a definite correlation between COVID-19 and elevated mucormycosis infection cases is now clear worldwide. In this review, we discuss the historical record and epidemiology of mucormycosis as well as pathogenesis and associated host immune response, risk factors, clinical presentation, diagnosis and treatment. Special emphasis is given to its association with the current COVID-19 pandemic, including latest updates on COVID-19-associated mucormycosis cases globally, with recommendations for efficacious management. A definite correlation between COVID-19 and elevated mucormycosis infection cases is now clear worldwide. This article can be used as comprehensive tool to help clinicians and the healthcare team in getting a clearer look on the historical record and epidemiology of mucormycosis as well as pathogenesis and associated host immune response. Risk factors, clinical presentation, diagnosis, treatment options and also the latest updates on COVID-19-associated mucormycosis are also discussed, which will help in the understanding of the fatal mucormycosis infection.
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Slavin MA, Chen YC, Cordonnier C, Cornely OA, Cuenca-Estrella M, Donnelly JP, Groll AH, Lortholary O, Marty FM, Nucci M, Rex JH, Rijnders BJA, Thompson GR, Verweij PE, White PL, Hargreaves R, Harvey E, Maertens JA. When to change treatment of acute invasive aspergillosis: an expert viewpoint. J Antimicrob Chemother 2021; 77:16-23. [PMID: 34508633 PMCID: PMC8730679 DOI: 10.1093/jac/dkab317] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Invasive aspergillosis (IA) is an acute infection affecting patients who are immunocompromised, as a result of receiving chemotherapy for malignancy, or immunosuppressant agents for transplantation or autoimmune disease. Whilst criteria exist to define the probability of infection for clinical trials, there is little evidence in the literature or clinical guidelines on when to change antifungal treatment in patients who are receiving prophylaxis or treatment for IA. To try and address this significant gap, an advisory board of experts was convened to develop criteria for the management of IA for use in designing clinical trials, which could also be used in clinical practice. For primary treatment failure, a change in antifungal therapy should be made: (i) when mycological susceptibility testing identifies an organism from a confirmed site of infection, which is resistant to the antifungal given for primary therapy, or a resistance mutation is identified by molecular testing; (ii) at, or after, 8 days of primary antifungal treatment if there is increasing serum galactomannan, or galactomannan positivity in serum, or bronchoalveolar lavage fluid when the antigen was previously undetectable, or there is sudden clinical deterioration, or a new clearly distinct site of infection is detected; and (iii) at, or after, 15 days of primary antifungal treatment if the patient is clinically stable but with ≥2 serum galactomannan measurements persistently elevated compared with baseline or increasing, or if the original lesions on CT or other imaging, show progression by >25% in size in the context of no apparent change in immune status.
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Affiliation(s)
- Monica A Slavin
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, National Centre for Infections in Cancer, Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Yee-Chun Chen
- Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 100, Taiwan
| | - Catherine Cordonnier
- Service d'Hématologie clinique et de Thérapie cellulaire, DMU Cancer, CHU Henri Mondor, 94000 Créteil, France
| | - Oliver A Cornely
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); Clinical Trials Centre Cologne (ZKS Köln), Kerpener Str. 62, 50937 Cologne, Germany
| | - Manuel Cuenca-Estrella
- Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo Km2, Majadahonda, Madrid 28220, Spain
| | | | - Andreas H Groll
- Infectious Disease Research Program, Center for Bone Marrow Transplantation and Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, Building A1, 48149 Münster, Germany
| | - Olivier Lortholary
- Paris University, Necker Pasteur Center for Infectious Diseases and Tropical Medicine, IHU Imagine, Necker Enfants Malades University Hospital, and Institute Pasteur, CNRS, Molecular Mycology Unit, APHP 149, rue de Sèvres, 75015 Paris, France
| | | | - Marcio Nucci
- University Hospital, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - John H Rex
- F2G Ltd, Lankro Way, Eccles, Manchester, M30 0LX, UK.,McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Bart J A Rijnders
- Department of Internal Medicine, Section of Infectious Diseases and Department of Medical Microbiology and Infectious Diseases Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - George R Thompson
- Department of Internal Medicine, Division of Infectious Diseases, 4150 V Street, Suite G500, Sacramento, CA 95817, USA
| | - Paul E Verweij
- Radboudumc-CWZ Center of Expertise for Mycology, Radboud University Nijmegen Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.,Center for Infectious Disease Research, Diagnostics and Laboratory Surveillance National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - P Lewis White
- Public Health Wales Mycology Reference Laboratory, University Hospital of Wales, Heath Park, Cardiff, UK
| | | | - Emma Harvey
- F2G Ltd, Lankro Way, Eccles, Manchester, M30 0LX, UK
| | - Johan A Maertens
- Department of Microbiology, Immunology, and Transplantation, K.U. Leuven, Leuven, Belgium.,Department of Hematology, U.Z. Leuven, Leuven, Belgium
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Culture Cell Block Controls as a Tool to the Biomolecular Diagnosis of Infectious Diseases. Appl Immunohistochem Mol Morphol 2021; 28:484-487. [PMID: 31633490 DOI: 10.1097/pai.0000000000000811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The cell block (CB) technique has allowed easy obtainment of samples such as cellular and culture suspensions, to perform specific molecular tests such as immunohistochemistry and in situ hybridization. It has been improved along time, accuracy, and quality of the diagnoses, however, the cost of a commercial gel matrix for the preparation of CB is high and not suitable depending on the situation. The objective of this study is to test agarose as an alternative to the commercial gel matrix in the preparation of Aspergillus fumigatus' CB.
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Skusa R, Skusa C, Wohlfarth M, Hahn A, Frickmann H, Weber MA, Podbielski A, Warnke P. How to Handle CT-Guided Abscess Drainages in Microbiological Analyses? Sterile Vials vs. Blood Culture Bottles for Transport and Processing. Microorganisms 2021; 9:microorganisms9071510. [PMID: 34361944 PMCID: PMC8306503 DOI: 10.3390/microorganisms9071510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/29/2022] Open
Abstract
The aim of this investigation was to compare microbiological analyses of 100 computed tomography-guided drainages from infectious foci (thoracic, abdominal, musculoskeletal), transported and analyzed by two widely established techniques, that are (i) sterile vials or (ii) inoculated blood culture bottles. The mean number of detected microorganisms from blood culture (aerobic/anaerobic) or conventional method (sterile vial, solid and broth media) per specimen were comparable with 1.29 and 1.41, respectively (p = 1.0). The conventional method showed a trend towards shorter time-to-result (median 28.62 h) in comparison to blood culture incubation (median 43.55 h) (p = 0.0722). Of note, detection of anaerobes (13% vs. 36%) and the number of detected microorganisms in polymicrobial infections (2.76 vs. 3.26) differed significantly with an advantage towards conventional techniques (p = 0.0015; p = 0.035), especially in abdominal aspirations. Despite substantially overlapping results from both techniques, the conventional approach includes some benefits which justify its role as standard approach.
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Affiliation(s)
- Romy Skusa
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany; (A.H.); (H.F.); (A.P.); (P.W.)
- Correspondence: ; Tel.: +49-(0)3-814-945-943
| | - Christopher Skusa
- Institute of Diagnostic and Interventional Radiology, Pediatric Radiology and Neuroradiology, Rostock University Medical Center, 18057 Rostock, Germany; (C.S.); (M.W.); (M.-A.W.)
| | - Moritz Wohlfarth
- Institute of Diagnostic and Interventional Radiology, Pediatric Radiology and Neuroradiology, Rostock University Medical Center, 18057 Rostock, Germany; (C.S.); (M.W.); (M.-A.W.)
| | - Andreas Hahn
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany; (A.H.); (H.F.); (A.P.); (P.W.)
| | - Hagen Frickmann
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany; (A.H.); (H.F.); (A.P.); (P.W.)
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 22767 Hamburg, Germany
| | - Marc-André Weber
- Institute of Diagnostic and Interventional Radiology, Pediatric Radiology and Neuroradiology, Rostock University Medical Center, 18057 Rostock, Germany; (C.S.); (M.W.); (M.-A.W.)
| | - Andreas Podbielski
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany; (A.H.); (H.F.); (A.P.); (P.W.)
| | - Philipp Warnke
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany; (A.H.); (H.F.); (A.P.); (P.W.)
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Zhang M, Liu J, Shen Z, Liu Y, Song Y, Liang Y, Li Z, Nie L, Fang Y, Zhao Y. A newly developed paper embedded microchip based on LAMP for rapid multiple detections of foodborne pathogens. BMC Microbiol 2021; 21:197. [PMID: 34182947 PMCID: PMC8240391 DOI: 10.1186/s12866-021-02223-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/30/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Microfluidic chip detection technology is considered a potent tool for many bioanalytic applications. Rapid detection of foodborne pathogens in the early stages is imperative to prevent the outbreak of foodborne diseases, known as a severe threat to human health. Conventional bacterial culture methods for detecting foodborne pathogens are time-consuming, laborious, and lacking in pathogen diagnosis. To overcome this problem, we have created an embedded paper-based microchip based on isothermal loop amplification (LAMP), which can rapidly and sensitively detect foodborne pathogens. RESULTS We embed paper impregnated with LAMP reagent and specific primers in multiple reaction chambers of the microchip. The solution containing the target pathogen was injected into the center chamber and uniformly distributed into the reaction chamber by centrifugal force. The purified DNA of Escherichia coli O157:H7, Salmonella spp., Staphylococcus aureus, and Vibrio parahaemolyticus has been successfully amplified and directly detected on the microchip. The E. coli O157:H7 DNA was identified as low as 0.0134 ng μL- 1. Besides, the potential of this microchip in point-of-care testing was further tested by combining the on-chip sample purification module and using milk spiked with Salmonella spp.. The pyrolyzed milk sample was filtered through a polydopamine-coated paper embedded in the inside of the sample chamber. It was transported to the reaction chamber by centrifugal force for LAMP amplification. Then direct chip detection was performed in the reaction chamber embedded with calcein-soaked paper. The detection limit of Salmonella spp. in the sample measured by the microchip was approximately 12 CFU mL- 1. CONCLUSION The paper embedded LAMP microchip offers inexpensive, user-friendly, and highly selective pathogen detection capabilities. It is expected to have great potential as a quick, efficient, and cost-effective solution for future foodborne pathogen detection.
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Affiliation(s)
- Mimi Zhang
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China.
| | - Jinfeng Liu
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
| | - Zhiqiang Shen
- Tianjin Institute of Health and Environmental Medicine, A Key Laboratory of Risk Assessment and Control for Environment and Food Safety, Tianjin, 300050, China.
| | - Yongxin Liu
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
| | - Yang Song
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
| | - Yu Liang
- Tianjin Institute of Health and Environmental Medicine, A Key Laboratory of Risk Assessment and Control for Environment and Food Safety, Tianjin, 300050, China
| | - Zhende Li
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
| | - Lingmei Nie
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
| | - Yanjun Fang
- Tianjin Institute of Health and Environmental Medicine, A Key Laboratory of Risk Assessment and Control for Environment and Food Safety, Tianjin, 300050, China
| | - Youquan Zhao
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China.
