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Rapid detection of giant salamander iridovirus by cross-priming amplification. J Virol Methods 2019; 274:113678. [PMID: 31442460 DOI: 10.1016/j.jviromet.2019.113678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/27/2019] [Accepted: 06/10/2019] [Indexed: 11/21/2022]
Abstract
Giant salamander iridovirus (GSIV) belongs to the epizootic genus Ranavirus, and is the cause of epidemic diseases associated with high mortality and great losses to artificial breeding and farming. Here, we established a simple, accurate, and reliable cross-priming amplification (CPA) method to detect GSIV. The CPA assay targets the major caspid protein gene of the GSIV genome to design crossing primer pairs, and the reaction conditions were optimized, including optimal concentrations of the primers, betaine, dNTPs, Mg2+, and Bst DNA polymerase, and reaction conditions. The sensitivity was shown to be 10 times higher than that of conventional polymerase chain reaction (PCR), and the specificity was 100%. The results were identified on nucleic acid strips within 3-5 min. Application of the CPA and PCR to 54 samples of giant salamander showed a positive rate of 72.22% and 74.07%, respectively, demonstrating high coincidence (94.44%, kappa = 8.7, P < 0.0001). The sensitivity of the CPA assay was 97.50% and the specificity was 92.86%. Thus, the CPA assay is as effective as conventional PCR, but with added practical advantages of simplicity and an almost instrument-free platform, which will be useful for both laboratories and giant salamander farms.
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Chylewska A, Ogryzek M, Makowski M. Modern Approach to Medical Diagnostics - the Use of Separation Techniques in Microorganisms Detection. Curr Med Chem 2019; 26:121-165. [DOI: 10.2174/0929867324666171023164813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 04/20/2017] [Accepted: 05/20/2016] [Indexed: 11/22/2022]
Abstract
Background:Analytical chemistry and biotechnology as an interdisciplinary fields of science have been developed during many years and are experiencing significant growth, to cover a wide range of microorganisms separation techniques and methods, utilized for medical therapeutic and diagnostic purposes. Currently scientific reports contribute by introducing electrophoretical and immunological methods and formation of devices applied in food protection (avoiding epidemiological diseases) and healthcare (safety ensuring in hospitals).Methods:Electrophoretic as well as nucleic-acid-based or specific immunological methods have contributed tremendously to the advance of analyses in recent three decades, particularly in relation to bacteria, viruses and fungi identifications, especially in medical in vitro diagnostics, as well as in environmental or food protection.Results:The paper presents the pathogen detection competitiveness of these methods against conventional ones, which are still too time consuming and also labor intensive. The review is presented in several parts following the current trends in improved pathogens separation and detection methods and their subsequent use in medical diagnosis.Discussion:Part one, consists of elemental knowledge about microorganisms as an introduction to their characterization: descriptions of divisions, sizes, membranes (cells) components. Second section includes the development, new technological and practical solution descriptions used in electrophoretical procedures during microbes analyses, with special attention paid to bio-samples analyses like blood, urine, lymph or wastewater. Third part covers biomolecular areas that have created a basis needed to identify the progress, limitations and challenges of nucleic-acid-based and immunological techniques discussed to emphasize the advantages of new separative techniques in selective fractionating of microorganisms.
