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Jenks JD, White PL, Kidd SE, Goshia T, Fraley SI, Hoenigl M, Thompson GR. An update on current and novel molecular diagnostics for the diagnosis of invasive fungal infections. Expert Rev Mol Diagn 2023; 23:1135-1152. [PMID: 37801397 PMCID: PMC10842420 DOI: 10.1080/14737159.2023.2267977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND Invasive fungal infections cause millions of infections annually, but diagnosis remains challenging. There is an increased need for low-cost, easy to use, highly sensitive and specific molecular assays that can differentiate between colonized and pathogenic organisms from different clinical specimens. AREAS COVERED We reviewed the literature evaluating the current state of molecular diagnostics for invasive fungal infections, focusing on current and novel molecular tests such as polymerase chain reaction (PCR), digital PCR, high-resolution melt (HRM), and metagenomics/next generation sequencing (mNGS). EXPERT OPINION PCR is highly sensitive and specific, although performance can be impacted by prior/concurrent antifungal use. PCR assays can identify mutations associated with antifungal resistance, non-Aspergillus mold infections, and infections from endemic fungi. HRM is a rapid and highly sensitive diagnostic modality that can identify a wide range of fungal pathogens, including down to the species level, but multiplex assays are limited and HRM is currently unavailable in most healthcare settings, although universal HRM is working to overcome this limitation. mNGS offers a promising approach for rapid and hypothesis-free diagnosis of a wide range of fungal pathogens, although some drawbacks include limited access, variable performance across platforms, the expertise and costs associated with this method, and long turnaround times in real-world settings.
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Affiliation(s)
- Jeffrey D Jenks
- Durham County Department of Public Health, Durham, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, USA
| | - P Lewis White
- Public Health Wales Microbiology Cardiff, UHW, United Kingdom and Centre for trials research/Division of Infection/Immunity, Cardiff University, Cardiff, UK
| | - Sarah E Kidd
- National Mycology Reference Centre, SA Pathology, Adelaide, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, Australia
| | - Tyler Goshia
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Stephanie I Fraley
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Martin Hoenigl
- Division of Infectious Diseases, Medical University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - George R Thompson
- University of California Davis Center for Valley Fever, Sacramento, CA, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of California Davis Medical Center, Sacramento, CA, USA
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
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Marcos‐Arias C, Mateo E, Jurado‐Martín I, Pena‐Fernández N, Cantón E, Pemán J, Quindós G, Eraso E. Utility of two PCR‐RFLP‐based techniques for identification of
Candida parapsilosis
complex blood isolates. Mycoses 2020; 63:461-470. [DOI: 10.1111/myc.13061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 02/06/2020] [Accepted: 02/08/2020] [Indexed: 12/29/2022]
Affiliation(s)
| | | | | | | | - Emilia Cantón
- Instituto de Investigación Sanitaria La Fe Valencia Spain
| | - Javier Pemán
- Instituto de Investigación Sanitaria La Fe Valencia Spain
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Fidler G, Kocsube S, Leiter E, Biro S, Paholcsek M. DNA Barcoding Coupled with High Resolution Melting Analysis Enables Rapid and Accurate Distinction of Aspergillus species. Med Mycol 2018; 55:642-659. [PMID: 27915305 DOI: 10.1093/mmy/myw127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 10/17/2016] [Indexed: 01/24/2023] Open
Abstract
We describe a high-resolution melting (HRM) analysis method that is rapid, reproducible, and able to identify reference strains and further 40 clinical isolates of Aspergillus fumigatus (14), A. lentulus (3), A. terreus (7), A. flavus (8), A. niger (2), A. welwitschiae (4), and A. tubingensis (2). Asp1 and Asp2 primer sets were designed to amplify partial sequences of the Aspergillus benA (beta-tubulin) genes in a closed-, single-tube system. Human placenta DNA, further Aspergillus (3), Candida (9), Fusarium (6), and Scedosporium (2) nucleic acids from type strains and clinical isolates were also included in this study to evaluate cross reactivity with other relevant pathogens causing invasive fungal infections. The barcoding capacity of this method proved to be 100% providing distinctive binomial scores; 14, 34, 36, 35, 25, 15, 26 when tested among species, while the within-species distinction capacity of the assay proved to be 0% based on the aligned thermodynamic profiles of the Asp1, Asp2 melting clusters allowing accurate species delimitation of all tested clinical isolates. The identification limit of this HRM assay was also estimated on Aspergillus reference gDNA panels where it proved to be 10-102 genomic equivalents (GE) except the A. fumigatus panel where it was 103 only. Furthermore, misidentification was not detected with human genomic DNA or with Candida, Fusarium, and Scedosporium strains. Our DNA barcoding assay introduced here provides results within a few hours, and it may possess further diagnostic utility when analyzing standard cultures supporting adequate therapeutic decisions.