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Krisko TI, Nicholls HT, Bare CJ, Holman CD, Putzel GG, Jansen RS, Sun N, Rhee KY, Banks AS, Cohen DE. Dissociation of Adaptive Thermogenesis from Glucose Homeostasis in Microbiome-Deficient Mice. Cell Metab 2020; 31:592-604.e9. [PMID: 32084379 PMCID: PMC7888548 DOI: 10.1016/j.cmet.2020.01.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 11/18/2019] [Accepted: 01/24/2020] [Indexed: 01/16/2023]
Abstract
Recent studies suggest that a key mechanism whereby the gut microbiome influences energy balance and glucose homeostasis is through the recruitment of brown and beige adipocytes, primary mediators of the adaptive thermogenic response. To test this, we assessed energy expenditure and glucose metabolism in two complementary mouse models of gut microbial deficiency, which were exposed to a broad range of thermal and dietary stresses. Neither ablation of the gut microbiome, nor the substantial microbial perturbations induced by cold ambient temperatures, influenced energy expenditure during cold exposure or high-fat feeding. Nevertheless, we demonstrated a critical role for gut microbial metabolism in maintaining euglycemia through the production of amino acid metabolites that optimized hepatic TCA (tricarboxylic acid) cycle fluxes in support of gluconeogenesis. These results distinguish the dispensability of the gut microbiome for the regulation of energy expenditure from its critical contribution to the maintenance of glucose homeostasis.
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Affiliation(s)
- Tibor I Krisko
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Hayley T Nicholls
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Curtis J Bare
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Corey D Holman
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Gregory G Putzel
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medical College, New York, NY 10021, USA
| | - Robert S Jansen
- Division of Infectious Diseases, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Natalie Sun
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Kyu Y Rhee
- Division of Infectious Diseases, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Alexander S Banks
- Division of Endocrinology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - David E Cohen
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA.
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Cruciani M, Mengoli C, Barnes R, Donnelly JP, Loeffler J, Jones BL, Klingspor L, Maertens J, Morton CO, White LP. Polymerase chain reaction blood tests for the diagnosis of invasive aspergillosis in immunocompromised people. Cochrane Database Syst Rev 2019; 9:CD009551. [PMID: 31478559 PMCID: PMC6719256 DOI: 10.1002/14651858.cd009551.pub4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND This is an update of the original review published in the Cochrane Database of Systematic Reviews Issue 10, 2015.Invasive aspergillosis (IA) is the most common life-threatening opportunistic invasive mould infection in immunocompromised people. Early diagnosis of IA and prompt administration of appropriate antifungal treatment are critical to the survival of people with IA. Antifungal drugs can be given as prophylaxis or empirical therapy, instigated on the basis of a diagnostic strategy (the pre-emptive approach) or for treating established disease. Consequently, there is an urgent need for research into both new diagnostic tools and drug treatment strategies. Increasingly, newer methods such as polymerase chain reaction (PCR) to detect fungal nucleic acids are being investigated. OBJECTIVES To provide an overall summary of the diagnostic accuracy of PCR-based tests on blood specimens for the diagnosis of IA in immunocompromised people. SEARCH METHODS We searched MEDLINE (1946 to June 2015) and Embase (1980 to June 2015). We also searched LILACS, DARE, Health Technology Assessment, Web of Science and Scopus to June 2015. We checked the reference lists of all the studies identified by the above methods and contacted relevant authors and researchers in the field. For this review update we updated electronic searches of the Cochrane Central Register of Controlled Trials (CENTRAL; 2018, Issue 3) in the Cochrane Library; MEDLINE via Ovid (June 2015 to March week 2 2018); and Embase via Ovid (June 2015 to 2018 week 12). SELECTION CRITERIA We included studies that: i) compared the results of blood PCR tests with the reference standard published by the European Organisation for Research and Treatment of Cancer/Mycoses Study Group (EORTC/MSG); ii) reported data on false-positive, true-positive, false-negative and true-negative results of the diagnostic tests under investigation separately; and iii) evaluated the test(s) prospectively in cohorts of people from a relevant clinical population, defined as a group of individuals at high risk for invasive aspergillosis. Case-control and retrospective studies were excluded from the analysis. DATA COLLECTION AND ANALYSIS Authors independently assessed quality and extracted data. For PCR assays, we evaluated the requirement for either one or two consecutive samples to be positive for diagnostic accuracy. We investigated heterogeneity by subgroup analyses. We plotted estimates of sensitivity and specificity from each study in receiver operating characteristics (ROC) space and constructed forest plots for visual examination of variation in test accuracy. We performed meta-analyses using the bivariate model to produce summary estimates of sensitivity and specificity. MAIN RESULTS We included 29 primary studies (18 from the original review and 11 from this update), corresponding to 34 data sets, published between 2000 and 2018 in the meta-analyses, with a mean prevalence of proven or probable IA of 16.3 (median prevalence 11.1% , range 2.5% to 57.1%). Most patients had received chemotherapy for haematological malignancy or had undergone hematopoietic stem cell transplantation. Several PCR techniques were used among the included studies. The sensitivity and specificity of PCR for the diagnosis of IA varied according to the interpretative criteria used to define a test as positive. The summary estimates of sensitivity and specificity were 79.2% (95% confidence interval (CI) 71.0 to 85.5) and 79.6% (95% CI 69.9 to 86.6) for a single positive test result, and 59.6% (95% CI 40.7 to 76.0) and 95.1% (95% CI 87.0 to 98.2) for two consecutive positive test results. AUTHORS' CONCLUSIONS PCR shows moderate diagnostic accuracy when used as screening tests for IA in high-risk patient groups. Importantly the sensitivity of the test confers a high negative predictive value (NPV) such that a negative test allows the diagnosis to be excluded. Consecutive positives show good specificity in diagnosis of IA and could be used to trigger radiological and other investigations or for pre-emptive therapy in the absence of specific radiological signs when the clinical suspicion of infection is high. When a single PCR positive test is used as the diagnostic criterion for IA in a population of 100 people with a disease prevalence of 16.3% (overall mean prevalence), three people with IA would be missed (sensitivity 79.2%, 20.8% false negatives), and 17 people would be unnecessarily treated or referred for further tests (specificity of 79.6%, 21.4% false positives). If we use the two positive test requirement in a population with the same disease prevalence, it would mean that nine IA people would be missed (sensitivity 59.6%, 40.4% false negatives) and four people would be unnecessarily treated or referred for further tests (specificity of 95.1%, 4.9% false positives). Like galactomannan, PCR has good NPV for excluding disease, but the low prevalence of disease limits the ability to rule in a diagnosis. As these biomarkers detect different markers of disease, combining them is likely to prove more useful.
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Affiliation(s)
- Mario Cruciani
- Azienda ULSS9 ScaligeraAntibiotic Stewardship ProgrammeVeronaItaly37135
| | - Carlo Mengoli
- Università di PadovaDepartment of Histology, Microbiology and Medical BiotechnologyVia Aristide Gabelli, 63PadovaItaly35121
| | - Rosemary Barnes
- Cardiff University School of MedicineInfection, Immunity and BiochemistryHeath ParkCardiffWalesUKCF14 4XN
| | - J Peter Donnelly
- Nijmegen Institute for InfectionDepartment of HaematologyInflammation and ImmunityRadboud University Nijmegen Medical CenterNijmegenNetherlands
| | - Juergen Loeffler
- Julius‐Maximilians‐UniversitatMedizinische Klinik IIKlinikstrasse 6‐8WurzburgGermany97070
| | - Brian L Jones
- Glasgow Royal Infirmary & University of GlasgowDepartment of Medical MicrobiologyGlasgowUK
| | - Lena Klingspor
- Division of Clinical MicrobiologyDepartment of Laboratory MedicineKarolinska University HospitalStockholmSweden
| | - Johan Maertens
- Acute Leukemia and Stem Cell Transplantation UnitDepartment of HematologyUniversity Hospitals LeuvenLeuvenBelgium
| | - Charles O Morton
- Western Sydney UniversitySchool of Science and HealthCampbelltown CampusCampbelltownNew South WalesAustralia2560
| | - Lewis P White
- Microbiology Cardiff, UHWPublic Health WalesHeath ParkCardiffUKCF37 1EN
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Fadhel M, Patel SV, Liu E, Fune L, Wasserman EJ, Asif A. Disseminated Pulmonary with Isolated Muscular Mucormycosis in an Acute Myeloid Leukemia Patient: A Case Report and Literature Review. AMERICAN JOURNAL OF CASE REPORTS 2019; 20:1210-1215. [PMID: 31417073 PMCID: PMC6711263 DOI: 10.12659/ajcr.916864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Patient: Female, 53 Final Diagnosis: Muscular mucormycosis Symptoms: Arm pain • leg pain • swelling Medication: — Clinical Procedure: — Specialty: Infectious Diseases
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Affiliation(s)
- Mustafa Fadhel
- Department of Medicine, Jersey Shore University Medical Center, Neptune, NJ, USA
| | - Swapnil V Patel
- Department of Medicine, Jersey Shore University Medical Center, Neptune, NJ, USA
| | - Edward Liu
- Department of Medicine, Jersey Shore University Medical Center, Neptune, NJ, USA
| | - Lito Fune
- Department of Medicine, Jersey Shore University Medical Center, Neptune, NJ, USA
| | - Ethan J Wasserman
- Department of Medicine, Jersey Shore University Medical Center, Neptune, NJ, USA
| | - Arif Asif
- Department of Medicine, Jersey Shore University Medical Center, Neptune, NJ, USA
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11
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Frickmann H, Künne C, Hagen RM, Podbielski A, Normann J, Poppert S, Looso M, Kreikemeyer B. Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples - a proof-of-principle assessment. BMC Microbiol 2019; 19:75. [PMID: 30961537 PMCID: PMC6454699 DOI: 10.1186/s12866-019-1448-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/28/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The potential of next-generation sequencing (NGS) for hypothesis-free pathogen diagnosis from (poly-)microbially contaminated, formalin-fixed, paraffin embedded tissue samples from patients with invasive fungal infections and amebiasis was investigated. Samples from patients with chromoblastomycosis (n = 3), coccidioidomycosis (n = 2), histoplasmosis (n = 4), histoplasmosis or cryptococcosis with poor histological discriminability (n = 1), mucormycosis (n = 2), mycetoma (n = 3), rhinosporidiosis (n = 2), and invasive Entamoeba histolytica infections (n = 6) were analyzed by NGS (each one Illumina v3 run per sample). To discriminate contamination from putative infections in NGS analysis, mean and standard deviation of the number of specific sequence fragments (paired reads) were determined and compared in all samples examined for the pathogens in question. RESULTS For matches between NGS results and histological diagnoses, a percentage of species-specific reads greater than the 4th standard deviation above the mean value of all 23 assessed sample materials was required. Potentially etiologically relevant pathogens could be identified by NGS in 5 out of 17 samples of patients with invasive mycoses and in 1 out of 6 samples of patients with amebiasis. CONCLUSIONS The use of NGS for hypothesis-free pathogen diagnosis from contamination-prone formalin-fixed, paraffin-embedded tissue requires further standardization.
