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Silva Zatti M, Domingos Arantes T, Cordeiro Theodoro R. Isothermal nucleic acid amplification techniques for detection and identification of pathogenic fungi: A review. Mycoses 2020; 63:1006-1020. [PMID: 32648947 DOI: 10.1111/myc.13140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Fungal infections have increased during the last years due to the AIDS epidemic and immunosuppressive therapies. The available diagnostic methods, such as culture, histopathology and serology, have several drawbacks regarding sensitivity, specificity and time-consuming, while molecular methods are still expensive and dependent on many devices. In order to overcome these challenges, isothermal nucleic acid amplification techniques (INAT) arose as promising diagnostic methods for infectious diseases. OBJECTIVE This review aimed to present and discuss the main contributions of the isothermal nucleic acid amplification techniques applied in medical mycology. METHODS Papers containing terms for each INAT (NASBA, RCA, LAMP, CPA, SDA, HAD or PSR) and the terms 'mycoses' or 'disease, fungal' were obtained from National Center for Biotechnology Information database until August 2019. RESULTS NASBA, RCA, LAMP and PSR are the INAT reported in the literature for detection and identification of pathogenic fungi. Despite the need of a previous conventional PCR, the RCA technique might also be used for genotyping or cryptic species differentiation, which may be important for the treatment of certain mycoses; nevertheless, LAMP is the most used INAT for pathogen detection. CONCLUSION Among all INATs herein reviewed, LAMP seems to be the most appropriate method for fungal detection, since it is affordable, sensitive, specific, user-friendly, rapid, robust, equipment-free and deliverable to end-users, fulfilling all ASSURED criteria of the World Health Organization for an ideal diagnostic method.
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Affiliation(s)
- Matheus Silva Zatti
- Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Thales Domingos Arantes
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiás, Brazil
| | - Raquel Cordeiro Theodoro
- Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, Brazil
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Posch W, Heimdörfer D, Wilflingseder D, Lass-Flörl C. Invasive candidiasis: future directions in non-culture based diagnosis. Expert Rev Anti Infect Ther 2017; 15:829-838. [PMID: 28829207 DOI: 10.1080/14787210.2017.1370373] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Delayed initial antifungal therapy is associated with high mortality rates caused by invasive candida infections, since accurate detection of the opportunistic pathogenic yeast and its identification display a diagnostic challenge. diagnosis of candida infections relies on time-consuming methods such as blood cultures, serologic and histopathologic examination. to allow for fast detection and characterization of invasive candidiasis, there is a need to improve diagnostic tools. trends in diagnostics switch to non-culture-based methods, which allow specified diagnosis within significantly shorter periods of time in order to provide early and appropriate antifungal treatment. Areas covered: within this review comprise novel pathogen- and host-related testing methods, e.g. multiplex-PCR analyses, T2 magnetic resonance, fungus-specific DNA microarrays, microRNA characterization or analyses of IL-17 as biomarker for early detection of invasive candidiasis. Expert commentary: Early recognition and diagnosis of fungal infections is a key issue for improved patient management. As shown in this review, a broad range of novel molecular based tests for the detection and identification of Candida species is available. However, several assays are in-house assays and lack standardization, clinical validation as well as data on sensitivity and specificity. This underscores the need for the development of faster and more accurate diagnostic tests.
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Affiliation(s)
- Wilfried Posch
- a Division of Hygiene and Medical Microbiology , Medical University of Innsbruck , Innsbruck , Austria
| | - David Heimdörfer
- a Division of Hygiene and Medical Microbiology , Medical University of Innsbruck , Innsbruck , Austria
| | - Doris Wilflingseder
- a Division of Hygiene and Medical Microbiology , Medical University of Innsbruck , Innsbruck , Austria
| | - Cornelia Lass-Flörl
- a Division of Hygiene and Medical Microbiology , Medical University of Innsbruck , Innsbruck , Austria
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Preuner S, Lion T. Towards molecular diagnostics of invasive fungal infections. Expert Rev Mol Diagn 2014; 9:397-9. [DOI: 10.1586/erm.09.27] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Yurdakul P, Colakoglu S. Molecular methods for detection of invasive fungal infections and mycobacteria and their clinical significance in hematopoietic stem cell transplantation. Methods Mol Biol 2014; 1109:239-70. [PMID: 24473787 DOI: 10.1007/978-1-4614-9437-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Infection remains an important source of morbidity and mortality in patients who undergo hematopoietic stem cell transplantation (HSCT). In the immune reconstitution period after transplantation, HSCT recipients are most likely to have bacterial or fungal infections. Invasive fungal infections (IFIs) and mycobacterial infections (MBIs) are among the complications of HSCT, with high morbidity and mortality rates. Early diagnosis of both is crucial in order to manipulate the disease and to avoid fulminant outcomes. This chapter reviews the current knowledge on the molecular diagnosis of IFIs and MBIs in HSCT recipients, describing two different polymerase chain reaction (PCR)-based methods, one commercial (qPCR, Roche) and one in-house IS6110-based protocol.
