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Thambugala KM, Daranagama DA, Tennakoon DS, Jayatunga DPW, Hongsanan S, Xie N. Humans vs. Fungi: An Overview of Fungal Pathogens against Humans. Pathogens 2024; 13:426. [PMID: 38787278 PMCID: PMC11124197 DOI: 10.3390/pathogens13050426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Human fungal diseases are infections caused by any fungus that invades human tissues, causing superficial, subcutaneous, or systemic diseases. Fungal infections that enter various human tissues and organs pose a significant threat to millions of individuals with weakened immune systems globally. Over recent decades, the reported cases of invasive fungal infections have increased substantially and research progress in this field has also been rapidly boosted. This review provides a comprehensive list of human fungal pathogens extracted from over 850 recent case reports, and a summary of the relevant disease conditions and their origins. Details of 281 human fungal pathogens belonging to 12 classes and 104 genera in the divisions ascomycota, basidiomycota, entomophthoromycota, and mucoromycota are listed. Among these, Aspergillus stands out as the genus with the greatest potential of infecting humans, comprising 16 species known to infect humans. Additionally, three other genera, Curvularia, Exophiala, and Trichophyton, are recognized as significant genera, each comprising 10 or more known human pathogenic species. A phylogenetic analysis based on partial sequences of the 28S nrRNA gene (LSU) of human fungal pathogens was performed to show their phylogenetic relationships and clarify their taxonomies. In addition, this review summarizes the recent advancements in fungal disease diagnosis and therapeutics.
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Affiliation(s)
- Kasun M. Thambugala
- Genetics and Molecular Biology Unit, Faculty of Applied Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda 10250, Sri Lanka; (K.M.T.); (D.P.W.J.)
- Center for Biotechnology, Department of Zoology, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
- Center for Plant Materials and Herbal Products Research, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
| | - Dinushani A. Daranagama
- Department of Plant and Molecular Biology, Faculty of Science, University of Kelaniya, Kelaniya 11300, Sri Lanka;
| | - Danushka S. Tennakoon
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Dona Pamoda W. Jayatunga
- Genetics and Molecular Biology Unit, Faculty of Applied Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda 10250, Sri Lanka; (K.M.T.); (D.P.W.J.)
- Center for Biotechnology, Department of Zoology, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
- Center for Plant Materials and Herbal Products Research, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
| | - Sinang Hongsanan
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Ning Xie
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, China
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Development of a Simple DNA Extraction Method and Candida Pan Loop-Mediated Isothermal Amplification Assay for Diagnosis of Candidemia. Pathogens 2022; 11:pathogens11020111. [PMID: 35215055 PMCID: PMC8878442 DOI: 10.3390/pathogens11020111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 01/27/2023] Open
Abstract
To reduce the morbidity and mortality of candidemia patients through rapid treatment, the development of a simple, rapid molecular diagnostic method that is based on nucleic acid extraction and is superior to conventional methods for detecting Candida in the blood is necessary. We developed a multiplex Candida Pan/internal control (IC) loop-mediated isothermal amplification (LAMP) assay and a simple DNA extraction boiling protocol using Chelex-100 that could extract yeast DNA in blood within 20 min. The Chelex-100/boiling method for DNA extraction showed comparable efficiency to that of the commercial QIAamp UCP Pathogen Mini Kit using Candida albicans qPCR. In addition, the Candida Pan/IC LAMP assay showed superior sensitivity to that of general Candida Pan and species qPCRs against clinical DNA samples extracted with the QIAamp UCP Pathogen Mini Kit and Chelex-100/boiling method. The Candida Pan/IC LAMP assay followed by Chelex-100/boiling-mediated DNA extraction showed high sensitivity (100%) and specificity (100%) against clinical samples infected with Candida. These results suggest that the Candida Pan/IC LAMP assay could be used as a rapid molecular diagnostic test for candidemia.