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Affiliation(s)
- Agnieszka Chylewska
- Laboratory of Intermolecular Interactions, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80- 308 Gdansk, Poland
| | - Małgorzata Ogryzek
- Laboratory of Intermolecular Interactions, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80- 308 Gdansk, Poland
| | - Mariusz Makowski
- Laboratory of Intermolecular Interactions, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80- 308 Gdansk, Poland
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Arantes TD, Theodoro RC, Teixeira MDM, Bagagli E. Use of fluorescent oligonucleotide probes for differentiation between Paracoccidioides brasiliensis and Paracoccidioides lutzii in yeast and mycelial phase. Mem Inst Oswaldo Cruz 2017; 112:140-145. [PMID: 28177048 PMCID: PMC5293123 DOI: 10.1590/0074-02760160374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/31/2016] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Fluorescence in situ hybridisation (FISH) associated with Tyramide Signal Amplification (TSA) using oligonucleotides labeled with non-radioactive fluorophores is a promising technique for detection and differentiation of fungal species in environmental or clinical samples, being suitable for microorganisms which are difficult or even impossible to culture. OBJECTIVE In this study, we aimed to standardise an in situ hybridisation technique for the differentiation between the pathogenic species Paracoccidioides brasiliensis and Paracoccidioides lutzii, by using species-specific DNA probes targeting the internal transcribed spacer-1 (ITS-1) of the rRNA gene. METHODS Yeast and mycelial phase of each Paracoccidioides species, were tested by two different detection/differentiation techniques: TSA-FISH for P. brasiliensis with HRP (Horseradish Peroxidase) linked to the probe 5' end; and FISH for P. lutzii with the fluorophore TEXAS RED-X® also linked to the probe 5' end. After testing different protocols, the optimised procedure for both techniques was accomplished without cross-positivity with other pathogenic fungi. FINDINGS The in silico and in vitro tests show no reaction with controls, like Candida and Cryptococcus (in silico) and Histoplasma capsulatum and Aspergillus spp. (in vitro). For both phases (mycelial and yeast) the in situ hybridisation showed dots of hybridisation, with no cross-reaction between them, with a lower signal for Texas Red probe than HRP-TSA probe. The dots of hybridisation was confirmed with genetic material marked with 4',6-diamidino-2-phenylindole (DAPI), visualised in a different filter (WU) on fluorescent microscopic. MAIN CONCLUSION Our results indicated that TSA-FISH and/or FISH are suitable for in situ detection and differentiation of Paracoccidioides species. This approach has the potential for future application in clinical samples for the improvement of paracoccidioidomycosis patients prognosis.
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Affiliation(s)
- Thales Domingos Arantes
- Universidade Estadual Paulista, Instituto de Biociências de Botucatu, Departamento de Microbiologia e Imunologia, Botucatu, SP, Brasil.,Universidade Federal do Rio Grande do Norte, Centro de Biociências, Instituto de Medicina Tropical, Programa de Pós-Graduação em Bioquímica, Campus Universitário Lagoa Nova, Natal, RN, Brasil
| | - Raquel Cordeiro Theodoro
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Instituto de Medicina Tropical, Programa de Pós-Graduação em Bioquímica, Campus Universitário Lagoa Nova, Natal, RN, Brasil.,Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Biologia Celular e Genética, Natal, RN, Brasil
| | - Marcus de Melo Teixeira
- Northern Arizona Center for Valley Fever Research, Translational Genomics Research Institute - Tgen North, Phoenix, AZ, US
| | - Eduardo Bagagli
- Universidade Estadual Paulista, Instituto de Biociências de Botucatu, Departamento de Microbiologia e Imunologia, Botucatu, SP, Brasil
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Zhao Y, Paderu P, Railkar R, Douglas C, Iannone R, Shire N, Perlin DS. Blood Aspergillus RNA is a promising alternative biomarker for invasive aspergillosis. Med Mycol 2016; 54:801-7. [PMID: 27335056 DOI: 10.1093/mmy/myw043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/21/2016] [Indexed: 01/20/2023] Open
Abstract
A critical challenge for the successful application of antifungal therapies for invasive aspergillosis (IA) is a lack of reliable biomarkers to assess early treatment response. Patients with proven or probable IA were prospectively enrolled, and serial blood samples were collected at 8 specified time points during 12-week antifungal therapy. Total nucleic acid was extracted from 2.5 ml blood and tested for Aspergillus-specific RNA by a pan-Aspergillus real-time nucleic acid sequence-based amplification (NASBA) assay. Serum 1, 3-β-D-glucan (BG) and galactomannan (GM) were measured in parallel. Clinical outcome was evaluated at 6 and 12 weeks. Overall, 48/328 (14.6%) blood samples from 29/46 (63%) patients had positive NASBA detection at baseline and/or some point during the study. Positive NASBA results during the first 4 and 6 weeks of treatment are significantly associated with the 12-week outcome. Blood RNA load change during weeks 4-6 may be informative to predict outcome at 12 weeks. While independent of serum GM, the kinetic change of circulating Aspergillus RNA appears to be well correlated with that of BG on some patient individuals. Monitoring blood Aspergillus RNA during the first 4-6 weeks of antifungal treatment may help assess therapeutic response. Combination of circulating Aspergillus RNA and BG may be a useful adjunct to assess response.