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Affiliation(s)
- Gabor Fidler
- University of Debrecen, Faculty of Medicine, Department of Human Genetics, Debrecen, Hungary
| | - Sandor Kocsube
- University of Szeged, Faculty of Science & Informatics, Department of Microbiology, Szeged, Hungary
| | - Eva Leiter
- University of Debrecen, Faculty of Science and Technology, Department of Biotechnology and Microbiology, Debrecen, Hungary
| | - Sandor Biro
- University of Debrecen, Faculty of Medicine, Department of Human Genetics, Debrecen, Hungary
| | - Melinda Paholcsek
- University of Debrecen, Faculty of Medicine, Department of Human Genetics, Debrecen, Hungary
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Lu S, Mirchevska G, Phatak SS, Li D, Luka J, Calderone RA, Fonzi WA. Dynamic time warping assessment of high-resolution melt curves provides a robust metric for fungal identification. PLoS One 2017; 12:e0173320. [PMID: 28264030 PMCID: PMC5338801 DOI: 10.1371/journal.pone.0173320] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/17/2017] [Indexed: 12/16/2022] Open
Abstract
Fungal infections are a global problem imposing considerable disease burden. One of the unmet needs in addressing these infections is rapid, sensitive diagnostics. A promising molecular diagnostic approach is high-resolution melt analysis (HRM). However, there has been little effort in leveraging HRM data for automated, objective identification of fungal species. The purpose of these studies was to assess the utility of distance methods developed for comparison of time series data to classify HRM curves as a means of fungal species identification. Dynamic time warping (DTW), first introduced in the context of speech recognition to identify temporal distortion of similar sounds, is an elastic distance measure that has been successfully applied to a wide range of time series data. Comparison of HRM curves of the rDNA internal transcribed spacer (ITS) region from 51 strains of 18 fungal species using DTW distances allowed accurate classification and clustering of all 51 strains. The utility of DTW distances for species identification was demonstrated by matching HRM curves from 243 previously identified clinical isolates against a database of curves from standard reference strains. The results revealed a number of prior misclassifications, discriminated species that are not resolved by routine phenotypic tests, and accurately identified all 243 test strains. In addition to DTW, several other distance functions, Edit Distance on Real sequence (EDR) and Shape-based Distance (SBD), showed promise. It is concluded that DTW-based distances provide a useful metric for the automated identification of fungi based on HRM curves of the ITS region and that this provides the foundation for a robust and automatable method applicable to the clinical setting.
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Affiliation(s)
- Sha Lu
- Dermatology Department, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Gordana Mirchevska
- Institute for Microbiology and Parasitology, University Sts Cyril and Methodius, Skopje, Macedonia
| | - Sayali S. Phatak
- Department of Microbiology & Immunology, Georgetown University, Washington, DC, United States of America
| | - Dongmei Li
- Department of Microbiology & Immunology, Georgetown University, Washington, DC, United States of America
| | - Janos Luka
- Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States of America
| | - Richard A. Calderone
- Department of Microbiology & Immunology, Georgetown University, Washington, DC, United States of America
| | - William A. Fonzi
- Department of Microbiology & Immunology, Georgetown University, Washington, DC, United States of America
- * E-mail:
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Barbedo LS, Figueiredo-Carvalho MHG, Muniz MDM, Zancopé-Oliveira RM. Comparison of four molecular approaches to identify Candida parapsilosis complex species. Mem Inst Oswaldo Cruz 2017; 112:214-219. [PMID: 28225905 PMCID: PMC5319372 DOI: 10.1590/0074-02760160412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/08/2016] [Indexed: 12/11/2022] Open
Abstract
Since the description of Candida orthopsilosis and C. metapsilosis in 2005, several methods have been proposed to identify and differentiate these species from C. parapsilosis sensu stricto. Species-specific uniplex polymerase chain reaction (PCR) was performed and compared with sequencing of the D1/D2 region of the LSU 28S rDNA gene, microsatellite typing of C. parapsilosis sensu stricto, and PCR-restriction fragment length polymorphism patterns in the ITS1-5.8S-ITS2 region of the rDNA gene. There was agreement between results of testing of 98 clinical isolates with the four PCR-based methods, with 59 isolates identified as C. parapsilosis sensu stricto, 37 as C. orthopsilosis, and two as C. metapsilosis.