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Dastidar MG, Roy S. Public health management during COVID-19 and applications of point-of-care based biomolecular detection approaches. ENVIRONMENTAL AND HEALTH MANAGEMENT OF NOVEL CORONAVIRUS DISEASE (COVID-19 ) 2021. [PMCID: PMC8237533 DOI: 10.1016/b978-0-323-85780-2.00009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The emergence of the novel human coronavirus, characterized as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a worldwide pandemic. The outbreak of SARS-CoV-2 was first reported at a local wet market in the city of Wuhan in the Hubei province of China at a local wet market. This virus is highly contagious, which gives it the potential for rapid transmission across the world. The transmission of SARS-CoV-2 can be triggered via respiratory droplets in the air from an infected individual to a healthy individual. Thus, to restrict the transmission of the virus, proper public health management and early diagnosis of infected individual is extremely essential. Considering this, the development of various point-of-care (POC) biomolecular assays lead to the importance of early diagnoses at a larger scale during this pandemic situation. Detecting a minimum level of specific target analytes to a particular disease with less instrumentation and minimum reagents, as well as immidiate outcomes, has appeared a challenging path for researchers. Apart from early-stage diagnosis, public awareness is also important to prevent the spread of the virus. Proper intensive care units, isolation rooms, maintaining hygiene, and wearing masks in public areas are necessary. In this chapter, we have discussed the public health management steps and current clinical diagnostics processes and various advanced technology including, molecular, serological, and nanobiosensing approaches for SARS-CoV-2 detection. Furthermore, we have highlighted the various challenges and limitations associated with health management and early diagnostics technologies during SARS-CoV-2 pandemic. Additionally, we have summarized various technical aspects of the development of such POC strategies including biomarkers selections, sensing platforms, unit fabrication, and device incorporation.
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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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Arastehfar A, Wickes BL, Ilkit M, Pincus DH, Daneshnia F, Pan W, Fang W, Boekhout T. Identification of Mycoses in Developing Countries. J Fungi (Basel) 2019; 5:E90. [PMID: 31569472 PMCID: PMC6958481 DOI: 10.3390/jof5040090] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/22/2019] [Accepted: 09/26/2019] [Indexed: 12/12/2022] Open
Abstract
Extensive advances in technology offer a vast variety of diagnostic methods that save time and costs, but identification of fungal species causing human infections remains challenging in developing countries. Since the echinocandins, antifungals widely used to treat invasive mycoses, are still unavailable in developing countries where a considerable number of problematic fungal species are present, rapid and reliable identification is of paramount importance. Unaffordability, large footprints, lack of skilled personnel, and high costs associated with maintenance and infrastructure are the main factors precluding the establishment of high-precision technologies that can replace inexpensive yet time-consuming and inaccurate phenotypic methods. In addition, point-of-care lateral flow assay tests are available for the diagnosis of Aspergillus and Cryptococcus and are highly relevant for developing countries. An Aspergillus galactomannan lateral flow assay is also now available. Real-time PCR remains difficult to standardize and is not widespread in countries with limited resources. Isothermal and conventional PCR-based amplification assays may be alternative solutions. The combination of real-time PCR and serological assays can significantly increase diagnostic efficiency. However, this approach is too expensive for medical institutions in developing countries. Further advances in next-generation sequencing and other innovative technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic tools may lead to efficient, alternate methods that can be used in point-of-care assays, which may supplement or replace some of the current technologies and improve the diagnostics of fungal infections in developing countries.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.
| | - Brian L Wickes
- The Department of Microbiology, Immunology, and Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana 01330, Turkey.
| | | | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China.
| | - Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China.
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China.
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1012 WX Amsterdam, The Netherlands.
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Gabaldón T. Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. FEMS Microbiol Rev 2019; 43:517-547. [PMID: 31158289 PMCID: PMC8038933 DOI: 10.1093/femsre/fuz015] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/31/2019] [Indexed: 12/29/2022] Open
Abstract
The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.