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Affiliation(s)
- Yanan Zhao
- Public Health Research Institute, New Jersey Medical School-Rutgers Biomedical and Health Sciences, Newark, NJ 07103
| | - Padmaja Paderu
- Public Health Research Institute, New Jersey Medical School-Rutgers Biomedical and Health Sciences, Newark, NJ 07103
| | | | | | | | | | - David S Perlin
- Public Health Research Institute, New Jersey Medical School-Rutgers Biomedical and Health Sciences, Newark, NJ 07103
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Demir T, Ergenoglu MU, Ekinci A, Tanrikulu N, Sahin M, Demirsoy E. Aspergillus flavus endocarditis of the native mitral valve in a bone marrow transplant patient. AMERICAN JOURNAL OF CASE REPORTS 2015; 16:25-30. [PMID: 25603977 PMCID: PMC4311906 DOI: 10.12659/ajcr.892428] [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] [Indexed: 11/09/2022]
Abstract
Patient: Male, 36 Final Diagnosis: Aspergillus flavus endocarditis Symptoms: Malaise • fatigue and dyspnea Medication: — Clinical Procedure: Mitral vale replacemnet Specialty: Cardiology
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Affiliation(s)
- Tolga Demir
- Department of Cardiovascular Surgery, Beylikduzu Kolan Hospital, Istanbul, Turkey
| | - Mehmet Umit Ergenoglu
- Department of Cardiovascular Surgery, Kolan International Hospital, Istanbul, Turkey
| | - Abdurrahman Ekinci
- Department of Cardiovascular Surgery, Kolan International Hospital, Istanbul, Turkey
| | - Nursen Tanrikulu
- Department of Anesthesiology, Kolan International Hospital, Istanbul, Turkey
| | - Mazlum Sahin
- Department of Cardiovascular Surgery, Beylikduzu Kolan Hospital, Istanbul, Turkey
| | - Ergun Demirsoy
- Department of Cardiovascular Surgery, Kolan International Hospital, Istanbul, Turkey
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6
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In vitro and in vivo antifungal activity of Cassia surattensis flower against Aspergillus niger. Microb Pathog 2014; 77:7-12. [DOI: 10.1016/j.micpath.2014.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 10/10/2014] [Accepted: 10/12/2014] [Indexed: 01/16/2023]
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7
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Wang L, He Y, Xia Y, Su X, Wang H, Liang S. Retrospective Comparison of Nucleic Acid Sequence–Based Amplification, Real-Time PCR, and Galactomannan Test for Diagnosis of Invasive Aspergillosis. J Mol Diagn 2014; 16:584-590. [DOI: 10.1016/j.jmoldx.2014.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 05/14/2014] [Accepted: 05/27/2014] [Indexed: 10/24/2022] Open
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Paholcsek M, Leiter É, Markovics A, Biró S. Novel and sensitive qPCR assays for the detection and identification of aspergillosis causing species. Acta Microbiol Immunol Hung 2014; 61:273-84. [PMID: 25261942 DOI: 10.1556/amicr.61.2014.3.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Despite concerted efforts, diagnosis of aspergillosis is still a great challenge to clinical microbiology laboratories. Along with the requirement for high sensitivity and specificity, species-specific identification is important. We developed rapid, sensitive and species-specific qPCR assays using the TaqMan technology for the detection and identification of Aspergillus fumigatus and Aspergillus terreus. The assays were designed to target orthologs of the Streptomyces factor C gene that are only found in a few species of filamentous fungi. Fungi acquired this gene through horizontal gene transfer and divergence of the gene allows identification of species. The assays have potential as a molecular diagnosis tool for the early detection of fungal infection caused by Aspergillus fumigatus and Aspergillus terreus, which merits future diagnostic studies. The assays were sensitive enough to detect a few genomic equivalents in blood samples.