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Affiliation(s)
- Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Bernhard-Nocht Str. 74, 20359, Hamburg, Germany. .,Institute for Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany.
| | - Carsten Künne
- Department of Bioinformatics, Max-Planck Institute for Heart and Lung Research Bad Nauheim, Parkstraße 1, 61231, Bad Nauheim, Germany
| | - Ralf Matthias Hagen
- Department of Preventive Medicine, Bundeswehr Medical Academy, Neuherbergstraße 11, 80937, Munich, Germany
| | - Andreas Podbielski
- Institute for Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany
| | - Jana Normann
- Institute for Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany
| | - Sven Poppert
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland.,Faculty of Medicine, University Basel, Socinstrasse 57, 4051, Basel, Switzerland
| | - Mario Looso
- Department of Bioinformatics, Max-Planck Institute for Heart and Lung Research Bad Nauheim, Parkstraße 1, 61231, Bad Nauheim, Germany
| | - Bernd Kreikemeyer
- Institute for Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany
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12
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Kumar M, Mugunthan M, Kapoor R, Pandalanghat S. Speciation of fungi using real time PCR with molecular beacons: Can we solve the enigma of diagnosis of invasive fungal disease? Med J Armed Forces India 2019; 75:41-49. [PMID: 30705477 PMCID: PMC6349607 DOI: 10.1016/j.mjafi.2017.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 12/15/2017] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Invasive fungal diseases (IFDs) are difficult to diagnose and associated with high mortality rates, especially in the immunosuppressed. Species of Aspergillus and Candida are the cause of majority of invasive fungal disease however IFDs are also caused by Fusarium, Zygomycetes, Trichosporon, etc. Early detection is crucial for appropriate antifungal therapy. Blood cultures usually fail to isolate filamentous fungi, while detection of circulating beta-d-glucan or galactomannan antigens show variable sensitivity and specificity. There is a need of reliable, sensitive and specific diagnostic tests for IFDs. METHODS A real-time Polymerase Chain Reaction (PCR) assay with a universal primer/molecular beacon system was developed for detecting and speciating most of the pathogenic fungi implicated in IFD. A single-reaction assay was designed targeting a carefully selected region of the ITS2 and ITS5 subunits of the fungal rDNA gene along with four molecular beacons capable of differential hybridization to the amplicons of different species. This generated a signature set of melting temperatures using the standard strains. The assay was tested on clinical specimens from patients with suspected invasive fungal disease. RESULTS The assay was tested on 72 clinical samples and 72 healthy controls. Of these, 22 clinical samples (6/8 proven; 13/29 probable; 3/35 possible IFD, classified by the EORTC/MSG criteria) were positive by PCR and generated a set of melting temperatures enabling identification of the causative fungus. The assay was negative in all healthy controls. CONCLUSION The molecular beacon assay is a promising tool providing a rapid method for detection and monitoring of invasive fungal disease in immunosuppressed patients.
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Affiliation(s)
- Mahadevan Kumar
- Professor (Microbiology), Army Hospital (R&R), Delhi Cantt 110010, India
| | - M. Mugunthan
- Consultant (Microbiologist), Yashoda Hospital, Hyderabad, Telengana, India
| | - Rajan Kapoor
- Senior Adviser (Haematology), Army Hospital (R&R), Delhi Cantt 110010, India
| | - Suresh Pandalanghat
- Senior Adviser (Oncology), Command Hospital (Eastern Command), Kolkata, India
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13
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Álvarez-Mosquera I, Hernáez S, Sánchez J, Suárez MD, Cisterna R. Diagnosis of Superficial Mycoses by a Rapid and Effective PCR Method from Samples of Scales, Nails and Hair. Mycopathologia 2018; 183:777-783. [PMID: 30094709 DOI: 10.1007/s11046-018-0290-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/28/2018] [Indexed: 11/26/2022]
Abstract
Superficial mycoses are the most frequently diagnosed affections of the stratum corneum of the skin, nails and hair. It is generally caused by the presence of yeasts and dermatophytes. Onychomycosis is the most common infection with an incidence of 80-90% in Europe generally produced by Trichophyton rubrum. The aim of this study is to compare the traditional diagnostic techniques of superficial mycoses with a homemade and wide-spectrum fungal polymerase chain reaction (PCR) technique that amplifies a specific region of the 18S ribosomal RNA (rRNA) directly from samples of scales, nails and hair. A total of 626 clinical samples (obtained in the Basurto University Hospital, Bilbao, Spain) were analysed by traditional culture, microscopy and PCR. DNA extraction was carried out by using an extraction buffer and bovine serum, and amplification of samples and performance of the PCR were checked by conventional agarose gel electrophoresis with subsequent sequencing of amplified samples. A total of 211 samples (34%) resulted in positive diagnosis with at least one of the two applied methods: culture (21%) and PCR (22%). Despite the low percentage of identification achieved by the sequencing technique (40%), the value contributed by the amplification of the 18S region of the rRNA was considered important in the identification as it showed a high predictive values for both positive and negative diagnoses (90.9% and 94.6%, respectively). The proposed PCR method has been confirmed as a complementary, rapid, and effective method in the diagnosis of superficial mycoses. Additionally, it reduces the time to obtain satisfactory results from 4 weeks to 7 h.
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Affiliation(s)
- Irene Álvarez-Mosquera
- Immunology, Microbiology and Parasitology Department, School of Medicine, University of Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Bizkaia, Spain.
| | - Silvia Hernáez
- Clinical Microbiology and Infection Control Department, Basurto University Hospital, Avda.Montevideo 18, 48013, Bilbao, Bizkaia, Spain
| | - Juan Sánchez
- Clinical Microbiology and Infection Control Department, Basurto University Hospital, Avda.Montevideo 18, 48013, Bilbao, Bizkaia, Spain
| | - Maria Dolores Suárez
- Clinical Microbiology and Infection Control Department, Basurto University Hospital, Avda.Montevideo 18, 48013, Bilbao, Bizkaia, Spain
| | - Ramón Cisterna
- Clinical Microbiology and Infection Control Department, Basurto University Hospital, Avda.Montevideo 18, 48013, Bilbao, Bizkaia, Spain
- Immunology, Microbiology and Parasitology Department, School of Medicine, University of Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Bizkaia, Spain
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14
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Krohn S, Zeller K, Böhm S, Chatzinotas A, Harms H, Hartmann J, Heidtmann A, Herber A, Kaiser T, Treuheit M, Hoffmeister A, Berg T, Engelmann C. Molecular quantification and differentiation of Candida species in biological specimens of patients with liver cirrhosis. PLoS One 2018; 13:e0197319. [PMID: 29897895 PMCID: PMC5999271 DOI: 10.1371/journal.pone.0197319] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/29/2018] [Indexed: 12/26/2022] Open
Abstract
Patients with liver cirrhosis are susceptible to fungal infections. Due to low sensitivity of culture-based methods, we applied a real-time PCR assay targeting the 18S rRNA gene in combination with direct sequencing and terminal-restriction fragment length polymorphism (T-RFLP) in order to establish a novel tool to detect fungal DNA and to quantify and differentiate Candida DNA, also in polyfungal specimens. In total, 281 samples (blood n = 135, ascites n = 92, duodenal fluid n = 54) from 135 patients with liver cirrhosis and 52 samples (blood n = 26, duodenal fluid n = 26) from 26 control patients were collected prospectively. Candida DNA was quantified in all samples. Standard microbiological culture was performed for comparison. Blood and ascites samples, irrespective of the patient cohort, showed a method-independent low fungal detection rate of approximately 1%, and the Candida DNA content level did not exceed 3.0x101 copies ml-1 in any sample. In contrast, in duodenal fluid of patients with liver cirrhosis high fungal detection rates were discovered by using both PCR- and culture-based techniques (81.5% vs. 66.7%; p = 0.123) and the median level of Candida DNA was 3.8x105 copies ml-1 (2.3x102-6.3x109). In cirrhosis and controls, fungal positive culture results were confirmed by PCR in 96% and an additional amount of 44% of culture negative duodenal samples were PCR positive. Using T-RFLP analysis in duodenal samples, overall 85% of results from microbial culture were confirmed and in 75% of culture-negative but PCR-positive samples additional Candida species could be identified. In conclusion, PCR-based methods and subsequent differentiation of Candida DNA might offer a quick approach to identifying Candida species without prior cultivation.
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Affiliation(s)
- Sandra Krohn
- University Hospital Leipzig, Section of Hepatology, Clinic of Gastroenterology and Rheumatology, University Hospital Leipzig, Leipzig, Germany
- Helmholtz Centre for Environmental Research—UFZ, Department of Environmental Microbiology, Leipzig, Germany
- * E-mail:
| | - Katharina Zeller
- University Hospital Leipzig, Section of Hepatology, Clinic of Gastroenterology and Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Stephan Böhm
- Ludwig Maximilians-University, Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Munich, Germany
| | - Antonis Chatzinotas
- Helmholtz Centre for Environmental Research—UFZ, Department of Environmental Microbiology, Leipzig, Germany
| | - Hauke Harms
- Helmholtz Centre for Environmental Research—UFZ, Department of Environmental Microbiology, Leipzig, Germany
| | - Jan Hartmann
- Department of Gastroenterology and Hepatology, Hospital and Outpatient Clinic for Internal Medicine A, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
| | - Anett Heidtmann
- Helmholtz Centre for Environmental Research—UFZ, Department of Environmental Microbiology, Leipzig, Germany
| | - Adam Herber
- University Hospital Leipzig, Section of Hepatology, Clinic of Gastroenterology and Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Thorsten Kaiser
- Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Maud Treuheit
- Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Albrecht Hoffmeister
- Interdisciplinary Endoscopy Unit, Clinic of Gastroenterology and Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Thomas Berg
- University Hospital Leipzig, Section of Hepatology, Clinic of Gastroenterology and Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Cornelius Engelmann
- University Hospital Leipzig, Section of Hepatology, Clinic of Gastroenterology and Rheumatology, University Hospital Leipzig, Leipzig, Germany
- University College London, Institute for Liver and Digestive Health, Royal Free Campus, London, United Kingdom
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15
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Das P, Pandey P, Harishankar A, Chandy M, Bhattacharya S, Chakrabarti A. Standardization of a two-step real-time polymerase chain reaction based method for species-specific detection of medically important Aspergillus species. Indian J Med Microbiol 2018; 35:381-388. [PMID: 29063883 DOI: 10.4103/ijmm.ijmm_17_190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
PURPOSE Standardization of Aspergillus polymerase chain reaction (PCR) poses two technical challenges (a) standardization of DNA extraction, (b) optimization of PCR against various medically important Aspergillus species. Many cases of aspergillosis go undiagnosed because of relative insensitivity of conventional diagnostic methods such as microscopy, culture or antigen detection. The present study is an attempt to standardize real-time PCR assay for rapid sensitive and specific detection of Aspergillus DNA in EDTA whole blood. MATERIALS AND METHODS Three nucleic acid extraction protocols were compared and a two-step real-time PCR assay was developed and validated following the recommendations of the European Aspergillus PCR Initiative in our setup. In the first PCR step (pan-Aspergillus PCR), the target was 28S rDNA gene, whereas in the second step, species specific PCR the targets were beta-tubulin (for Aspergillus fumigatus, Aspergillus flavus, Aspergillus terreus), gene and calmodulin gene (for Aspergillus niger). RESULTS Species specific identification of four medically important Aspergillus species, namely, A. fumigatus, A. flavus, A. niger and A. terreus were achieved by this PCR. Specificity of the PCR was tested against 34 different DNA source including bacteria, virus, yeast, other Aspergillus sp., other fungal species and for human DNA and had no false-positive reactions. The analytical sensitivity of the PCR was found to be 102 CFU/ml. CONCLUSION The present protocol of two-step real-time PCR assays for genus- and species-specific identification for commonly isolated species in whole blood for diagnosis of invasive Aspergillus infections offers a rapid, sensitive and specific assay option and requires clinical validation at multiple centers.