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Affiliation(s)
- Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- ICREA, Pg Lluís Companys 23, 08010 Barcelona, Spain
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Asghar W, Sher M, Khan NS, Vyas JM, Demirci U. Microfluidic Chip for Detection of Fungal Infections. ACS OMEGA 2019; 4:7474-7481. [PMID: 31080939 PMCID: PMC6504191 DOI: 10.1021/acsomega.9b00499] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/27/2019] [Indexed: 05/08/2023]
Abstract
Fungal infections can lead to severe clinical outcomes such as multiple organ failure and septic shock. Rapid detection of fungal infections allows clinicians to treat patients in a timely manner and improves clinical outcomes. Conventional detection methods include blood culture followed by plate culture and polymerase chain reaction. These methods are time-consuming and require expensive equipment, hence, they are not suitable for point-of-care and clinical settings. There is an unmet need to develop a rapid and inexpensive detection method for fungal infections such as candidemia. We developed an innovative immuno-based microfluidic device that can rapidly detect and capture Candida albicans from phosphate-buffered saline (PBS) and human whole blood. Our microchip technology showed an efficient capture of C. albicans in PBS with an efficiency of 61-78% at various concentrations ranging from 10 to 105 colony-forming units per milliliter (cfu/mL). The presented microfluidic technology will be useful to screen for various pathogens at the point-of-care and clinical settings.
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Affiliation(s)
- Waseem Asghar
- Ashgar
Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, Florida 33431, United States
- Department
of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431, United States
- E-mail: (W.A.)
| | - Mazhar Sher
- Ashgar
Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, Florida 33431, United States
- Department
of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Nida S. Khan
- Division
of Infectious Disease, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts 02115, United States
| | - Jatin M. Vyas
- Division
of Infectious Disease, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts 02115, United States
| | - Utkan Demirci
- Bio-Acoustic
MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for
Cancer Early Detection, Department of Radiology, School of Medicine, Stanford University, Palo Alto, California 94305, United States
- E-mail: (U.D.)
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Lee SH, Ahn G, Kim MS, Jeong OC, Lee JH, Kwon HG, Kim YH, Ahn JY. Poly-adenine-Coupled LAMP Barcoding to Detect Apple Scar Skin Viroid. ACS COMBINATORIAL SCIENCE 2018; 20:472-481. [PMID: 30011183 DOI: 10.1021/acscombsci.8b00022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Apple Scar Skin Viroid (ASSVd), a nonprotein coding, circular RNA pathogen is relatively difficult to detect by immunoassay. We report here a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to improve selectivity for diagnostic use in detecting ASSVd in plants. ASSVd RT-LAMP was accelerated using loop primers and was found to be highly sensitive with a detection limit of 104 copies of cDNA-ASSVd within 30 min. Real-time LAMP and melting curve analysis could differentiate between the true-positive LAMP amplicons and false-positive nonspecific primer amplification products. The optimized RT-LAMP was then followed by the addition of nonthiolated AuNP:poly-adenine (A10)-ASSVd LAMP barcodes, showing a high authentication capacity with colorimetric changes. This type of barcoding assay is a potential alternative for rapid and multiple viroid diagnosis, providing for visible sensing in the field that can be applied to viroid-free planting.