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Affiliation(s)
- Melinda Paholcsek
- 1 University of Debrecen Department of Human Genetics, Faculty of Medicine Debrecen Hungary
| | - Éva Leiter
- 2 University of Debrecen Department of Microbial Biotechnology and Cell Biology, Faculty of Science and Technology Debrecen Hungary
| | - Arnold Markovics
- 1 University of Debrecen Department of Human Genetics, Faculty of Medicine Debrecen Hungary
| | - Sándor Biró
- 1 University of Debrecen Department of Human Genetics, Faculty of Medicine Debrecen Hungary
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9
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Posteraro B, Sanguinetti M. The future of fungal susceptibility testing. Future Microbiol 2014; 9:947-67. [DOI: 10.2217/fmb.14.55] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
ABSTRACT The antifungal treatment failures and the emergence of resistant fungal strains have stimulated the need for reproducible and clinically relevant antifungal susceptibility testing (AFST). While the standard reference methods are not intended for routine use, commercial methods are widely used for performing AFST. However, to accelerate AFST and to improve the detection of antifungal resistance, which is the most challenging goal of AFST, novel assays have been developed. Following brief drug exposures of fungal cells, the new antifungal susceptibility end points seem to provide a reliable means of identifying fungal isolates, which harbor mutations that have been associated with antifungal resistance. This article summarizes the recent progress in AFST that is destined to enhance its clinical utility in the near future.
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Affiliation(s)
- Brunella Posteraro
- Institute of Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, Rome, Italy
| | - Maurizio Sanguinetti
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
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Thomas PA, A Teresa P, Theodore J, Geraldine P. PCR for the molecular diagnosis of mycotic keratitis. Expert Rev Mol Diagn 2013; 12:703-18. [PMID: 23153238 DOI: 10.1586/erm.12.65] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Mycotic keratitis, an infection of the cornea caused by fungi, is a medical emergency, with patients presenting with considerable pain and distress. For effective management of the condition, a specific diagnosis must be made rapidly to permit early initiation of antifungal therapy. Currently, direct microscopic examination and culture of corneal material constitute the 'gold standard' for diagnosis. However, rapid, sensitive yet specific tests are needed to detect a small number of, or nonviable, fungi. PCR has many potential advantages when used as a diagnostic aid for mycotic keratitis; the present review covers these advantages, and possible limitations. An expert assessment is also made of studies that have used PCR for the diagnosis of mycotic keratitis. The review concludes with a Five-year view of the potential impact of PCR in management of mycotic keratitis.
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Affiliation(s)
- Philip A Thomas
- Institute of Ophthalmology, Joseph Eye Hospital, Tiruchirapalli 620001, India.
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11
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Barton RC. Laboratory diagnosis of invasive aspergillosis: from diagnosis to prediction of outcome. SCIENTIFICA 2013; 2013:459405. [PMID: 24278780 PMCID: PMC3820361 DOI: 10.1155/2013/459405] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 11/14/2012] [Indexed: 06/02/2023]
Abstract
Invasive aspergillosis (IA), an infection caused by fungi in the genus Aspergillus, is seen in patients with immunological deficits, particularly acute leukaemia and stem cell transplantation, and has been associated with high rates of mortality in previous years. Diagnosing IA has long been problematic owing to the inability to culture the main causal agent A. fumigatus from blood. Microscopic examination and culture of respiratory tract specimens have lacked sensitivity, and biopsy tissue for histopathological examination is rarely obtainable. Thus, for many years there has been a great interest in nonculture-based techniques such as the detection of galactomannan, β -D-glucan, and DNA by PCR-based methods. Recent meta-analyses suggest that these approaches have broadly similar performance parameters in terms of sensitivity and specificity to diagnose IA. Improvements have been made in our understanding of the limitations of antigen assays and the standardisation of PCR-based DNA detection. Thus, in more recent years, the debate has focussed on how these assays can be incorporated into diagnostic strategies to maximise improvements in outcome whilst limiting unnecessary use of antifungal therapy. Furthermore, there is a current interest in applying these tests to monitor the effectiveness of therapy after diagnosis and predict clinical outcomes. The search for improved markers for the early and sensitive diagnosis of IA continues to be a challenge.
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Affiliation(s)
- Richard C. Barton
- Mycology Reference Centre, Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds LS1 3EX, UK
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Abstract
Nucleic acids are the ultimate biomarker and real-time PCR (qPCR) is firmly established as the method of choice for nucleic acid detection. Together, they allow the accurate, sensitive and specific identification of pathogens, and the use of qPCR has become routine in diagnostic laboratories. The reliability of qPCR-based assays relies on a combination of optimal sample selection, assay design and validation as well as appropriate data analysis and the "Minimal Information for the Publication of real-time PCR" (MIQE) guidelines aim to improve both the reliability of assay design as well as the transparency of reporting, essential conditions if qPCR is to remain the benchmark technology for molecular diagnosis.