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Affiliation(s)
- P Das
- Department of Microbiology, Tata Medical Center, Kolkata, West Bengal, India
| | - P Pandey
- Department of Microbiology, Tata Medical Center, Kolkata, West Bengal, India
| | - A Harishankar
- Department of Microbiology, Tata Medical Center, Kolkata, West Bengal, India
| | - M Chandy
- Department of Clinical Hematology, Tata Medical Center, Kolkata, West Bengal, India
| | - S Bhattacharya
- Department of Microbiology, Tata Medical Center, Kolkata, West Bengal, India
| | - A Chakrabarti
- Department of Microbiology, WHO Collaborating Center for Reference and Research of Fungi of Medical Importance, PGIMER, Chandigarh, India
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16
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Wagner K, Springer B, Pires VP, Keller PM. Molecular detection of fungal pathogens in clinical specimens by 18S rDNA high-throughput screening in comparison to ITS PCR and culture. Sci Rep 2018; 8:6964. [PMID: 29725065 PMCID: PMC5934447 DOI: 10.1038/s41598-018-25129-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/13/2018] [Indexed: 12/30/2022] Open
Abstract
The rising incidence of invasive fungal infections and the expanding spectrum of fungal pathogens makes early and accurate identification of the causative pathogen a daunting task. Diagnostics using molecular markers enable rapid identification of fungi, offer new insights into infectious disease dynamics, and open new possibilities for infectious disease control and prevention. We performed a retrospective study using clinical specimens (N = 233) from patients with suspected fungal infection previously subjected to culture and/or internal transcribed spacer (ITS) PCR. We used these specimens to evaluate a high-throughput screening method for fungal detection using automated DNA extraction (QIASymphony), fungal ribosomal small subunit (18S) rDNA RT-PCR and amplicon sequencing. Fungal sequences were compared with sequences from the curated, commercially available SmartGene IDNS database for pathogen identification. Concordance between 18S rDNA RT-PCR and culture results was 91%, and congruence between 18S rDNA RT-PCR and ITS PCR results was 94%. In addition, 18S rDNA RT-PCR and Sanger sequencing detected fungal pathogens in culture negative (N = 13) and ITS PCR negative specimens (N = 12) from patients with a clinically confirmed fungal infection. Our results support the use of the 18S rDNA RT-PCR diagnostic workflow for rapid and accurate identification of fungal pathogens in clinical specimens.
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Affiliation(s)
- K Wagner
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - B Springer
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Graz, Austria
| | - V P Pires
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - P M Keller
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
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17
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Esashika K, Saiki T. DNA Hybridization Assay Using Gold Nanoparticles and Electrophoresis Separation Provides 1 pM Sensitivity. Bioconjug Chem 2017; 29:182-189. [DOI: 10.1021/acs.bioconjchem.7b00682] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Keiko Esashika
- Department of Electronics
and Electrical Engineering, Keio University, Yokohama 223-8522, Japan
| | - Toshiharu Saiki
- Department of Electronics
and Electrical Engineering, Keio University, Yokohama 223-8522, Japan
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18
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Agha Kuchak Afshari S, Rahimi H, Hashemi SJ, Daie Ghazvini R, Badali H, Aghaei Gharehbolagh S, Rezaie S. Evaluation of PCR-reverse line blot hybridization assay for simultaneous identification of medically important saprophytic fungi. J Mycol Med 2017; 28:173-179. [PMID: 29100947 DOI: 10.1016/j.mycmed.2017.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 09/05/2017] [Accepted: 09/11/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND In immunocompromised patients suffering from invasive fungal infections, rapid identification of fungal species is important since the appropriate treatment is usually related to the responsible species. We describe here, an assay based on combination of PCR and reverse line blot hybridization (PCR/RLB) for differentiation causative agent of fungal infections. MATERIALS AND METHODS We performed PCR/RLB assay on 10 reference strains, which include Aspergillus species (A. fumigatus, A. flavus, A. niger, A. terreus, and A. clavatus), Mucor circnelloides, Rhizopus oryzae, Alternaria alternata, Cladosporium herbarum, and Fusarium solani. Besides, twenty-two clinical specimens from patients with proven fungal infections were analyzed for the identification of species. The obtained results were then compared with the results of culture and sequence analysis. RESULTS The fungal species-specific oligonucleotide probes were able to distinguish between all species represented in this study with the exception of cross-reactivity between A. niger and A. fumigatus species. Two specimens, which were represented as mixed fungi in culture, were identified properly by this method. Results of the RLB assay were concordant with the culture and ITS sequencing results. CONCLUSION Our result demonstrate that the RLB assay potentially is suitable for rapid and simultaneous identification of variety fungal pathogens directly from culture as well as from clinical specimens.
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Affiliation(s)
- S Agha Kuchak Afshari
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - H Rahimi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - S J Hashemi
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - R Daie Ghazvini
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - H Badali
- Department of Medical Mycology and Parasitology, Antimicrobial Resistance Research Center (ARRC), Mazandaran University of Medical Science, Sari, Iran
| | - S Aghaei Gharehbolagh
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - S Rezaie
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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19
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Molecular Identification of Saprochaete capitata in Human Blood and Paraffinized Tissue Samples. J Clin Microbiol 2017; 55:2556-2559. [PMID: 28592551 DOI: 10.1128/jcm.00876-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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20
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Safavieh M, Coarsey C, Esiobu N, Memic A, Vyas JM, Shafiee H, Asghar W. Advances in Candida detection platforms for clinical and point-of-care applications. Crit Rev Biotechnol 2017; 37:441-458. [PMID: 27093473 PMCID: PMC5083221 DOI: 10.3109/07388551.2016.1167667] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Invasive candidiasis remains one of the most serious community and healthcare-acquired infections worldwide. Conventional Candida detection methods based on blood and plate culture are time-consuming and require at least 2-4 days to identify various Candida species. Despite considerable advances for candidiasis detection, the development of simple, compact and portable point-of-care diagnostics for rapid and precise testing that automatically performs cell lysis, nucleic acid extraction, purification and detection still remains a challenge. Here, we systematically review most prominent conventional and nonconventional techniques for the detection of various Candida species, including Candida staining, blood culture, serological testing and nucleic acid-based analysis. We also discuss the most advanced lab on a chip devices for candida detection.
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Affiliation(s)
- Mohammadali Safavieh
- Division of Biomedical Engineering, Division of Renal medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Chad Coarsey
- Department of Computer Engineering and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, USA
- College of Engineering and Computer Science, Asghar-Lab, Micro and Nanotechnologies for Medicine, Boca Raton, FL, USA
| | - Nwadiuto Esiobu
- Biological Sciences Department, Florida Atlantic University, Davie, FL, USA
| | - Adnan Memic
- Center of Nanotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jatin Mahesh Vyas
- Department of Medicine, Division of Infectious Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Hadi Shafiee
- Division of Biomedical Engineering, Division of Renal medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Waseem Asghar
- Department of Computer Engineering and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, USA
- College of Engineering and Computer Science, Asghar-Lab, Micro and Nanotechnologies for Medicine, Boca Raton, FL, USA
- Biological Sciences Department, Florida Atlantic University, Davie, FL, USA
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21
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Galactofuranose antigens, a target for diagnosis of fungal infections in humans. Future Sci OA 2017; 3:FSO199. [PMID: 28883999 PMCID: PMC5583699 DOI: 10.4155/fsoa-2017-0030] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 03/20/2017] [Indexed: 12/02/2022] Open
Abstract
The use of biomarkers for the detection of fungal infections is of interest to complement histopathological and culture methods. Since the production of antibodies in immunocompromised patients is scarce, detection of a specific antigen could be effective for early diagnosis. D-Galactofuranose (Galf) is the antigenic epitope in glycoconjugates of several pathogenic fungi. Since Galf is not biosynthesized by mammals, it is an attractive candidate for diagnosis of infection. A monoclonal antibody that recognizes Galf is commercialized for detection of aspergillosis. The linkage of Galf in the natural glycans and the chemical structures of the synthesized Galf-containing oligosaccharides are described in this paper. The oligosaccharides could be used for the synthesis of artificial carbohydrate-based antigens, not enough exploited for diagnosis. D-Galactofuranose (Galf) is the unit in polysaccharides and glycoconjugates of several pathogenic fungi that is recognized by the immune system. Since Galf is not synthesized by mammals, it is an attractive candidate for diagnosis of infection. Since the production of antibodies in immunocompromised patients is scarce, detection of a specific antigen could be effective for early diagnosis. An antibody that recognizes Galf is commercialized for the detection of aspergillosis. Chemically synthesized Galf-containing oligosaccharides, reviewed in this paper, could therefore be used for the synthesis of artificial carbohydrate-based antigens and in diagnosis.
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22
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Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C, Wilmes P. Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life. Front Microbiol 2017; 8:738. [PMID: 28512451 PMCID: PMC5411419 DOI: 10.3389/fmicb.2017.00738] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/10/2017] [Indexed: 12/26/2022] Open
Abstract
Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus, and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides. Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not only bacteria but also archaea and microeukaryotes. This further highlights the need for resolving bacterial, archaeal, and microeukaryotic dynamics in future longitudinal studies of microbial colonization and succession within the neonatal gastrointestinal tract.
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Affiliation(s)
- Linda Wampach
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Anna Heintz-Buschart
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Angela Hogan
- Integrated BioBank of LuxembourgLuxembourg, Luxembourg
| | - Emilie E L Muller
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Cedric C Laczny
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Luisa W Hugerth
- Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, Royal Institute of TechnologyStockholm, Sweden
| | - Lutz Bindl
- Centre Hospitalier de LuxembourgLuxembourg, Luxembourg
| | - Jean Bottu
- Centre Hospitalier de LuxembourgLuxembourg, Luxembourg
| | - Anders F Andersson
- Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, Royal Institute of TechnologyStockholm, Sweden
| | - Carine de Beaufort
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg.,Centre Hospitalier de LuxembourgLuxembourg, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
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Abstract
PCR-based detection of fungal pathogens offers a sensitive and specific tool for the diagnosis of invasive fungal infections. A large variety of different clinical specimen types can be used as original material. However, certain precautions, in addition to the published MIQE guidelines [1], need to be taken to prevent contaminations from airborne fungal spores and PCR reagents. In addition, the European Aspergillus PCR Initiative (EAPCRI) recently defined standards for Aspergillus PCR [2, 3], following these recommendations leads to superior sensitivity. The combination of fungal PCR with the galactomannan ELISA assay increases the sensitivity for the detection of Aspergillus DNA from blood, compared to a single assay only [4, 5].
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Affiliation(s)
- Jan Springer
- Medizinische Klinik II, Universitätklinikum Würzburg, Josef-Schneider-Str. 2, Würzburg, 97080, Germany
| | - Jürgen Löffler
- Medizinische Klinik II, Universitätklinikum Würzburg, Josef-Schneider-Str. 2, Würzburg, 97080, Germany.