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Affiliation(s)
- Se Hee Lee
- School of Biological Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea
| | - Gna Ahn
- School of Biological Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea
| | - Myung-Su Kim
- Apple Research Institute, National Institute of Horticultural & Herbal Science, Rural Development Administration, Gunwi 39000, Korea
| | - Ok Chan Jeong
- Department of Biomedical Engineering, Inje University, Gimhae, South Korea
- Institute of Digital Anti-Aging Healthcare, Inje University, Gimhae, South Korea
| | - Jong Hyun Lee
- Institute of Digital Anti-Aging Healthcare, Inje University, Gimhae, South Korea
| | - Hyuck Gi Kwon
- Institute of Digital Anti-Aging Healthcare, Inje University, Gimhae, South Korea
| | - Yang-Hoon Kim
- School of Biological Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea
| | - Ji-Young Ahn
- School of Biological Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea
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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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Ray M, Ray A, Dash S, Mishra A, Achary KG, Nayak S, Singh S. Fungal disease detection in plants: Traditional assays, novel diagnostic techniques and biosensors. Biosens Bioelectron 2016; 87:708-723. [PMID: 27649327 DOI: 10.1016/j.bios.2016.09.032] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 08/25/2016] [Accepted: 09/10/2016] [Indexed: 11/19/2022]
Abstract
Fungal diseases in commercially important plants results in a significant reduction in both quality and yield, often leading to the loss of an entire plant. In order to minimize the losses, it is essential to detect and identify the pathogens at an early stage. Early detection and accurate identification of pathogens can control the spread of infection. The present article provides a comprehensive overview of conventional methods, current trends and advances in fungal pathogen detection with an emphasis on biosensors. Traditional techniques are the "gold standard" in fungal detection which relies on symptoms, culture-based, morphological observation and biochemical identifications. In recent times, with the advancement of biotechnology, molecular and immunological approaches have revolutionized fungal disease detection. But the drawback lies in the fact that these methods require specific and expensive equipments. Thus, there is an urgent need for rapid, reliable, sensitive, cost effective and easy to use diagnostic methods for fungal pathogen detection. Biosensors would become a promising and attractive alternative, but they still have to be subjected to some modifications, improvements and proper validation for on-field use.
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Affiliation(s)
- Monalisa Ray
- Centre of Biotechnology, Siksha O Anusandhan University, Kalinga Nagar, Ghatikia, Bhubaneswar, Odisha, India
| | - Asit Ray
- Centre of Biotechnology, Siksha O Anusandhan University, Kalinga Nagar, Ghatikia, Bhubaneswar, Odisha, India
| | - Swagatika Dash
- Centre of Biotechnology, Siksha O Anusandhan University, Kalinga Nagar, Ghatikia, Bhubaneswar, Odisha, India
| | - Abtar Mishra
- Centre of Biotechnology, Siksha O Anusandhan University, Kalinga Nagar, Ghatikia, Bhubaneswar, Odisha, India
| | | | - Sanghamitra Nayak
- Centre of Biotechnology, Siksha O Anusandhan University, Kalinga Nagar, Ghatikia, Bhubaneswar, Odisha, India
| | - Shikha Singh
- Centre of Biotechnology, Siksha O Anusandhan University, Kalinga Nagar, Ghatikia, Bhubaneswar, Odisha, India.
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Park C, Kwon EY, Shin NY, Choi SM, Kim SH, Park SH, Lee DG, Choi JH, Yoo JH. Evaluation of nucleic acid sequence based amplification using fluorescence resonance energy transfer (FRET-NASBA) in quantitative detection of Aspergillus 18S rRNA. Med Mycol 2010; 49:73-9. [PMID: 20718604 DOI: 10.3109/13693786.2010.507604] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We attempted to apply fluorescence resonance energy transfer technology to nucleic acid sequence-based amplification (FRET-NASBA) on the platform of the LightCycler system to detect Aspergillus species. Primers and probes for the Aspergillus 18S rRNA were newly designed to avoid overlapping with homologous sequences of human 18s rRNA. NASBA using molecular beacon (MB) showed non-specific results which have been frequently observed from controls, although it showed higher sensitivity (10(-2) amol) than the FRET. FRET-NASBA showed a sensitivity of 10(-1) amol and a high fidelity of reproducibility from controls. As FRET technology was successfully applied to the NASBA assay, it could contribute to diverse development of the NASBA assay. These results suggest that FRET-NASBA could replace previous NASBA techniques in the detection of Aspergillus.
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Affiliation(s)
- Chulmin Park
- Catholic Research Institutes of Medical Science, The Catholic University of Korea, College of Medicine, Seoul, South Korea
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Abstract
Neonatal candidiasis is serious and often fatal. Blood culture, the standard for diagnosis, has a sensitivity of 50% or less, and isolate speciation and susceptibility takes several days. This review explores recent advances in Candida detection using various diagnostic strategies.