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Affiliation(s)
- Gemma Johnson
- Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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Johnson GL, Bibby DF, Wong S, Agrawal SG, Bustin SA. A MIQE-compliant real-time PCR assay for Aspergillus detection. PLoS One 2012; 7:e40022. [PMID: 22808087 PMCID: PMC3393739 DOI: 10.1371/journal.pone.0040022] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 05/30/2012] [Indexed: 01/06/2023] Open
Abstract
The polymerase chain reaction (PCR) is widely used as a diagnostic tool in clinical laboratories and is particularly effective for detecting and identifying infectious agents for which routine culture and microscopy methods are inadequate. Invasive fungal disease (IFD) is a major cause of morbidity and mortality in immunosuppressed patients, and optimal diagnostic criteria are contentious. Although PCR-based methods have long been used for the diagnosis of invasive aspergillosis (IA), variable performance in clinical practice has limited their value. This shortcoming is a consequence of differing sample selection, collection and preparation protocols coupled with a lack of standardisation of the PCR itself. Furthermore, it has become clear that the performance of PCR-based assays in general is compromised by the inadequacy of experimental controls, insufficient optimisation of assay performance as well as lack of transparency in reporting experimental details. The recently published "Minimum Information for the publication of real-time Quantitative PCR Experiments" (MIQE) guidelines provide a blueprint for good PCR assay design and unambiguous reporting of experimental detail and results. We report the first real-time quantitative PCR (qPCR) assay targeting Aspergillus species that has been designed, optimised and validated in strict compliance with the MIQE guidelines. The hydrolysis probe-based assay, designed to target the 18S rRNA DNA sequence of Aspergillus species, has an efficiency of 100% (range 95-107%), a dynamic range of at least six orders of magnitude and limits of quantification and detection of 6 and 0.6 Aspergillus fumigatus genomes, respectively. It does not amplify Candida, Scedosporium, Fusarium or Rhizopus species and its clinical sensitivity is demonstrated in histological material from proven IA cases, as well as concordant PCR and galactomannan data in matched broncho-alveolar lavage and blood samples. The robustness, specificity and sensitivity of this assay make it an ideal molecular diagnostic tool for clinical use.
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Affiliation(s)
- Gemma L Johnson
- Blizard Institute of Cell and Molecular Science, Queen Mary University, London, United Kingdom.
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Aigner M, Mutschlechner W, Lass-Flörl C. [Diagnosis of Aspergillus infections in hematology and oncology]. Mycoses 2012; 55 Suppl 2:3-9. [PMID: 22519626 DOI: 10.1111/j.1439-0507.2012.02177.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Maria Aigner
- Department für Hygiene, Mikrobiologie und Sozialmedizin, Medizinische Universität Innsbruck, Innsbruck, Österreich
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Morton CO, de Luca A, Romani L, Rogers TR. RT-qPCR detection of Aspergillus fumigatus RNA in vitro and in a murine model of invasive aspergillosis utilizing the PAXgene® and Tempus™ RNA stabilization systems. Med Mycol 2012; 50:661-6. [PMID: 22263641 DOI: 10.3109/13693786.2011.652200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Molecular diagnosis of invasive aspergillosis (IA) is a potentially life-saving tool in the care of at-risk individuals. To date, the development of PCR-based diagnostic tests has been hampered by the lack of standardization in the methods for such critical activities. In this study, we used both spiked volunteer blood samples and a murine model of IA to test the utility of the PAXgene and Tempus systems for stabilization and isolation of fungal RNA from blood as part of an evaluation of a new diagnostic strategy. In spiking experiments, RNA isolation followed by RT-qPCR that targeted the 18S gene was compared to a standard DNA isolation and qPCR assay that targeted the ITS ribosomal region. We demonstrated that both PAXgene and Tempus RNA stabilization and extraction systems followed by RT-qPCR had similar performance in detecting fungal RNA in blood samples from Aspergillus fumigates-infected mice. In spiked samples, the Tempus system performed better than the PAXgene system as it detected 100% of all samples spiked with 10 or 20 germinated Aspergillus conidia/ml blood sample as compared to the PAXgene system which detected 33% and 56% of the samples spiked with 10 or 20 conidia/ml, respectively. The stabilization of fungal nucleic acids in blood samples and its efficient isolation by a commercial method is an important step in the development of standardized molecular diagnostic tools that are needed to improve the outcomes for individuals with IA.