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Shamim M, Kumar P, Kumar RR, Kumar M, Kumar RR, Singh KN. Assessing Fungal Biodiversity Using Molecular Markers. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Kotrotsiou T, Chatzimichaloglou A, Nasr A, Spandou E, Patsatsi A, Sotiriadis D, Vyzantiadis TA. A comparative study of three extraction protocols of DNA from nails: Potential use in the diagnosis of onychomycoses. Mycoses 2016; 60:183-187. [DOI: 10.1111/myc.12581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/06/2016] [Accepted: 10/08/2016] [Indexed: 11/27/2022]
Affiliation(s)
- T. Kotrotsiou
- 1st Department of Microbiology; Medical School; Aristotle University of Thessaloniki; Thessaloniki Greece
| | - A. Chatzimichaloglou
- 1st Department of Microbiology; Medical School; Aristotle University of Thessaloniki; Thessaloniki Greece
| | - A. Nasr
- 2nd Department of Dermatology; Medical School; Aristotle University of Thessaloniki; Thessaloniki Greece
| | - E. Spandou
- Department of Experimental Physiology; Medical School; Aristotle University of Thessaloniki; Greece
| | - A. Patsatsi
- 2nd Department of Dermatology; Medical School; Aristotle University of Thessaloniki; Thessaloniki Greece
| | - D. Sotiriadis
- 2nd Department of Dermatology; Medical School; Aristotle University of Thessaloniki; Thessaloniki Greece
| | - T.-A. Vyzantiadis
- 1st Department of Microbiology; Medical School; Aristotle University of Thessaloniki; Thessaloniki Greece
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Aspergillus galactomannan detection in comparison to a real-time PCR assay in serum samples from a high-risk group of patients. Cent Eur J Immunol 2016; 40:454-60. [PMID: 26862310 PMCID: PMC4737742 DOI: 10.5114/ceji.2015.56968] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/28/2015] [Indexed: 11/17/2022] Open
Abstract
Invasive aspergillosis (IA) is a severe infection with a 70% mortality rate. Aspergillus fumigatus is responsible for over 90% of those infections. The diagnosis of invasive aspergillosis is based on clinical sample culture and detection of fungal hyphae in histopathological examination. Additional tests may include the detection of the galactomannan antigen and of fungal genetic material in serum and bronchoalveolar washings. The present study was to assess the use of these two rapid tests in the diagnosis of invasive aspergillosis: serological one - to detect the galactomannan antigen (ELISA assay), and real-time PCR, and to establish a possible correlation between these two methods.
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28
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Springer J, Goldenberger D, Schmidt F, Weisser M, Wehrle-Wieland E, Einsele H, Frei R, Löffler J. Development and application of two independent real-time PCR assays to detect clinically relevant Mucorales species. J Med Microbiol 2016; 65:227-234. [PMID: 26743820 DOI: 10.1099/jmm.0.000218] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
PCR-based detection of Mucorales species could improve diagnosis of suspected invasive fungal infection, leading to a better patient outcome. This study describes two independent probe-based real-time PCR tests for detection of clinically relevant Mucorales, targeting specific fragments of the 18S and the 28S rRNA genes. Both assays have a short turnaround time, allow fast, specific and very sensitive detection of clinically relevant Mucorales and have the potential to be used as quantitative tests. They were validated on various clinical samples (fresh and formalin-fixed paraffin-embedded specimens, mainly biopsies, n = 17). The assays should be used as add-on tools to complement standard techniques; a combined approach of both real-time PCR assays has 100 % sensitivity. Genus identification by subsequent sequencing is possible for amplicons of the 18S PCR assay. In conclusion, combination of the two independent Mucorales assays described in this study, 18S and 28S, detected all clinical samples associated with proven Mucorales infection (n = 10). Reliable and specific identification of Mucorales is a prerequisite for successful antifungal therapy as these fungi show intrinsic resistance to voriconazole and caspofungin.
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Affiliation(s)
- Jan Springer
- Department for Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Daniel Goldenberger
- Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland
| | - Friderike Schmidt
- Department for Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Maja Weisser
- Clinic of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Elisabeth Wehrle-Wieland
- Clinic of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Hermann Einsele
- Department for Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Reno Frei
- Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland
| | - Jürgen Löffler
- Department for Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
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Rivera V, Gaviria M, Muñoz-Cadavid C, Cano L, Naranjo T. Validation and clinical application of a molecular method for the identification of Cryptococcus neoformans/Cryptococcus gattii complex DNA in human clinical specimens. Braz J Infect Dis 2015; 19:563-70. [PMID: 26365230 PMCID: PMC9425379 DOI: 10.1016/j.bjid.2015.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 07/07/2015] [Accepted: 07/07/2015] [Indexed: 12/26/2022] Open
Abstract
The diagnosis of cryptococcosis is usually performed based on cultures of tissue or body fluids and isolation of the fungus, but this method may require several days. Direct microscopic examination, although rapid, is relatively insensitive. Biochemical and immunodiagnostic rapid tests are also used. However, all of these methods have limitations that may hinder final diagnosis. The increasing incidence of fungal infections has focused attention on tools for rapid and accurate diagnosis using molecular biological techniques. Currently, PCR-based methods, particularly nested, multiplex and real-time PCR, provide both high sensitivity and specificity. In the present study, we evaluated a nested PCR targeting the gene encoding the ITS-1 and ITS-2 regions of rDNA in samples from a cohort of patients diagnosed with cryptococcosis. The results showed that in our hands, this Cryptococcus nested PCR assay has 100% specificity and 100% sensitivity and was able to detect until 2 femtograms of Cryptococcus DNA.
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30
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Boch T, Reinwald M, Postina P, Cornely OA, Vehreschild JJ, Heußel CP, Heinz WJ, Hoenigl M, Eigl S, Lehrnbecher T, Hahn J, Claus B, Lauten M, Egerer G, Müller MC, Will S, Merker N, Hofmann WK, Buchheidt D, Spiess B. Identification of invasive fungal diseases in immunocompromised patients by combining an Aspergillus specific PCR with a multifungal DNA-microarray from primary clinical samples. Mycoses 2015; 58:735-45. [PMID: 26497302 DOI: 10.1111/myc.12424] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2015] [Indexed: 12/21/2022]
Abstract
The increasing incidence of invasive fungal diseases (IFD), most of all invasive aspergillosis (IA) in immunocompromised patients emphasises the need to improve the diagnostic tools for detection of fungal pathogens. We investigated the diagnostic performance of a multifungal DNA-microarray detecting 15 different fungi [Aspergillus, Candida, Fusarium, Mucor, Rhizopus, Scedosporium and Trichosporon species (spp.)] in addition to an Aspergillus specific polymerase chain reaction (PCR) assay. Biopsies, bronchoalveolar lavage and peripheral blood samples of 133 immunocompromised patients (pts) were investigated by a multifungal DNA-microarray as well as a nested Aspergillus specific PCR assay. Patients had proven (n = 18), probable (n = 29), possible (n = 48) and no IFD (n = 38) and were mostly under antifungal therapy at the time of sampling. The results were compared to culture, histopathology, imaging and serology, respectively. For the non-Aspergillus IFD the microarray analysis yielded in all samples a sensitivity of 64% and a specificity of 80%. Best results for the detection of all IFD were achieved by combining DNA-microarray and Aspergillus specific PCR in biopsy samples (sensitivity 79%; specificity 71%). The molecular assays in combination identify genomic DNA of fungal pathogens and may improve identification of causative pathogens of IFD and help overcoming the diagnostic uncertainty of culture and/or histopathology findings, even during antifungal therapy.
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Affiliation(s)
- T Boch
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | - M Reinwald
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | - P Postina
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | - O A Cornely
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany.,Clinical Trials Centre Cologne, ZKS Köln, BMBF 01KN1106, Centre for Integrated Oncology CIO Köln Bonn, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - J J Vehreschild
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany.,German Centre for Infection Research, Partner site Bonn-Cologne, Cologne, Germany
| | - C P Heußel
- Department of Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - W J Heinz
- Department II of Internal Medicine, Würzburg University Hospital, Würzburg, Germany
| | - M Hoenigl
- Section of Infectious Diseases and Tropical Medicine and Division of Pulmonology, Medical University of Graz, Graz, Austria
| | - S Eigl
- Section of Infectious Diseases and Tropical Medicine and Division of Pulmonology, Medical University of Graz, Graz, Austria
| | - T Lehrnbecher
- Pediatric Hematology and Oncology, Children's Hospital, University of Frankfurt, Frankfurt, Germany
| | - J Hahn
- Regensburg University Hospital, Regensburg, Germany
| | - B Claus
- Ludwigshafen General Hospital, Ludwigshafen, Germany
| | - M Lauten
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - G Egerer
- Department V of Internal Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - M C Müller
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | - S Will
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | - N Merker
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | - W-K Hofmann
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | - D Buchheidt
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | - B Spiess
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
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31
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Cruciani M, Mengoli C, Loeffler J, Donnelly P, Barnes R, Jones BL, Klingspor L, Morton O, Maertens J. Polymerase chain reaction blood tests for the diagnosis of invasive aspergillosis in immunocompromised people. Cochrane Database Syst Rev 2015:CD009551. [PMID: 26424726 DOI: 10.1002/14651858.cd009551.pub3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND Invasive aspergillosis (IA) is the most common life-threatening opportunistic invasive mould infection in immunocompromised people. Early diagnosis of IA and prompt administration of appropriate antifungal treatment are critical to the survival of people with IA. Antifungal drugs can be given as prophylaxis or empirical therapy, instigated on the basis of a diagnostic strategy (the pre-emptive approach) or for treating established disease. Consequently there is an urgent need for research into both new diagnostic tools and drug treatment strategies. Newer methods such as polymerase chain reaction (PCR) to detect fungal nucleic acids are increasingly being investigated. OBJECTIVES To provide an overall summary of the diagnostic accuracy of PCR-based tests on blood specimens for the diagnosis of IA in immunocompromised people. SEARCH METHODS We searched MEDLINE (1946 to June 2015) and EMBASE (1980 to June 2015). We also searched LILACS, DARE, Health Technology Assessment, Web of Science and Scopus to June 2015. We checked the reference lists of all the studies identified by the above methods and contacted relevant authors and researchers in the field. SELECTION CRITERIA We included studies that: i) compared the results of blood PCR tests with the reference standard published by the European Organisation for Research and Treatment of Cancer/Mycoses Study Group (EORTC/MSG); ii) reported data on false-positive, true-positive, false-negative and true-negative results of the diagnostic tests under investigation separately; and iii) evaluated the test(s) prospectively in cohorts of people from a relevant clinical population, defined as a group of individuals at high risk for invasive aspergillosis. Case-control studies were excluded from the analysis. DATA COLLECTION AND ANALYSIS Authors independently assessed quality and extracted data. For PCR assays, we evaluated the requirement for either one or two consecutive samples to be positive for diagnostic accuracy. We investigated heterogeneity by subgroup analyses. We plotted estimates of sensitivity and specificity from each study in receiver operating characteristics (ROC) space and constructed forest plots for visual examination of variation in test accuracy. We performed meta-analyses using the bivariate model to produce summary estimates of sensitivity and specificity. MAIN RESULTS Eighteen primary studies, corresponding to 19 cohorts and 22 data sets, published between 2000 and 2013 were included in the meta-analyses, with a median prevalence of IA (proven or probable) of 12.0% (range 2.5 to 30.8 %). The majority of people had received chemotherapy for a haematological malignancy or had undergone a hematopoietic stem cell transplant. Several PCR techniques were used among the included studies. The sensitivity and specificity of PCR for the diagnosis of IA varied according to the interpretative criteria used to define a test as positive. The mean sensitivity and specificity were 80.5% (95% CI; 73.0 to 86.3) and 78.5% (67.8 to 86.4) for a single positive test result, and 58.0% (36.5 to 76.8) and 96.2% (89.6 to 98.6) for two consecutive positive test results. AUTHORS' CONCLUSIONS PCR shows moderate diagnostic accuracy when used as screening tests for IA in high-risk patient groups. Importantly the sensitivity of the test confers a high negative predictive value (NPV) such that a negative test allows the diagnosis to be excluded. Consecutive positives show good specificity in diagnosis of IA and could be used to trigger radiological and other investigations or for pre-emptive therapy in the absence of specific radiological signs when the clinical suspicion of infection is high. When a single PCR positive test is used as diagnostic criterion for IA in a population of 100 people with a disease prevalence of 13.0% (overall mean prevalence), three people with IA would be missed (sensitivity 80.5%, 19.5% false negatives), and 19 people would be unnecessarily treated or referred for further tests (specificity of 78.5%, 21.5% false positives). If we use the two positive test requirement in a population with the same disease prevalence, it would mean that six IA people would be missed (sensitivity 58.0%, 42.1% false negatives) and three people would be unnecessarily treated or referred for further tests (specificity of 96.2%, 3.8% false positives). Galactomannan and PCR have good NPV for excluding disease but the low prevalence of disease limits the ability to rule in a diagnosis. The biomarkers are detecting different aspects of disease and the combination of both together is likely to be more useful.