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Affiliation(s)
- Pinar Yurdakul
- Ankara University Faculty of Medicine, Cord Blood Bank, Ankara, Turkey
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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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Lau A, Chen S, Sleiman S, Sorrell T. Current status and future perspectives on molecular and serological methods in diagnostic mycology. Future Microbiol 2009; 4:1185-222. [DOI: 10.2217/fmb.09.70] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Invasive fungal infections are an important cause of infectious morbidity. Nonculture-based methods are increasingly used for rapid, accurate diagnosis to improve patient outcomes. New and existing DNA amplification platforms have high sensitivity and specificity for direct detection and identification of fungi in clinical specimens. Since laboratories are increasingly reliant on DNA sequencing for fungal identification, measures to improve sequence interpretation should support validation of reference isolates and quality control in public gene repositories. Novel technologies (e.g., isothermal and PNA FISH methods), platforms enabling high-throughput analyses (e.g., DNA microarrays and Luminex® xMAP™) and/or commercial PCR assays warrant further evaluation for routine diagnostic use. Notwithstanding the advantages of molecular tests, serological assays remain clinically useful for patient management. The serum Aspergillus galactomannan test has been incorporated into diagnostic algorithms of invasive aspergillosis. Both the galactomannan and the serum β-D-glucan test have value for diagnosing infection and monitoring therapeutic response.
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Affiliation(s)
- Anna Lau
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia
| | - Sharon Chen
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia and Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Sue Sleiman
- Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Tania Sorrell
- Centre for Infectious Diseases & Microbiology, Westmead Hospital, Darcy and Hawkesbury Roads, Westmead, NSW 2145, Australia
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Rapid real-time nucleic Acid sequence-based amplification-molecular beacon platform to detect fungal and bacterial bloodstream infections. J Clin Microbiol 2009; 47:2067-78. [PMID: 19403758 DOI: 10.1128/jcm.02230-08] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bloodstream infections (BSIs) are a significant cause of morbidity and mortality. Successful patient outcomes are diminished by a failure to rapidly diagnose these infections and initiate appropriate therapy. A rapid and reliable diagnostic platform of high sensitivity is needed for the management of patients with BSIs. The combination of an RNA-dependent nucleic acid sequence-based amplification and molecular beacon (NASBA-MB) detection system in multiplex format was developed to rapidly detect medically important BSI organisms. Probes and primers representing pan-gram-negative, pan-gram-positive, pan-fungal, pan-Candida, and pan-Aspergillus organisms were established utilizing 16S and 28S rRNA targets for bacteria and fungi, respectively. Two multiplex panels were developed to rapidly discriminate bacterial or fungal infections at the subkingdom/genus level with a sensitivity of 1 to 50 genomes. A clinical study was performed to evaluate the accuracy of this platform by evaluating 570 clinical samples from a tertiary-care hospital group using blood bottle samples. The sensitivity, specificity, and Youden's index values for pan-gram-positive detection and pan-gram-negative detection were 99.7%, 100%, 0.997 and 98.6%, 95.9%, 0.945, respectively. The positive predictive values (PPV) and the negative predictive values (NPV) for these two probes were 100, 90.7, and 99.4, 99.4, respectively. Pan-fungal and pan-Candida probes showed 100% sensitivity, specificity, PPV, and NPV, and the pan-Aspergillus probe showed 100% NPV. Robust signals were observed for all probes in the multiplex panels, with signal detection in <15 min. The multiplex real-time NASBA-MB assay provides a valuable platform for the rapid and specific diagnosis of bloodstream pathogens, and reliable pathogen identification and characterization can be obtained in under 3 h.