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Affiliation(s)
- Leonardo Silva Barbedo
- Fundação Oswaldo Cruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Micologia, Rio de Janeiro, RJ, Brasil
| | | | - Mauro de Medeiros Muniz
- Fundação Oswaldo Cruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Micologia, Rio de Janeiro, RJ, Brasil
| | - Rosely Maria Zancopé-Oliveira
- Fundação Oswaldo Cruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Micologia, Rio de Janeiro, RJ, Brasil
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Gago S, Serrano C, Alastruey-Izquierdo A, Cuesta I, Martín-Mazuelos E, Aller AI, Gómez-López A, Mellado E. Molecular identification, antifungal resistance and virulence ofCryptococcus neoformansandCryptococcus deneoformansisolated in Seville, Spain. Mycoses 2016; 60:40-50. [DOI: 10.1111/myc.12543] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 07/09/2016] [Accepted: 07/11/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Sara Gago
- Mycology Reference Laboratory; Centro Nacional de Microbiología; Instituto de Salud Carlos III; Madrid Spain
- Manchester Fungal Infection Group; Institute of Inflammation and Repair; University of Manchester; Manchester UK
| | - Carmen Serrano
- Sección Micología; Hospital San Juan de Dios del Aljarafe; Sevilla Spain
| | - Ana Alastruey-Izquierdo
- Mycology Reference Laboratory; Centro Nacional de Microbiología; Instituto de Salud Carlos III; Madrid Spain
- Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015); Instituto de Salud Carlos III; Madrid Spain
| | - Isabel Cuesta
- Mycology Reference Laboratory; Centro Nacional de Microbiología; Instituto de Salud Carlos III; Madrid Spain
- Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015); Instituto de Salud Carlos III; Madrid Spain
| | | | - Ana Isabel Aller
- Unidad de Gestión de Enfermedades Infecciosas y Microbiología; Hospital de Valme; Sevilla Spain
| | - Alicia Gómez-López
- Mycology Reference Laboratory; Centro Nacional de Microbiología; Instituto de Salud Carlos III; Madrid Spain
- Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015); Instituto de Salud Carlos III; Madrid Spain
| | - Emilia Mellado
- Mycology Reference Laboratory; Centro Nacional de Microbiología; Instituto de Salud Carlos III; Madrid Spain
- Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015); Instituto de Salud Carlos III; Madrid Spain
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Neji S, Trabelsi H, Hadrich I, Cheikhrouhou F, Sellami H, Makni F, Ayadi A. Molecular study of the Candida parapsilosis complex in Sfax, Tunisia. Med Mycol 2016; 55:137-144. [PMID: 27555560 DOI: 10.1093/mmy/myw063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 03/04/2016] [Accepted: 06/25/2016] [Indexed: 11/14/2022] Open
Abstract
Candida parapsilosis, which was previously considered to be a complex of three genetically distinct groups, has emerged as a significant agent of nosocomial infections. Recently, this complex was separated into three species: C. parapsilosis sensu stricto, C. orthopsilosis, and C. metapsilosis In Tunisia, data pertaining to these fungi are limited. Thus, the purpose of our study was to determine by BanI PCR-RFLP and ITS sequencing, the occurrence of Candida parapsilosis complex among 182 isolates identified as C. parapsilosis by phenotypical methods. C. parapsilosis sensu stricto represented 94.5% of all isolates, while C. metapsilosis and. C. orthopsilosis were identified in 3.3% and 2.2%, respectively. Sequence analysis of internal transcribed spacer region confirmed and revealed only one genotype among the C. parapsilosis sensu stricto strains, three genotypes among six C. metapsilosis strains and two genotypes among four C. orthopsilosis strains.