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Affiliation(s)
- Mario Cruciani
- Center of Community Medicine and Infectious Diseases Service, ULSS 20 Verona, Via Germania, 20, Verona, Italy, 37135
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Cruciani M, Mengoli C, Loeffler J, Donnelly P, Barnes R, Jones BL, Klingspor L, Morton O, Maertens J. Polymerase chain reaction blood tests for the diagnosis of invasive aspergillosis in immunocompromised people. Cochrane Database Syst Rev 2015:CD009551. [PMID: 26343815 DOI: 10.1002/14651858.cd009551.pub2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Invasive aspergillosis (IA) is the most common life-threatening opportunistic invasive mould infection in immunocompromised people. Early diagnosis of IA and prompt administration of appropriate antifungal treatment are critical to the survival of people with IA. Antifungal drugs can be given as prophylaxis or empirical therapy, instigated on the basis of a diagnostic strategy (the pre-emptive approach) or for treating established disease. Consequently there is an urgent need for research into both new diagnostic tools and drug treatment strategies. Newer methods such as polymerase chain reaction (PCR) to detect fungal nucleic acids are increasingly being investigated. OBJECTIVES To provide an overall summary of the diagnostic accuracy of PCR-based tests on blood specimens for the diagnosis of IA in immunocompromised people. SEARCH METHODS We searched MEDLINE (1946 to June 2015) and EMBASE (1980 to June 2015). We also searched LILACS, DARE, Health Technology Assessment, Web of Science and Scopus to June 2015. We checked the reference lists of all the studies identified by the above methods and contacted relevant authors and researchers in the field. SELECTION CRITERIA We included studies that: i) compared the results of blood PCR tests with the reference standard published by the European Organisation for Research and Treatment of Cancer/Mycoses Study Group (EORTC/MSG); ii) reported data on false-positive, true-positive, false-negative and true-negative results of the diagnostic tests under investigation separately; and iii) evaluated the test(s) prospectively in cohorts of people from a relevant clinical population, defined as a group of individuals at high risk for invasive aspergillosis. Case-control studies were excluded from the analysis. DATA COLLECTION AND ANALYSIS Authors independently assessed quality and extracted data. For PCR assays, we evaluated the requirement for either one or two consecutive samples to be positive for diagnostic accuracy. We investigated heterogeneity by subgroup analyses. We plotted estimates of sensitivity and specificity from each study in receiver operating characteristics (ROC) space and constructed forest plots for visual examination of variation in test accuracy. We performed meta-analyses using the bivariate model to produce summary estimates of sensitivity and specificity. MAIN RESULTS Eighteen primary studies, corresponding to 19 cohorts and 22 data sets, published between 2000 and 2013 were included in the meta-analyses, with a median prevalence of IA (proven or probable) of 12.0% (range 2.5 to 30.8 %). The majority of people had received chemotherapy for a haematological malignancy or had undergone a hematopoietic stem cell transplant. Several PCR techniques were used among the included studies. The sensitivity and specificity of PCR for the diagnosis of IA varied according to the interpretative criteria used to define a test as positive. The mean sensitivity and specificity were 80.5% (95% CI; 73.0 to 86.3) and 78.5% (67.8 to 86.4) for a single positive test result, and 58.0% (36.5 to 76.8) and 96.2% (89.6 to 98.6) for two consecutive positive test results. AUTHORS' CONCLUSIONS PCR shows moderate diagnostic accuracy when used as screening tests for IA in high-risk patient groups. Importantly the sensitivity of the test confers a high negative predictive value (NPV) such that a negative test allows the diagnosis to be excluded. Consecutive positives show good specificity in diagnosis of IA and could be used to trigger radiological and other investigations or for pre-emptive therapy in the absence of specific radiological signs when the clinical suspicion of infection is high. When a single PCR positive test is used as diagnostic criterion for IA in a population of 100 people with a disease prevalence of 13.0% (overall mean prevalence), three people with IA would be missed (sensitivity 80.5%, 19.5% false negatives), and 19 people would be unnecessarily treated or referred for further tests (specificity of 78.5%, 21.5% false negatives). If we use the two positive test requirement in a population with the same disease prevalence, it would mean that six IA people would be missed (sensitivity 58.0%, 42.1% false negatives) and three people would be unnecessarily treated or referred for further tests (specificity of 96.2%, 3.8% false negatives). Galactamannan and PCR have good NPV for excluding disease but the low prevalence of disease limits the ability to rule in a diagnosis. The biomarkers are detecting different aspects of disease and the combination of both together is likely to be more useful.
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Affiliation(s)
- Mario Cruciani
- Center of Community Medicine and Infectious Diseases Service, ULSS 20 Verona, Via Germania, 20, Verona, Italy, 37135
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Application of Culture-Independent Rapid Diagnostic Tests in the Management of Invasive Candidiasis and Cryptococcosis. J Fungi (Basel) 2015; 1:217-251. [PMID: 29376910 PMCID: PMC5753112 DOI: 10.3390/jof1020217] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/17/2015] [Accepted: 08/17/2015] [Indexed: 12/26/2022] Open
Abstract
The diagnosis of invasive candidiasis (IC) and cryptococcosis is often complicated by slow and insensitive culture-based methods. Such delay results in poor outcomes due to the lack of timely therapeutic interventions. Advances in serological, biochemical, molecular and proteomic approaches have made a favorable impact on this process, improving the timeliness and accuracy of diagnosis with resultant improvements in outcome. This paper will serve as an overview of recent developments in the diagnostic approaches to infections due to these important yeast-fungi.
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Gaviria M, Rivera V, Muñoz-Cadavid C, Cano LE, Naranjo TW. Validation and clinical application of a nested PCR for paracoccidioidomycosis diagnosis in clinical samples from Colombian patients. Braz J Infect Dis 2015; 19:376-83. [PMID: 26100437 PMCID: PMC9427526 DOI: 10.1016/j.bjid.2015.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/08/2015] [Accepted: 04/22/2015] [Indexed: 11/30/2022] Open
Abstract
Paracoccidioidomycosis is a systemic and endemic mycosis, restricted to tropical and subtropical areas of Latin America. The infection is caused by the thermal dimorphic fungus Paracoccidioides brasiliensis and Paracoccidioides lutzii. The diagnosis of paracoccidioidomycosis is usually performed by microscopic examination, culture and immunodiagnostic tests to respiratory specimens, body fluids and/or biopsies; however these methods require laboratory personnel with experience and several days to produce a result. In the present study, we have validated and evaluated a nested PCR assay targeting the gene encoding the Paracoccidioides gp43 membrane protein in 191 clinical samples: 115 samples from patients with proven infections other than paracoccidioidomycosis, 51 samples as negative controls, and 25 samples from patients diagnosed with paracoccidioidomycosis. Additionally, the specificity of the nested PCR assay was also evaluated using purified DNA isolated from cultures of different microorganisms (n=35) previously identified by culture and/or sequencing. The results showed that in our hands, this nested PCR assay for gp43 protein showed specificity and sensitivity rates of 100%. The optimized nested PCR conditions in our laboratory allowed detection down to 1fg of P. brasiliensis DNA.
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Affiliation(s)
- Marcela Gaviria
- Corporación para Investigaciones Biológicas, Medellín, Colombia
| | - Vanessa Rivera
- Corporación para Investigaciones Biológicas, Medellín, Colombia
| | | | - Luz Elena Cano
- Corporación para Investigaciones Biológicas, Medellín, Colombia; Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Tonny Williams Naranjo
- Corporación para Investigaciones Biológicas, Medellín, Colombia; Escuela de Ciencias de la Salud, Universidad Pontifica Bolivariana, Medellín, Colombia.
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Ambasta A, Carson J, Church DL. The use of biomarkers and molecular methods for the earlier diagnosis of invasive aspergillosis in immunocompromised patients. Med Mycol 2015; 53:531-57. [DOI: 10.1093/mmy/myv026] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 04/08/2015] [Indexed: 12/15/2022] Open
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Detection of tropical fungi in formalin-fixed, paraffin-embedded tissue: still an indication for microscopy in times of sequence-based diagnosis? BIOMED RESEARCH INTERNATIONAL 2015; 2015:938721. [PMID: 25961048 PMCID: PMC4417575 DOI: 10.1155/2015/938721] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 02/27/2015] [Accepted: 03/09/2015] [Indexed: 01/31/2023]
Abstract
INTRODUCTION The aim of the study was the evaluation of panfungal PCR protocols with subsequent sequence analysis for the diagnostic identification of invasive mycoses in formalin-fixed, paraffin-embedded tissue samples with rare tropical mycoses. MATERIALS AND METHODS Five different previously described panfungal PCR/sequencing protocols targeting 18S and 28S ribosomal RNA gene fragments as well as internal transcribed spacer 1 and 2 fragments were evaluated with a collection of 17 formalin-fixed, paraffin-embedded tissue samples of patients with rare and/or tropical invasive mycoses, comprising chromoblastomycosis, coccidioidomycosis, cryptococcosis, histoplasmosis, mucormycosis, mycetoma/maduromycosis, and rhinosporidiosis, in a proof-of-principle analysis. RESULTS The primers of the panfungal PCRs readily and predominantly reacted with contaminating environmental fungi that had deposited on the paraffin blocks. Altogether three sequence results of histoplasmosis and mycetoma samples that matched the histological assessment were associated with sample age <10 years and virtually without PCR inhibition. CONCLUSIONS The high risk of amplifying environmental contaminants severely reduces the usefulness of the assessed panfungal PCR/sequencing protocols for the identification of rare and/or tropical mycoses in stored formalin-fixed, paraffin-embedded tissues. Histological assessment remains valuable for such indications if cultural differentiation is impossible from inactivated sample material.