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McMullan R, Metwally L, Coyle PV, Hedderwick S, McCloskey B, O'Neill HJ, Patterson CC, Thompson G, Webb CH, Hay RJ. A Prospective Clinical Trial of a Real-Time Polymerase Chain Reaction Assay for the Diagnosis of Candidemia in Nonneutropenic, Critically Ill Adults. Clin Infect Dis 2008; 46:890-6. [DOI: 10.1086/528690] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Inácio J, Flores O, Spencer-Martins I. Efficient identification of clinically relevant Candida yeast species by use of an assay combining panfungal loop-mediated isothermal DNA amplification with hybridization to species-specific oligonucleotide probes. J Clin Microbiol 2008; 46:713-20. [PMID: 18077626 PMCID: PMC2238081 DOI: 10.1128/jcm.00514-07] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 05/29/2007] [Accepted: 12/04/2007] [Indexed: 11/20/2022] Open
Abstract
The occurrence of invasive mycoses has progressively increased in recent years. Yeasts of the genus Candida remain the leading etiologic agents of those infections. Early identification of opportunistic yeasts may contribute significantly to improved disease management and the selection of appropriate antifungal therapy. We developed a rapid and reliable molecular identification system for clinically relevant yeasts that makes use of nonspecific primers to amplify a region of the 26S rRNA gene, followed by reverse hybridization of the digoxigenin-labeled products to a panel of species-specific oligonucleotide probes arranged on a nylon membrane macroarray format. DNA amplification was achieved by the recently developed loop-mediated isothermal DNA amplification technology, a promising option for the development of improved laboratory diagnostic kits. The newly developed method was successful in distinguishing among the major clinically relevant yeasts associated with bloodstream infections by using simple, rapid, and cost-effective procedures and equipment.
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Affiliation(s)
- João Inácio
- Centro de Recursos Microbiológicos, Department of Life Sciences, Faculty of Sciences and Technology, New University of Lisbon, 2829-516 Caparica, Portugal
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Abstract
The focus of this review is the evolution of biochemical phenotypic yeast identification methods with emphasis on conventional approaches, rapid screening tests, chromogenic agars, comprehensive commercial methods, and the eventual migration to genotypic methods. As systemic yeast infections can be devastating and resistance is common in certain species, accurate identification to the species level is paramount for successful therapy and appropriate patient care.
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Affiliation(s)
- D H Pincus
- bioMérieux, Inc., Hazelwood, Missouri 63042, USA.
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Somogyvari F, Doczi I, Serly J, Ahmad S, Nagy E. Rapid discrimination between Candida albicans and Candida dubliniensis by using real-time polymerase chain reaction. Diagn Microbiol Infect Dis 2007; 58:367-9. [PMID: 17376634 DOI: 10.1016/j.diagmicrobio.2007.01.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Revised: 01/15/2007] [Accepted: 01/23/2007] [Indexed: 11/28/2022]
Abstract
Several phenotypic methods have been used for the differentiation of Candida albicans and Candida dubliniensis, but molecular investigations are considered most reliable in their diagnostic value. Here, we suggest a rapid real-time polymerase chain reaction assay where the discrimination was achieved through melting point analysis with the help of the nonspecific fluorescent dye SybrGreen.
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Affiliation(s)
- Ferenc Somogyvari
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Szeged 6725, Hungary.
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Trtkova J, Raclavsky V. MOLECULAR-GENETIC APPROACHES TO IDENTIFICATION AND TYPING OF PATHOGENIC CANDIDA YEASTS. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2006; 150:51-61. [PMID: 16936901 DOI: 10.5507/bp.2006.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Currently, invasive candidal infections represent an increasing cause of morbidity and mortality in seriously ill hospitalised patients. Because the accurate diagnosis of candidiasis remains difficult, a fast and reliable assay for characterization of fungal pathogens is critical for the early initiation of adequate antifungal therapy and/or for introduction of preventive measures. As novel molecular genetic techniques are continuously introduced, their role in the management of infectious diseases has also been growing. Today, molecular strategies complement conventional methods and provide more accurate and detailed insight. It can be expected that future technical development will improve their potential furthermore. In this article, we provide a critical review on the value and limitations of molecular tools in pathogenic Candida species identification and strain typing regarding their sensitivity, discriminatory power, reproducibility, cost and ease of performance.