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Affiliation(s)
- Charles Oliver Morton
- Department of Clinical Microbiology, Sir Patrick Dun Research Laboratory, Trinity College Dublin, St James's Hospital, Dublin, Ireland.
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Kim SH, Park C, Kwon EY, Shin NY, Kwon JC, Park SH, Choi SM, Lee DG, Choi JH, Yoo JH. Real-time nucleic acid sequence-based amplification to predict the clinical outcome of invasive aspergillosis. J Korean Med Sci 2012; 27:10-5. [PMID: 22219607 PMCID: PMC3247764 DOI: 10.3346/jkms.2012.27.1.10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 11/07/2011] [Indexed: 11/23/2022] Open
Abstract
Monitoring the response to therapy for invasive aspergillosis (IA) is essential for the management of patients with hematologic diseases. We evaluated the correlation between the outcome of real-time nucleic acid sequence-based amplification (RTi-NASBA) for Aspergillus 18S rRNA and the clinical outcome of IA. A total of 157 serum samples from 29 patients with IA were tested for RTi-NASBA. The treatment response and mortality were compared with the NASBA outcome (whether the NASBA value was converted to negative or not) at 12 weeks after the start of antifungal therapy. At 12 weeks, there was a moderate correlation between the treatment failure and persistently positive NASBA (κ = 0.482; P = 0.019). Deaths attributable to IA were more prevalent in patients without negative conversion of NASBA than in those with negative conversion (50% vs 5%; P = 0.013). Significant factors of treatment failure at 12 weeks were the status of hematologic disease (nonremission; P = 0.041) and the NASBA outcome (failure of negative conversion; P = 0.024). Survival was significantly better in patients with negative conversion of NASBA than those with persistently positive values (P = 0.036). This study suggests that the serial monitoring of RTi-NASBA could be useful for prediction of the clinical outcome in hematologic patients with IA.
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Affiliation(s)
- Si-Hyun Kim
- Division of Infectious Diseases, Department of Internal Medicine, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Chulmin Park
- Clinical Research Institutes of Medical Science, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Eun-Young Kwon
- Clinical Research Institutes of Medical Science, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Na-Young Shin
- Clinical Research Institutes of Medical Science, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Jae-Cheol Kwon
- Division of Infectious Diseases, Department of Internal Medicine, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Sun Hee Park
- Division of Infectious Diseases, Department of Internal Medicine, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Su-Mi Choi
- Division of Infectious Diseases, Department of Internal Medicine, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Dong-Gun Lee
- Division of Infectious Diseases, Department of Internal Medicine, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Jung-Hyun Choi
- Division of Infectious Diseases, Department of Internal Medicine, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Jin-Hong Yoo
- Division of Infectious Diseases, Department of Internal Medicine, The Catholic University of Korea College of Medicine, Seoul, Korea
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Rosa C, Araujo R, Rodrigues AG, Pinto-de-Sousa MI, Pina-Vaz C. Detection of Aspergillus species in BACTEC blood cultures. J Med Microbiol 2011; 60:1467-1471. [DOI: 10.1099/jmm.0.030601-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Carla Rosa
- Microbiology Laboratory, Department of Clinical Pathology, Hospital São João, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Microbiology, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Ricardo Araujo
- IPATIMUP – Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr Roberto Frias s/n, 4200-465 Porto, Portugal
- Department of Microbiology, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Acácio G. Rodrigues
- Cardiovascular Research and Development Unit, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
- Burn Unit, Department of Plastic and Reconstructive Surgery, Hospital São João, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Microbiology, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - M. Isaura Pinto-de-Sousa
- Department of Microbiology, Faculty of Pharmacy, University of Porto, Rua Aníbal Cunha 164, 4050-047 Porto, Portugal
| | - Cidália Pina-Vaz
- Cardiovascular Research and Development Unit, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
- Microbiology Laboratory, Department of Clinical Pathology, Hospital São João, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Microbiology, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
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Diagnosis of Antifungal Drug Resistance Mechanisms in Fungal Pathogens: Transcriptional Gene Regulation. CURRENT FUNGAL INFECTION REPORTS 2011. [DOI: 10.1007/s12281-011-0055-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Harrison E, Stalhberger T, Whelan R, Sugrue M, Wingard JR, Alexander BD, Follett SA, Bowyer P, Denning DW. Aspergillus DNA contamination in blood collection tubes. Diagn Microbiol Infect Dis 2010; 67:392-4. [PMID: 20638611 DOI: 10.1016/j.diagmicrobio.2010.02.028] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 02/27/2010] [Indexed: 10/19/2022]
Abstract
Fungal polymerase chain reaction (PCR)-based diagnostic methods are at risk for contamination. Sample collection containers were investigated for fungal DNA contamination using real-time PCR assays. Up to 18% of blood collection tubes were contaminated with fungal DNA, probably Aspergillus fumigatus. Lower proportions of contamination in other vessels were observed.