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Affiliation(s)
- Sourour Neji
- Laboratory of Parasitology-Mycology, Habib Bourguiba, University Hospital, Sfax, Tunisia.,Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Tunisia
| | - Houaida Trabelsi
- Laboratory of Parasitology-Mycology, Habib Bourguiba, University Hospital, Sfax, Tunisia.,Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Tunisia
| | - Ines Hadrich
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Tunisia
| | - Fatma Cheikhrouhou
- Laboratory of Parasitology-Mycology, Habib Bourguiba, University Hospital, Sfax, Tunisia.,Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Tunisia
| | - Hayet Sellami
- Laboratory of Parasitology-Mycology, Habib Bourguiba, University Hospital, Sfax, Tunisia.,Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Tunisia
| | - Fattouma Makni
- Laboratory of Parasitology-Mycology, Habib Bourguiba, University Hospital, Sfax, Tunisia.,Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Tunisia
| | - Ali Ayadi
- Laboratory of Parasitology-Mycology, Habib Bourguiba, University Hospital, Sfax, Tunisia .,Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Tunisia
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Asadzadeh M, Ahmad S, Hagen F, Meis JF, Al-Sweih N, Khan Z. Simple, Low-Cost Detection of Candida parapsilosis Complex Isolates and Molecular Fingerprinting of Candida orthopsilosis Strains in Kuwait by ITS Region Sequencing and Amplified Fragment Length Polymorphism Analysis. PLoS One 2015; 10:e0142880. [PMID: 26580965 PMCID: PMC4651534 DOI: 10.1371/journal.pone.0142880] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 10/28/2015] [Indexed: 12/19/2022] Open
Abstract
Candida parapsilosis has now emerged as the second or third most important cause of healthcare-associated Candida infections. Molecular studies have shown that phenotypically identified C. parapsilosis isolates represent a complex of three species, namely, C. parapsilosis, C. orthopsilosis and C. metapsilosis. Lodderomyces elongisporus is another species phenotypically closely related to the C. parapsilosis-complex. The aim of this study was to develop a simple, low cost multiplex (m) PCR assay for species-specific identification of C. parapsilosis complex isolates and to study genetic relatedness of C. orthopsilosis isolates in Kuwait. Species-specific amplicons from C. parapsilosis (171 bp), C. orthopsilosis (109 bp), C. metapsilosis (217 bp) and L. elongisporus (258 bp) were obtained in mPCR. Clinical isolates identified as C. parapsilosis (n = 380) by Vitek2 in Kuwait and an international collection of 27 C. parapsilosis complex and L. elongisporus isolates previously characterized by rDNA sequencing were analyzed to evaluate mPCR. Species-specific PCR and DNA sequencing of internal transcribed spacer (ITS) region of rDNA were performed to validate the results of mPCR. Fingerprinting of 19 clinical C. orthopsilosis isolates (including 4 isolates from a previous study) was performed by amplified fragment length polymorphism (AFLP) analysis. Phenotypically identified C. parapsilosis isolates (n = 380) were identified as C. parapsilosis sensu stricto (n = 361), C. orthopsilosis (n = 15), C. metapsilosis (n = 1) and L. elongisporus (n = 3) by mPCR. The mPCR also accurately detected all epidemiologically unrelated C. parapsilosis complex and L. elongisporus isolates. The 19 C. orthopsilosis isolates obtained from 16 patients were divided into 3 haplotypes based on ITS region sequence data. Seven distinct genotypes were identified among the 19 C. orthopsilosis isolates by AFLP including a dominant genotype (AFLP1) comprising 11 isolates recovered from 10 patients. A rapid, low-cost mPCR assay for detection and differentiation of C. parapsilosis, C. orthopsilosis, C. metapsilosis and L. elongisporus has been developed.
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Affiliation(s)
- Mohammad Asadzadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Ferry Hagen
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboudumc, Nijmegen, The Netherlands
| | - Noura Al-Sweih
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Ziauddin Khan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- * E-mail:
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Criseo G, Scordino F, Romeo O. Current methods for identifying clinically important cryptic Candida species. J Microbiol Methods 2015; 111:50-6. [PMID: 25659326 DOI: 10.1016/j.mimet.2015.02.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/03/2015] [Accepted: 02/03/2015] [Indexed: 01/12/2023]
Abstract
In recent years, the taxonomy of the most important pathogenic Candida species (Candida albicans, Candida parapsilosis and Candida glabrata) has undergone profound changes due to the description of new closely-related species. This has resulted in the establishment of cryptic species complexes difficult to recognize in clinical diagnostic laboratories. The identification of these novel Candida species seems to be clinically relevant because it is likely that they differ in virulence and drug resistance. Nevertheless, current phenotypic methods are not suitable to accurately distinguish all the species belonging to a specific cryptic complex and therefore their recognition still requires molecular methods. Since traditional mycological techniques have not been useful, a number of molecular based methods have recently been developed. These range from simple PCR-based methods to more sophisticated real-time PCR and/or MALDI-TOF methods. In this article, we review the current methods designed for discriminating among closely related Candida species by highlighting, in particular, the limits of the existing phenotypic tests and the development of rapid and specific molecular tools for their proper identification.
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Affiliation(s)
- Giuseppe Criseo
- Department of Environmental and Biological Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Fabio Scordino
- Department of Environmental and Biological Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Orazio Romeo
- Department of Environmental and Biological Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy.
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