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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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White PL, Perry MD, Barnes RA. An update on the molecular diagnosis of invasive fungal disease. FEMS Microbiol Lett 2009; 296:1-10. [PMID: 19416355 DOI: 10.1111/j.1574-6968.2009.01575.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Despite improvements in medical technology, the definitive diagnosis of invasive fungal disease (IFD) is limited. The prevalence of disease is relatively low but many cases are undiagnosed. With the diagnosis of proven IFD dependent on histopathology or culture from a sterile site, clinicians have become more reliant on noninvasive nonculture diagnostic techniques. PCR technology has the capacity to overcome classical limitations but has its own drawbacks, resulting from an incomplete knowledge of the various disease processes and subsequent shortage of optimal specimens, leading to a lack of methodological standardization. This review will consider the general principles and limitations of fungal PCR before discussing genus-specific PCR applications. It is by no means a systematic review of the literature but is intended, where possible, to provide the reader with access to assays with proficient clinical performance.
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Affiliation(s)
- P Lewis White
- NPHS Microbiology Cardiff, UHW, Heath Park, Cardiff, UK.
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Abstract
Direct detection technologies for pathogenic microorganisms are emerging to be applied in the diagnosis of serious bloodstream infections and infections at sterile body sites, as well as for quality control measures prior to the release of sterile blood products and to ascertain microbial safety of food. Standard blood cultures as the current gold standard for detection of bacteraemia/sepsis and other culture-based microbiological identification procedures are comparatively slow and have limited sensitivity for fastidious or slow-growing microorganisms. Rapid nucleic acid-based technologies with PCR amplification or hybridisation probes for specific pathogens, broad-range bacterial or fungal assays, flow cytometry, as well as protein-based characterisation by mass spectrometry, aim at identification of pathogenic microorganisms within minutes to hours. Interpretation of direct detection of panbacterial or panfungal nucleic acids instead of living microorganisms in blood is complex, given the risk of contamination, the ubiquitous presence of bacterial and fungal DNA, and the lack of a gold standard. Since many of the infections at sterile sites, particularly sepsis, are medical emergencies requiring immediate therapeutic responses, rapid technologies could contribute to reduction of morbidity, mortality, and of the economic burden. This review summarises the currently available data on rapid non-culture-based technologies and outlines the potential clinical usefulness in infectious disease diagnosis.
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Affiliation(s)
- Mariam Klouche
- Bremer Zentrum für Laboratoriumsmedizin GmbH and LADR GmbH Medizinisches Versorgungszentrum Bremen, Bremen, Germany.
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Metwally L, Fairley DJ, Coyle PV, Hay RJ, Hedderwick S, McCloskey B, O'Neill HJ, Webb CH, Elbaz W, McMullan R. Improving molecular detection of Candida DNA in whole blood: comparison of seven fungal DNA extraction protocols using real-time PCR. J Med Microbiol 2008; 57:296-303. [DOI: 10.1099/jmm.0.47617-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The limitations of classical diagnostic methods for invasive Candida infections have led to the development of molecular techniques such as real-time PCR to improve diagnosis. However, the detection of low titres of Candida DNA in blood from patients with candidaemia requires the use of extraction methods that efficiently lyse yeast cells and recover small amounts of DNA suitable for amplification. In this study, a Candida-specific real-time PCR assay was used to detect Candida albicans DNA in inoculated whole blood specimens extracted using seven different extraction protocols. The yield and quality of total nucleic acids were estimated using UV absorbance, and specific recovery of C. albicans genomic DNA was estimated quantitatively in comparison with a reference (Qiagen kit/lyticase) method currently in use in our laboratory. The extraction protocols were also compared with respect to sensitivity, cost and time required for completion. The TaqMan PCR assay used to amplify the DNA extracts achieved high levels of specificity, sensitivity and reproducibility. Of the seven extraction protocols evaluated, only the MasterPure yeast DNA extraction reagent kit gave significantly higher total nucleic acid yields than the reference method, although nucleic acid purity was highest using either the reference or YeaStar genomic DNA kit methods. More importantly, the YeaStar method enabled C. albicans DNA to be detected with highest sensitivity over the entire range of copy numbers evaluated, and appears to be an optimal method for extracting Candida DNA from whole blood.