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Affiliation(s)
- Elizabeth Harrison
- Manchester Academic Health Science Centre, University Hospital of South Manchester, The University of Manchester, Southmoor Road, Manchester M23 9LT, United Kingdom.
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Diagnostic value of PCR analysis of bacteria and fungi from blood in empiric-therapy-resistant febrile neutropenia. J Clin Microbiol 2010; 48:2030-6. [PMID: 20392911 DOI: 10.1128/jcm.01700-09] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
This study aimed to assess the clinical utility of PCR for the analysis of bacteria and fungi from blood for the management of febrile neutropenic patients with hematologic malignancies. Using a PCR system able to detect a broad range of bacteria and fungi, we conducted a prospective pilot study of periodic analyses of blood from patients following intensive chemotherapy. When fever occurred, it was treated with empirical antibiotic therapy, basically without knowledge of the PCR results. In 23 febrile episodes during the neutropenic period, bacteria were detected by PCR in 11 cases, while the same species were identified by blood culture in 3 cases. In 10 out of 11 PCR-positive cases, fever could be managed by empirical therapy. In the empirical-therapy-resistant case, the identification of Stenotrophomonas maltophilia by PCR led to improvement of fever. No fungi were detected by PCR in febrile cases, while Aspergillus fumigatus was detected in one afebrile patient, several days before a clinical diagnosis was made. In subsequent sporadic PCR analyses in 15 cases of febrile neutropenia, bacteria were detected by both PCR and blood culture in 7 cases and by PCR alone in 6. Fungi were not detected. While fever was improved by empirical therapy in 12 out of the 13 PCR-positive cases, the identification of Pseudomonas aeruginosa by PCR in one therapy-resistant case contributed to the successful treatment of persistent fever. Our results indicate that PCR analysis of bacteria from blood provides essential information for managing empirical-therapy-resistant febrile neutropenia.
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Morton CO, Loeffler J, De Luca A, Frost S, Kenny C, Duval S, Romani L, Rogers TR. Dynamics of extracellular release of Aspergillus fumigatus DNAand galactomannan during growth in blood and serum. J Med Microbiol 2010; 59:408-413. [DOI: 10.1099/jmm.0.017418-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Aspergillus fumigatus is the major cause of invasive aspergillosis (IA),a disease associated with high rates of morbidity and mortality in patientsundergoing treatment for haematological malignancies. This study investigated A. fumigatus growth in vitro and in a murine model of IA inorder to provide insights into the dynamics of extracellular DNA and galactomannan (GM)release and their relevance to early diagnosis of IA. Following inoculationof whole blood with 20 A. fumigatus conidia ml−1,DNA that corresponded to the inoculum could be detected by PCR but GM wasnot detected in plasma separated from the blood sample, indicating that thefungus did not grow in whole blood. The quantities of DNA detected by PCR,and GM, were proportional to the amount of fungal biomass present in vitro. Fungal DNA could be detected in the sera of mice experimentally infectedwith A. fumigatus with maximum detection in cyclophosphamide-treatedmice.