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Affiliation(s)
- Jitka Trtkova
- Department of Biology, Faculty of Medicine, Palacký University, Hnevotínská 3, Olomouc, Czech Republic.
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Bretagne S, Costa JM. Towards a nucleic acid-based diagnosis in clinical parasitology and mycology. Clin Chim Acta 2006; 363:221-8. [PMID: 16102739 DOI: 10.1016/j.cccn.2005.05.051] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2005] [Accepted: 05/05/2005] [Indexed: 12/22/2022]
Abstract
BACKGROUND Multiple in-house polymerase chain reaction (PCR) assays for the diagnosis of parasitic and fungal diseases have been reported. Encouraging results have been published to anticipate or improve the diagnosis. However, the absence of standardized methods has led to discrepant results. As a consequence, these tests are not recognized as consensual diagnostic criteria. METHODS The major breakthrough for improving the results of these methods is the emergence of real-time technologies. This markedly improves the reliability of the PCR results by dramatically decreasing the risk of false positive results due to PCR products carryover. Moreover, the quantitative results provided by these techniques allow to compare rapidly the efficiency of primers, probes, and DNA extraction. Therefore, one can expect a more consensual method to implement comparisons between laboratories. Automated DNA extraction should also be useful to achieve this goal. Whatever sophisticated technology is used, the meaning of detecting nucleic acids in a given clinical sample still needs to be defined. This requires well-designed studies with clinical consensual criteria and PCR techniques that are as similar as possible. CONCLUSIONS The development of real-time technology should improve our knowledge in order to give the clinicians informative clues for decision-making.
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Affiliation(s)
- Stéphane Bretagne
- Laboratoire de Parasitologie-Mycologie and UMR BIPAR 956, Hôpital Henri Mondor, Créteil, France.
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Bretagne S, Costa JM. Towards a molecular diagnosis of invasive aspergillosis and disseminated candidosis. ACTA ACUST UNITED AC 2005; 45:361-8. [PMID: 16054349 DOI: 10.1016/j.femsim.2005.05.012] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Accepted: 05/27/2005] [Indexed: 12/25/2022]
Abstract
A lot of in-house polymerase chain reaction assays have been reported for diagnosis of invasive aspergillosis and disseminated candidosis. Encouraging results have been published to anticipate the diagnosis over the conventional microbiological methods. However, the absence of standardized methods has led to diverging results. As a consequence, these tests are not recognized as consensual diagnostic criteria, in contrast with some antigenemia detection kits. The major breakthrough for improving the results of these methods is the emergence of real-time technologies. This markedly improves the reliability of the PCR results by dramatically decreasing the risk of false positive results due to PCR products carryover. Moreover, using the quantitative results provided by this technique, this allows to rapidly compare the efficiency of primers, probes, and DNA extraction methods. Therefore, the hope is to identify the more specific and sensitive parameters to implement comparative studies. Automated DNA extraction should also be useful to achieve this goal. Whatever sophisticated technology is used, we still have to define the meaning of detecting nucleic acids in a given clinical sample. This seems simple in normally sterile anatomical sites but less obvious for example in respiratory specimens for invasive aspergillosis or in blood for candidosis in heavily colonized patients. Additional studies of the kinetics of fungal DNA are needed. The development of real-time technology should improve our knowledge in order to give the clinicians informative clues for making a decision.
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Affiliation(s)
- Stéphane Bretagne
- Laboratoire de Parasitologie-Mycologie and UMR BIPAR 956, Hôpital Henri Mondor, De Lattre de Tassigny, AP-HP, Créteil, France.
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Current awareness on yeast. Yeast 2003; 20:1007-14. [PMID: 14587515 DOI: 10.1002/yea.948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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