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Maschmeyer G, Carratalà J, Buchheidt D, Hamprecht A, Heussel CP, Kahl C, Lorenz J, Neumann S, Rieger C, Ruhnke M, Salwender H, Schmidt-Hieber M, Azoulay E. Diagnosis and antimicrobial therapy of lung infiltrates in febrile neutropenic patients (allogeneic SCT excluded): updated guidelines of the Infectious Diseases Working Party (AGIHO) of the German Society of Hematology and Medical Oncology (DGHO). Ann Oncol 2015; 26:21-33. [PMID: 24833776 PMCID: PMC4269340 DOI: 10.1093/annonc/mdu192] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 04/29/2014] [Accepted: 05/02/2014] [Indexed: 12/13/2022] Open
Abstract
Up to 25% of patients with profound neutropenia lasting for >10 days develop lung infiltrates, which frequently do not respond to broad-spectrum antibacterial therapy. While a causative pathogen remains undetected in the majority of cases, Aspergillus spp., Pneumocystis jirovecii, multi-resistant Gram-negative pathogens, mycobacteria or respiratory viruses may be involved. In at-risk patients who have received trimethoprim-sulfamethoxazole (TMP/SMX) prophylaxis, filamentous fungal pathogens appear to be predominant, yet commonly not proven at the time of treatment initiation. Pathogens isolated from blood cultures, bronchoalveolar lavage (BAL) or respiratory secretions are not always relevant for the etiology of pulmonary infiltrates and should therefore be interpreted critically. Laboratory tests for detecting Aspergillus galactomannan, β-D-glucan or DNA from blood, BAL or tissue samples may facilitate the diagnosis; however, most polymerase chain reaction assays are not yet standardized and validated. Apart from infectious agents, pulmonary side-effects from cytotoxic drugs, radiotherapy or pulmonary involvement by the underlying malignancy should be included into differential diagnosis and eventually be clarified by invasive diagnostic procedures. Pre-emptive treatment with mold-active systemic antifungal agents improves clinical outcome, while other microorganisms are preferably treated only when microbiologically documented. High-dose TMP/SMX is first choice for treatment of Pneumocystis pneumonia, while cytomegalovirus pneumonia is treated primarily with ganciclovir or foscarnet in most patients. In a considerable number of patients, clinical outcome may be favorable despite respiratory failure, so that intensive care should be unrestrictedly provided in patients whose prognosis is not desperate due to other reasons.
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Affiliation(s)
- G Maschmeyer
- Department of Hematology, Oncology and Palliative Care, Klinikum Ernst von Bergmann, Potsdam, Germany.
| | - J Carratalà
- Department of Infectious Diseases, Bellvitge University Hospital, University of Barcelona, Barcelona, Spain
| | - D Buchheidt
- Department of Hematology and Oncology, Mannheim University Hospital, Mannheim
| | - A Hamprecht
- Institution for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne
| | - C P Heussel
- Department of Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik, University Hospital, Heidelberg
| | - C Kahl
- Department of Hematology and Oncology, Klinikum Magdeburg, Magdeburg
| | - J Lorenz
- Department of Pneumology, Infectious Diseases, Sleep Medicine and Intensive Care, Klinikum Lüdenscheid, Lüdenscheid
| | - S Neumann
- Medical Oncology, AMO MVZ, Wolfsburg
| | - C Rieger
- Department of Medicine III, University Hospital Großhadern, München
| | - M Ruhnke
- Department of Medical Oncology and Hematology, Charité University Medicine Campus Mitte, Berlin
| | - H Salwender
- Department of Hematology, Oncology, Stem Cell Transplantation, Asklepios Klinik Altona, Hamburg
| | - M Schmidt-Hieber
- Department of Hematology, Oncology and Tumor Immunology, Helios-Klinikum Berlin-Buch, Berlin, Germany
| | - E Azoulay
- AP-HP, Hopital Saint-Louis, Service de Réanimation Médicale, Université Paris-Diderot, Sorbonne Paris-Cité, Faculté de Médecine, Paris, France
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Houshyarfard M, Rouhani H, Falahati-Rastegar M, Malekzadeh-Shafaroudi S, Mahdikhani-Moghaddam E. Characterization of Iranian nonaflatoxigenic strains of Aspergillus flavus based on microsatellite-primed PCR. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2015; 4:43-55. [PMID: 27843995 PMCID: PMC5019298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Out of fifty-two Iranian nonaflatoxigenic strains of Aspergillus flavus,collected from various substrates (soil and kernel) and sources (peanut, corn and pistachio), fifteen representatives were selected according to their different geographical origins (six provinces: Guilan and Golestan, Ardebil, Fars, Kerman and Semnan) and vegetative compatibility groups (VCGs, IR1 to IR15) for microsatellite-primed PCR analysis. Two inter-simple sequence repeat (ISSR) primers AFMPP and AFM13 were used to determine polymorphism and the relationship among strain isolates. A. flavus isolates were identified by their morphologies and their identities were confirmed by PCR amplification using the specific primer pair ITS1 and ITS4. The results revealed variations in the percentages of polymorphisms. In the ISSR analysis, primers AFMPP and AFM13 generated a total of 18 and 23 amplicons among the fungal strains, out of which 12 (66.7%) and 22 (95.7%) were polymorphic, respectively. Cluster analysis of the ISSR data was carried out using 1 D DNA gel image analysis. The two dendrograms obtained through these markers showed six different clusterings of testing nonaflatoxigenic A. flavus L strains, but we noticed that some clusters were different in some cases. The microsatellite-primed PCR data revealed that the Iranian nonaflatoxigenic isolates of A. flavus were not clustered according to their origins and sources. This study is the first to characterize Iranian nonaflatoxigenic isolates of A. flavus using ISSR markers.
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Affiliation(s)
- Mahmoud Houshyarfard
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Iran
| | - Hamid Rouhani
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Iran
| | | | - Saeid Malekzadeh-Shafaroudi
- Department of Crop Biotechnology and Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Iran,Address for correspondence:Department of Crop Biotechnology and Breeding, Faculty of Agriculture, Ferdowsi University, Mashhad, Iran, Tel: +98 (051) 8662101, E-mail:
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Ashrafi M, Nabili M, Shokohi T, Janbabaie G, Hedayati MT, Ali-Moghaddam K. A real time PCR assay on blood for diagnosis of invasive candidiasis in immunocompromised patient. Curr Med Mycol 2015; 1:35-41. [PMID: 28680979 PMCID: PMC5490320 DOI: 10.18869/acadpub.cmm.1.1.35] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background and Purpose: Invasive candidiasis (IC) is a significant cause of morbidity and mortality in patients with hematologic disorders and bone marrow transplant recipients. Rapid, specific and sensitive test for the timely accuracy in immunocompromised patients to reduce mortality rates and prevent IC progress is necessary. We established a real-time PCR assay on blood for the diagnosis and differentiation of the causative Candida species. Materials and Methods: Whole blood samples were collected twice, from 72 patients for Real Time PCR and blood culture assays. The primers and hybridization probes were designed to potentiate the specific sequence of 18S rRNA genes using Light Cycler system and Fluorescence Resonance Energy Transfer (FERT). The patients with hematologic malignancies and bone marrow transplant recipients were evaluated for IC based on the revised European Organization for Research and Treatment of Cancer/ Mycoses Study Group (EORTC/MSG) criteria. Results: From 2009 to 2011, 72 patients with hematologic malignancies and bone marrow transplant recipients were evaluated for IC. The female to male ratio was 27:45; the mean age was 32.1 years. The most common malignancy in this patient was acute myeloid leukemia (AML) (27.8%) and acute lymphoblastic leukemia (ALL) (26.4%). Out of 72 patients, 11 patients (15.3%) had positive real time PCR /probe results. Based on the melting temperature (Tm) analysis, 5 (45.4%) C. krusei, 3 (27.2%) C. tropicalis, 2 (18.1%) C. parapsilosis and 1 C. albicans (9%) were identified. According to the revised EORTC / MSG, 1 patient (9%) and 10 patients (91%) were defined as proven and possible groups of IC, respectively. The mortality rate in proven and possible IC patient was found 54.5%. Conclusion: The established Real-time PCR/FRET probe assay is an appropriate diagnostic tool for the detection of Candida species DNA and the management of patients suffering from hematologic malignancies and bone marrow recipient are at risk for IC
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Affiliation(s)
- M Ashrafi
- Student research committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - M Nabili
- Student research committee, Mazandaran University of Medical Sciences, Sari, Iran.,Social Security Organization, Golestan, Iran
| | - T Shokohi
- Invasive Fungi Research Center (IFRC), and Department of Medical Parasitology and Mycology, Mazandaran University of Medical Sciences, Sari, Iran
| | - G Janbabaie
- Department of Internal Medicine, Cell and Molecular Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - M T Hedayati
- Invasive Fungi Research Center (IFRC), and Department of Medical Parasitology and Mycology, Mazandaran University of Medical Sciences, Sari, Iran
| | - K Ali-Moghaddam
- Hematology-Oncology Research Center and Stem Cell Transplantation Research Center (HORCSCT), Tehran University of Medical Sciences, Iran
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Teranishi H, Ohzono N, Inamura N, Kato A, Wakabayashi T, Akaike H, Terada K, Ouchi K. Detection of bacteria and fungi in blood of patients with febrile neutropenia by real-time PCR with universal primers and probes. J Infect Chemother 2014; 21:189-93. [PMID: 25497674 DOI: 10.1016/j.jiac.2014.11.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/27/2014] [Accepted: 11/15/2014] [Indexed: 10/24/2022]
Abstract
Febrile neutropenia is the main treatment-related cause of mortality in cancer patients. During June 2012 to April 2014, 97 blood culture samples were collected from patients receiving chemotherapy for hematological malignancy and cancer with febrile neutropenia episodes (FNEs). The samples were examined for the presence of bacteria and fungi using real-time PCR amplification and sequencing of 16S and 18S rRNA genes. Bacteria were identified in 20 of 97 samples (20.6%) by the real-time PCR assay and in 10 of 97 (10.3%) samples by blood culture. In 6 blood culture-positive samples, the real-time PCR assay detected the same type of bacteria. No fungi were detected by the real-time PCR assay or blood culture. During antibiotic therapy, all samples were negative by blood culture, but the real-time PCR assay yielded a positive result in 2 cases of 2 (100%). The bacterial DNA copy number was not well correlated with the serum C-reactive protein titer of patients with FNEs. We conclude that a real-time PCR assay could provide better detection of causative microbes' in a shorter time, and with a smaller blood sample than blood culture. Using a real-time PCR assay in combination with blood culture could improve microbiological documentation of FNEs.
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Affiliation(s)
- Hideto Teranishi
- Department of Pediatrics, Kawasaki Medical School, Kurashiki-shi, Okayama, Japan.
| | - Nanae Ohzono
- Department of Pediatrics, Kawasaki Medical School, Kurashiki-shi, Okayama, Japan
| | - Norikazu Inamura
- Department of Pediatrics, Kawasaki Medical School, Kurashiki-shi, Okayama, Japan
| | - Atsushi Kato
- Department of Pediatrics, Kawasaki Medical School, Kurashiki-shi, Okayama, Japan
| | - Tokio Wakabayashi
- Department of Pediatrics, Kawasaki Medical School, Kurashiki-shi, Okayama, Japan
| | - Hiroto Akaike
- Department of Pediatrics, Kawasaki Medical School, Kurashiki-shi, Okayama, Japan
| | - Kihei Terada
- Department of Pediatrics, Kawasaki Medical School, Kurashiki-shi, Okayama, Japan
| | - Kazunobu Ouchi
- Department of Pediatrics, Kawasaki Medical School, Kurashiki-shi, Okayama, Japan
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Kothari A, Morgan M, Haake DA. Emerging technologies for rapid identification of bloodstream pathogens. Clin Infect Dis 2014; 59:272-8. [PMID: 24771332 DOI: 10.1093/cid/ciu292] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Technologies for rapid microbial identification are poised to revolutionize clinical microbiology and enable informed decision making for patients with life-threatening bloodstream infections. Species identification of microorganisms in positive blood cultures can be performed in minutes using commercial fluorescence in situ hybridization tests or mass spectroscopy. Microorganisms in positive blood cultures can also be identified within 1-2.5 hours using automated polymerase chain reaction-based systems that can also detect selected antibiotic resistance markers, such as methicillin resistance. When combined with antibiotic stewardship programs, these approaches improve clinical outcomes and reduce healthcare expenditures. Tests for direct detection in whole blood samples are highly desirable because of their potential to identify bloodstream pathogens without waiting 1-2 days for blood cultures to become positive. However, results for pathogen detection in whole blood do not overlap with those of conventional blood culture techniques and we are still learning how best to use these approaches.