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Affiliation(s)
- C. O. Morton
- Department of Clinical Microbiology, Sir PatrickDun Research Laboratory, Trinity College Dublin, St James's Hospital,Dublin 8, Ireland
| | - J. Loeffler
- Universität Würzburg, Medizinische Klinik &Poliklinik II, 97070 Würzburg, Germany
| | - A. De Luca
- Department of Experimental Medicine, University ofPerugia, 06126 Perugia, Italy
| | - S. Frost
- Department of Clinical Microbiology, Sir PatrickDun Research Laboratory, Trinity College Dublin, St James's Hospital,Dublin 8, Ireland
| | - C. Kenny
- Department of Clinical Microbiology, Sir PatrickDun Research Laboratory, Trinity College Dublin, St James's Hospital,Dublin 8, Ireland
| | - S. Duval
- Department of Clinical Microbiology, Sir PatrickDun Research Laboratory, Trinity College Dublin, St James's Hospital,Dublin 8, Ireland
| | - L. Romani
- Department of Experimental Medicine, University ofPerugia, 06126 Perugia, Italy
| | - T. R. Rogers
- Department of Clinical Microbiology, Sir PatrickDun Research Laboratory, Trinity College Dublin, St James's Hospital,Dublin 8, Ireland
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Detection of Aspergillus fumigatus in a rat model of invasive pulmonary aspergillosis by real-time nucleic acid sequence-based amplification. J Clin Microbiol 2010; 48:1378-83. [PMID: 20129972 DOI: 10.1128/jcm.02214-09] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid and sensitive detection of Aspergillus from clinical samples may facilitate the early diagnosis of invasive pulmonary aspergillosis (IPA). A real-time nucleic acid sequence-based amplification (NASBA) method was investigated by use of an inhalational rat model of IPA. Immunosuppressed male Sprague-Dawley rats were exposed to Aspergillus fumigatus spores for an hour in an aerosol chamber. Bronchoalveolar lavage (BAL) fluid, lung tissues, and whole blood were collected from five infected rats at 1, 24, 48, 72, and 96 h postinfection and five uninfected rats at the end of the experiment. Total nucleic acid (TNA) was extracted on an easyMAG instrument. A primer-molecular beacon set targeting 28S rRNA was designed to detect Aspergillus spp. The results were compared to those of quantitative PCR (qPCR) (18S rDNA) and quantitative culture. The analytical sensitivity of the real-time NASBA assay was <1 CFU/assay. A linear range of detection was demonstrated over 5 log units of conidia (10 to 10(5) spores). Both NASBA and qPCR showed a progressive increase in lung tissue burdens, while the CFU counts were stable over time. The fungal burdens in BAL fluid were more variable and not indicative of a progressive infection. The results of both real-time assays correlated well for both sample types (r = 0.869 and P < 0.0001 for lung tissue, r = 0.887 and P < 0.0001 for BAL fluid). For all whole-blood specimens, NASBA identified Aspergillus-positive samples in the group from which samples were collected at 72 h postinfection (three of five samples) and the group from which samples were collected at 96 h postinfection (five of five samples), but no positive results were obtained by culture or PCR. Real-time NASBA is highly sensitive and useful for the detection of Aspergillus in an experimental model of IPA.
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Abstract
PURPOSE OF REVIEW Antifungal drug resistance is a confounding factor that negatively impacts clinical outcome for patients with serious mycoses. Early detection of fungi in blood or other specimens with a rapid assessment of drug susceptibility could improve the survival of patients with invasive disease by accelerating the initiation of appropriate antifungal treatment. Recent years have seen the growth of molecular technology that is ideally suited for fungal identification and assessment of drug resistance mechanisms. RECENT FINDINGS Elucidation of the genetic mechanisms responsible for triazole and echinocandin resistance in prominent Candida spp. and Aspergillus spp. provides an opportunity to develop molecular diagnostic platforms suitable for rapid detection of primary and secondary drug resistance. Several highly dynamic and robust amplification/detection methodologies are now available that can provide simultaneous species identification and high fidelity discrimination of resistance alleles. SUMMARY Molecular diagnostic platforms are ideal for rapid detection of fungal pathogens and they provide an opportunity to develop in parallel molecular assays that can evaluate antifungal drug resistance.
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