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Affiliation(s)
- L. Metwally
- Department of Medical Microbiology, Royal Victoria Hospital, Belfast, Northern Ireland
| | - D. J. Fairley
- Department of Medical Microbiology, Royal Victoria Hospital, Belfast, Northern Ireland
| | - P. V. Coyle
- Department of Medical Microbiology, Royal Victoria Hospital, Belfast, Northern Ireland
| | - R. J. Hay
- Queen's University of Belfast, School of Medicine and Dentistry, Belfast, Northern Ireland
| | - S. Hedderwick
- Department of Infectious Diseases, Royal Victoria Hospital, Belfast, Northern Ireland
| | - B. McCloskey
- Regional Intensive Care Unit, Royal Victoria Hospital, Belfast, Northern Ireland
| | - H. J. O'Neill
- Department of Medical Microbiology, Royal Victoria Hospital, Belfast, Northern Ireland
| | - C. H. Webb
- Department of Medical Microbiology, Royal Victoria Hospital, Belfast, Northern Ireland
| | - W. Elbaz
- Department of Infectious Diseases, Royal Victoria Hospital, Belfast, Northern Ireland
| | - R. McMullan
- Department of Medical Microbiology, Royal Victoria Hospital, Belfast, Northern Ireland
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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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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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20
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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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21
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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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Gore HM, Wakeman CA, Hull RM, McKillip JL. Real-time molecular beacon NASBA reveals hblC expression from Bacillus spp. in milk. Biochem Biophys Res Commun 2003; 311:386-90. [PMID: 14592426 DOI: 10.1016/j.bbrc.2003.10.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Nucleic acid sequence-based amplification (NASBA) was applied in combination with a fluorescein-conjugated molecular beacon specific for a sequence flanked by transcript-specific primers in order to monitor hblC enterotoxin gene expression in real-time from milk separately contaminated with Bacillus amyloliquefaciens, Bacillus cereus, and Bacillus circulans. Maximal enterotoxin expression was noted following 16, 15, and 16 h, respectively, when grown in artificially contaminated nonfat dried milk incubated aerobically at 32 degrees C, corresponding to 1.6 x 10(5), 5 x 10(7), and 9.8 x 10(4)cfu/ml, for B. amyloliquefaciens, B. cereus, and B. circulans, respectively. This RNA amplification assay allows for simultaneous detection and confirmation of target transcripts in a closed tube format and may be performed in a high DNA background. The development of a rapid, sensitive, real-time method to quantitate the expression of virulence genes in pathogenic spore-formers is useful in shelf life determination of foods and other quality assurance measures.
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Affiliation(s)
- Hope M Gore
- Louisiana State University School of Dentistry, New Orleans, LA, USA
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23
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Greene SR, Moe CL, Jaykus LA, Cronin M, Grosso L, Aarle PV. Evaluation of the NucliSens Basic Kit assay for detection of Norwalk virus RNA in stool specimens. J Virol Methods 2003; 108:123-31. [PMID: 12565163 PMCID: PMC7119547 DOI: 10.1016/s0166-0934(02)00286-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Norwalk-like viruses (NLVs) are a genetically diverse group of human caliciviruses that are the most common cause of epidemic gastroenteritis and are detected typically in stool by reverse transcription (RT)-PCR or electron microscopy (EM). The application of a rapid nucleic acid sequence-based amplification (NASBA) assay for the detection of NLV RNA in stool is described using the NucliSens Basic Kit. Primers and probes for the NLV Basic Kit assay were based on the RNA polymerase region of the prototype NLV, Norwalk virus (NV) genome and could consistently detect 10(4) RT-PCR detectable units of NV RNA in a stool filtrate. When compared directly with RT-PCR on a dilution series of NV stool filtrate, the NucliSens Basic Kit assay was equally sensitive. Cross-reactivity studies with a representative panel of other enteric pathogens were negative. When applied to 15 stool specimens from NV-challenged volunteers, the NASBA Basic Kit application for NV detection yielded 100% sensitivity, 50% specificity, and 67% concordance, using RT-PCR as the 'gold standard'. Despite the specificity of the NASBA primer/probe sequences for NV, other representatives from both NLV genogroups I and II could be detected by the Basic Kit assay in outbreak stool specimens, although the results were inconsistent. Our results suggest that the NucliSens Basic Kit assay provides a rapid and sensitive alternative to RT-PCR for detecting NV RNA in stool specimens. However, improvements in test specificity and primer design will be needed before the assay can be used routinely in the clinical setting.