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Affiliation(s)
- Atul Kothari
- Division of Infectious Diseases, VA Greater Los Angeles Healthcare System
| | - Margie Morgan
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center
| | - David A Haake
- Division of Infectious Diseases, VA Greater Los Angeles Healthcare System Departments of Medicine, Urology, and Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California
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Scheel CM, Gómez BL. Diagnostic Methods for Histoplasmosis: Focus on Endemic Countries with Variable Infrastructure Levels. CURRENT TROPICAL MEDICINE REPORTS 2014; 1:129-137. [PMID: 31187020 DOI: 10.1007/s40475-014-0020-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Diagnosis of histoplasmosis remains challenging in resource-limited regions where HIV/AIDS is epidemic and histoplasmosis is endemic. Early and rapid detection of histoplasmosis is essential to preventing morbidity and mortality, yet few diagnostic options are available in low-resource areas of the world. The aim of this review is to provide an overview of the current status of the diagnosis of histoplasmosis, including an update on recent developments and utilization of new technologies. We discuss the specific diagnostic challenges faced in endemic regions, emphasizing the need for greater availability and standardization of rapid diagnostics for this endemic and neglected disease. While significant progress has been made in the development of new methods, clinical utility must be established by means of formal and extensive clinical studies.
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Affiliation(s)
- Christina M Scheel
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS G11, Atlanta, GA, USA
| | - Beatriz L Gómez
- Corporación para Investigaciones Biólogicas, Cra. 72 No 78 B 141, Medellín, Colombia
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Cordonnier C, Robin C, Alanio A, Bretagne S. Antifungal pre-emptive strategy for high-risk neutropenic patients: why the story is still ongoing. Clin Microbiol Infect 2014; 20 Suppl 6:27-35. [PMID: 24283975 DOI: 10.1111/1469-0691.12428] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Neutropenic patients with haematological malignancies are at high risk of invasive fungal disease (IFD). Due to limitations in specific procedures to establish an early diagnosis of IFD, two historical unpowered studies suggested, three decades ago, that giving an empirical antifungal treatment to patients with persistent or recurrent fever under broad-spectrum antibacterials, could reduce the risk of IFD. For cost and toxicity reasons, this strategy became debated when modern imaging and indirect biological markers became available. Different pre-emptive strategies, either based on lung imaging, galactomannan antigenaemia, fungal PCR, or a combination of several parameters, were designed with the goal of restricting the administration of antifungals to the more at-risk patients with early signs of IFD. Almost all pre-emptive studies showed or suggested a reduction of administration and cost of antifungals during neutropenic phases. However, the clinical pertinence and safety of the strategy, and mainly its optimal design, are still pending. This paper reviews the evolution of these strategies and how they may be implemented in the haematology ward.
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Affiliation(s)
- C Cordonnier
- Haematology Department, Henri Mondor Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP) and University Paris-Est-Créteil, Créteil, France
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Abstract
In susceptible patients, invasive aspergillosis has a high incidence and a mortality of up to 80%. The diagnosis of this condition is difficult, especially in the early stages of the disease and, as a consequence, antifungal therapy, despite its expense and toxicity, is often initiated empirically. Until recently, there were very few effective antifungal agents for established invasive aspergillosis, but the introduction of two new drugs, voriconazole and caspofungin, has increased the treatment options. These newer antifungal therapies, combined with improved early diagnosis due to the introduction of newer microbiologic techniques, offer the hope that there will be a significant improvement in the substantial morbidity and mortality associated with invasive aspergillosis over the next 5 years.
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Affiliation(s)
- S R Doffman
- Barts & the London NHS Trust, West Smithfield, London, EC1A 7BE, UK.
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Laín A, Elguezabal N, Moragues MD, García-Ruiz JC, del Palacio A, Pontón J. Contribution of serum biomarkers to the diagnosis of invasive candidiasis. Expert Rev Mol Diagn 2014; 8:315-25. [DOI: 10.1586/14737159.8.3.315] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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ISSHIKI ATSUNORI, TAKEHARU HITOSHI, AOKI SHUNSUKE, KOKAJI MAMI, TANABE SUGURU, KASETANI TAISUKE, YOSHIDA MITSUHIRO. Development of a Multiple Detection Technique for Fungi by DNA Microarray with the Simultaneous Use of Internal Transcribed Spacer Region of Ribosomal RNA Gene and β-Tubulin Gene Probes. Biocontrol Sci 2014; 19:139-45. [DOI: 10.4265/bio.19.139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Candida identification: a journey from conventional to molecular methods in medical mycology. World J Microbiol Biotechnol 2014; 30:1437-51. [PMID: 24379160 DOI: 10.1007/s11274-013-1574-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 12/02/2013] [Indexed: 12/17/2022]
Abstract
The incidence of Candida infections have increased substantially in recent years due to aggressive use of immunosuppressants among patients. Use of broad-spectrum antibiotics and intravascular catheters in the intensive care unit have also attributed with high risks of candidiasis among immunocompromised patients. Among Candida species, C. albicans accounts for the majority of superficial and systemic infections, usually associated with high morbidity and mortality often caused due to increase in antimicrobial resistance and restricted number of antifungal drugs. Therefore, early detection of candidemia and correct identification of Candida species are indispensable pre-requisites for appropriate therapeutic intervention. Since blood culture based methods lack sensitivity, and species-specific identification by conventional method is time-consuming and often leads to misdiagnosis within closely related species, hence, molecular methods may provide alternative for accurate and rapid identification of Candida species. Although, several molecular approaches have been developed for accurate identification of Candida species but the internal transcribed spacer 1 and 2 (ITS1 and ITS2) regions of the rRNA gene are being used extensively in a variety of formats. Of note, ITS sequencing and PCR-RFLP analysis of ITS region seems to be promising as a rapid, easy, and cost-effective method for identification of Candida species. Here, we review a number of existing techniques ranging from conventional to molecular approaches currently in use for the identification of Candida species. Further, advantages and limitations of these methods are also discussed with respect to their discriminatory power, reproducibility, and ease of performance.
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Alwakeel SS. Molecular identification of isolated fungi from stored apples in Riyadh, Saudi Arabia. Saudi J Biol Sci 2013; 20:311-7. [PMID: 24235866 DOI: 10.1016/j.sjbs.2013.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 05/01/2013] [Accepted: 05/10/2013] [Indexed: 10/26/2022] Open
Abstract
Fungi causes most plant disease. When fruits are stored at suboptimal conditions, fungi grows, and some produce mycotoxin which can be dangerous for human consumption. Studies have shown that the Penicillium and Monilinia species commonly cause spoilage of fruits, especially apples. Several other genera and species were reported to grow to spoil fruits. This study was conducted to isolate and identify fruit spoilage by fungi on apples collected in Riyadh, Saudi Arabia and conduct a molecular identification of the fungal isolates. Thus, we collected 30 samples of red delicious and Granny Smith apples with obvious spoilage from different supermarkets between February and March of 2012 in Riyadh, Saudi Arabia. Each apple was placed in a sterile plastic bag in room temperature (25-30 °C) for six days or until fungal growth was evident all over the sample. Growth of fungal colonies on PDA was counted and sent for molecular confirmation by PCR. Six fruit spoilage fungi were isolated, including Penicillium chrysogenum, Penicillium adametzii, Penicillium chrysogenum, Penicillium steckii, Penicillium chrysogenum, and Aspergillus oryzae. P. chrysogenum was the most frequent isolate which was seen in 14 of a total of 34 isolates (41.2%), followed by P. adametzii and A. oryzae with seven isolates each (20.6%) and the least was P. steckii with six isolates (17.6%). Penicillium species comprised 27 of the total 34 (79.4%) isolates. Sequence analysis of the ITS regions of the nuclear encoded rDNA showed significant alignments for P. chrysogenum, P. adametzii and A. oryzae. Most of these fungal isolates are useful and are rarely pathogenic; however they can still produce severe illness in immune-compromised individuals, and sometimes otherwise healthy people may also become infected. It is therefore necessary to evaluate the possible production of mycotoxins by these fungi to determine a potential danger and to establish its epidemiology in order to develop adequate methods of control.
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Affiliation(s)
- Suaad S Alwakeel
- University of Princess Nora Bent Abdul Rahman, Riyadh, Saudi Arabia
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Nabili M, Ashrafi M, Janbabaie G, Hedayati MT, Ali-Moghaddam K, Shokohi T. Quantification and optimization of Candida albicans DNA in blood samples using Real- Time PCR. Rep Biochem Mol Biol 2013; 2:42-47. [PMID: 26989719 PMCID: PMC4757066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 08/07/2013] [Indexed: 06/05/2023]
Abstract
BACKGROUND Candida albicans (C. albicans) is a major cause of candidaemia in people with impaired immunity. Blood culture is a "gold standard" for candidaemia detection but is time-consuming and relatively insensitive. We established a real-time PCR assay for C. albicans detection in blood by LightCycler PCR and melting curve analysis. METHODS Five milliliter blood samples from healthy volunteers were spiked with 10(0)-10(6) C. albicans cells to determine the detection limit of our method. DNA was extracted from whole blood using glass beads and the QIAamp DNA Blood Mini Kit (Qiagen, Hilden Germany). DNA from C. albicans isolates were amplified with primers and inserted into Escherichia coli (E. coli) DH5α.1 cells with the TA cloning vector (Invitrogen). The plasmid was used for standardization and optimization. A quantitative PCR assay with the LightCycler amplification and detection system based on fluorescence resonance energy transfer (FRET) with two different specific probes was established. To assess the precision and reproducibility of real-time PCR the intra-assay precision was determined in six consecutive assays. RESULTS No cross-reactivity of the hybridization probes with the DNA of non-C. albicans species or human genomic DNA was observed, which confirmed its 100% specificity. The minimum limit detected was one C. albicans cell or 10(0) CFU/ml (10 fg) per PCR reaction. The real-time PCR efficiency rate for Candida was high (E = 1.95). Melting curve analysis of C. albicans showed a specific melting peak temperature of 65.76 °C. CONCLUSION The real-time PCR assay we developed is highly specific and sufficiently sensitive to detect the fungal load for early diagnosis of invasive candidiasis.
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Affiliation(s)
- Mojtaba Nabili
- Department of Medical Parasitology and Mycology, Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
- Social Security Organization, Golestan, Iran
| | - Mohsen Ashrafi
- Department of Medical Parasitology and Mycology, Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
| | - Ghasem Janbabaie
- Department of Internal Medicine, Cell and Molecular Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohamad Taghi Hedayati
- Department of Medical Parasitology and Mycology, Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
| | - Kamran Ali-Moghaddam
- Hematology-Oncology Research Center and Stem Cell Transplantation Research Center (HORCSCT), Tehran University of Medical Sciences, Iran
| | - Tahereh Shokohi
- Department of Medical Parasitology and Mycology, Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
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