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Affiliation(s)
- Shermalyn R Greene
- Program in Infectious Diseases, Department of Epidemiology, School of Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7400, USA
| | - Christine L Moe
- Program in Infectious Diseases, Department of Epidemiology, School of Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7400, USA
- Corresponding author. Tel.: +1-404-727-9275; fax: +1-404-727-4590
| | - Lee-Ann Jaykus
- Department of Food Science, North Carolina State University, Raleigh, NC, USA
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Brinkman NE, Haugland RA, Wymer LJ, Byappanahalli M, Whitman RL, Vesper SJ. Evaluation of a rapid, quantitative real-time PCR method for enumeration of pathogenic Candida cells in water. Appl Environ Microbiol 2003; 69:1775-82. [PMID: 12620869 PMCID: PMC150045 DOI: 10.1128/aem.69.3.1775-1782.2003] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Quantitative PCR (QPCR) technology, incorporating fluorigenic 5' nuclease (TaqMan) chemistry, was utilized for the specific detection and quantification of six pathogenic species of Candida (C. albicans, C. tropicalis, C. krusei, C. parapsilosis, C. glabrata and C. lusitaniae) in water. Known numbers of target cells were added to distilled and tap water samples, filtered, and disrupted directly on the membranes for recovery of DNA for QPCR analysis. The assay's sensitivities were between one and three cells per filter. The accuracy of the cell estimates was between 50 and 200% of their true value (95% confidence level). In similar tests with surface water samples, the presence of PCR inhibitory compounds necessitated further purification and/or dilution of the DNA extracts, with resultant reductions in sensitivity but generally not in quantitative accuracy. Analyses of a series of freshwater samples collected from a recreational beach showed positive correlations between the QPCR results and colony counts of the corresponding target species. Positive correlations were also seen between the cell quantities of the target Candida species detected in these analyses and colony counts of Enterococcus organisms. With a combined sample processing and analysis time of less than 4 h, this method shows great promise as a tool for rapidly assessing potential exposures to waterborne pathogenic Candida species from drinking and recreational waters and may have applications in the detection of fecal pollution.
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Affiliation(s)
- Nichole E Brinkman
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268, USA
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White PL, Shetty A, Barnes RA. Detection of seven Candida species using the Light-Cycler system. J Med Microbiol 2003; 52:229-238. [PMID: 12621088 DOI: 10.1099/jmm.0.05049-0] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Due to the limitations of classical methods for the detection of systemic fungal infections and the high mortality rates associated with these infections, it has become essential to develop a quick, sensitive and specific detection assay. By using the Idaho Technologies Light-Cycler system, a qualitative real-time PCR system has been developed for the detection of the leading causes of systemic infection within the genus Candida. The sensitivity of the assay was comparable to previously described PCR methods (1-5 c.f.u. ml(-1)) and, by the use of a single Candida probe, it was able to detect, but not differentiate between, seven species of Candida (Candida albicans, Candida dubliniensis, Candida glabrata, Candida kefyr, Candida krusei, Candida parapsilosis and Candida tropicalis). Single-round amplification on the Light-Cycler allowed rapid turn-around of clinical samples (within one working day) and it was shown to be more sensitive than classical procedures, exposing 39 possible systemic infections that were not detected by blood culture.
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Affiliation(s)
- P Lewis White
- Department of Medical Microbiology and PHLS, University Hospital Wales, Heath Park, Cardiff CF14 4XN, UK
| | - Anjali Shetty
- Department of Medical Microbiology and PHLS, University Hospital Wales, Heath Park, Cardiff CF14 4XN, UK
| | - Rosemary A Barnes
- Department of Medical Microbiology and PHLS, University Hospital Wales, Heath Park, Cardiff CF14 4XN, UK
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Development and evaluation of the nuclisens basic kit NASBA for the detection of RNA from Candida species frequently resistant to antifungal drugs. Diagn Microbiol Infect Dis 2003; 45:217-20. [PMID: 12663165 DOI: 10.1016/s0732-8893(02)00510-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We describe a Nucleic Acid Sequence Based Amplification (NASBA) protocol to detect 6 different Candida species (Candida krusei, Candida glabrata, Candida inconspicua, Candida dubliniensis, Candida norvegensis, Candida lusitaniae) and compare it to a PCR assay. NASBA showed a sensitivity of 1 Colony Forming Unit and detected RNA from all 6 Candida species within 1 working day. All 5 patients with documented candidiasis showed identical results by both methods. This assay offers a sensitive, specific and fast possibility to detect yeast RNA.
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Loeffler J, Hebart H, Cox P, Flues N, Schumacher U, Einsele H. Nucleic acid sequence-based amplification of Aspergillus RNA in blood samples. J Clin Microbiol 2001; 39:1626-9. [PMID: 11283102 PMCID: PMC87985 DOI: 10.1128/jcm.39.4.1626-1629.2001] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Nucleic acid sequence-based amplification (NASBA), an isothermal amplification technique, was established and evaluated for the detection of Aspergillus RNA and compared with a previously published, well-defined real-time PCR assay amplifying a region of the Aspergillus 18S rRNA gene. NASBA showed a lower detection limit of 1 CFU and detected RNA from five different clinically relevant Aspergillus species, including Aspergillus fumigatus. All 77 blood samples tested by PCR and NASBA showed identical results in both assays. Results with the NASBA technique were obtained within 6 h. Thus, the NASBA technique provided a valuable tool for sensitive, specific, fast, and reliable detection of Aspergillus RNA with potential for routine diagnosis, including the possibility to test the viability of cells.
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Affiliation(s)
- J Loeffler
- Medizinische Klinik, Abteilung II, Eberhard-Karls-Universität Tübingen, 72076 Tübingen, Germany.
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Borst A, Leverstein-Van Hall MA, Verhoef J, Fluit AC. Detection of Candida spp. in blood cultures using nucleic acid sequence-based amplification (NASBA). Diagn Microbiol Infect Dis 2001; 39:155-60. [PMID: 11337181 DOI: 10.1016/s0732-8893(01)00211-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Candida spp. are the main causes of fungal infections in immunocompromised patients. It is known, that the routinely used automated blood culture systems may fail to detect yeasts. We therefore investigated, whether Nucleic Acid Sequence-Based Amplification (NASBA) can be used to improve the detection rate of Candida spp. in blood cultures. Culture-positive as well as negative blood cultures from patients with a proven candidaemia were analyzed, and the results of BacT/Alert monitoring were compared with the results of NASBA-based detection of yeast RNA. With the NASBA-assay, the number of positive blood cultures increased from 21% to 34%. The NASBA-assay may confirm the diagnosis and demonstrate the need for prolonged treatment. In addition it may shorten the time to detection. In summary, using NASBA for the detection of yeast RNA in blood cultures, we have shown for the first time that it is possible to improve the detection rate of yeasts in blood cultures by using amplification technology.
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Affiliation(s)
- A Borst
- Eijkman-Winkler Institute for Microbiology, Infectious Diseases and Inflammation, University Medical Center, Utrecht, The Netherlands.
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