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Associations between Cryptococcus Genotypes, Phenotypes, and Clinical Parameters of Human Disease: A Review. J Fungi (Basel) 2021; 7:jof7040260. [PMID: 33808500 PMCID: PMC8067209 DOI: 10.3390/jof7040260] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 12/11/2022] Open
Abstract
The genus Cryptococcus contains two primary species complexes that are significant opportunistic human fungal pathogens: C. neoformans and C. gattii. In humans, cryptococcosis can manifest in many ways, but most often results in either pulmonary or central nervous system disease. Patients with cryptococcosis can display a variety of symptoms on a spectrum of severity because of the interaction between yeast and host. The bulk of our knowledge regarding Cryptococcus and the mechanisms of disease stem from in vitro experiments and in vivo animal models that make a fair attempt, but do not recapitulate the conditions inside the human host. To better understand the dynamics of initiation and progression in cryptococcal disease, it is important to study the genetic and phenotypic differences in the context of human infection to identify the human and fungal risk factors that contribute to pathogenesis and poor clinical outcomes. In this review, we summarize the current understanding of the different clinical presentations and health outcomes that are associated with pathogenicity and virulence of cryptococcal strains with respect to specific genotypes and phenotypes.
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2
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Lewis PO, Lanier CG, Patel PD, Krolikowski WD, Krolikowski MA. False negative diagnostic errors with polymerase chain reaction for the detection of cryptococcal meningoencephalitis. Med Mycol 2020; 58:408-410. [PMID: 31212317 DOI: 10.1093/mmy/myz064] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/13/2019] [Accepted: 05/20/2019] [Indexed: 01/22/2023] Open
Abstract
The accuracy of the BioFire FilmArray Meningitis/Encephalitis (ME) panel for the identification of Cryptococcus has recently been called into question. The primary objective of this study was to assess the agreement between the BioFire ME polymerase chain reaction (PCR) and other markers of cryptococcal infection. This retrospective review identified five patients with cryptococcal meningoencephalitis, 4 of whom had a negative ME panel for Cryptococcus. All five cases had positive serum cryptococcal antigens, and three of five had a positive cerebrospinal fluid (CSF) culture for Cryptococcus. The BioFire ME panel does not appear to be reliable for ruling out Cryptococcus meningoencephalitis; multiple testing methods are recommended.
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Affiliation(s)
- Paul O Lewis
- Johnson City Medical Center, Department of Pharmacy, Johnson City, TN, 37604, USA
| | - Cameron G Lanier
- Bill Gatton College of Pharmacy at East Tennessee State University, Department of Pharmacy Practice, Johnson City, TN, 37614, USA
| | - Paras D Patel
- East Tennessee State University, Quillen College of Medicine, Division of Infectious Diseases, Johnson City TN, 37614, USA
| | - Whitney D Krolikowski
- East Tennessee State University, Quillen College of Medicine, Division of Infectious Diseases, Johnson City TN, 37614, USA
| | - Matthew A Krolikowski
- East Tennessee State University, Quillen College of Medicine, Division of Infectious Diseases, Johnson City TN, 37614, USA
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3
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Derbalah ASH, El-Banna A, Saad Allah M. Efficiency of Candida tropicalis for Potential Degradation of Metalaxyl in the Aqueous Media. Curr Microbiol 2020; 77:2991-2999. [PMID: 32683464 DOI: 10.1007/s00284-020-02121-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 07/07/2020] [Indexed: 10/23/2022]
Abstract
Biodegradation of pesticides by bacteria, fungi, algae, and other organisms is an eco-friendly, efficient, and economical method of detoxification. This study was conducted to evaluate the efficiency of Candida tropicalis for potential degradation of metalaxyl in the aqueous media. The yeast fungus from soil with a historical application of metalaxyl has been isolated. The identification of isolated fungus was carried out using 28S rRNA. The effect of pH, temperature, and metalaxyl concentration on the growth of C. tropicalis and its ability for metalaxyl degradation was also investigated. The isolated fungus was identified as C. tropicalis based on the sequencing of D1D2 region of the 28S rRNA and BLAST search of the nucleotide sequences. The growth of C. tropicalis in the presence of metalaxyl was significantly higher than in the absence of it. A temperature of 30 °C, a pH value of 7, and metalaxyl concentration of 5 mg/L were the optimal conditions for C. tropicalis to grow and to obtain the highest degradation rate of metalaxyl. At the optimum conditions, the degradation rate and the half-life value of metalaxyl were 0.065 d-1 and 10.7 days, respectively. Under the optimum conditions, a 98% degradation of metalaxyl initial concentration obtained within 36 days. This report is novel in showing the biodegradation of metalaxyl in water by the yeast C. tropicalis, which can be a promising method in this regard.
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Affiliation(s)
- Aly Soliman Hamed Derbalah
- Pesticides Chemistry and Toxicology Department, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt.
| | - Antar El-Banna
- Genetics Department, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
| | - Mostafa Saad Allah
- Pesticides Chemistry and Toxicology Department, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
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4
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Marinelli T, Anagnostou N, Daniel S, Wigg AJ, Teh J. Very early-onset of Cryptococcus neoformans disease following liver transplantation: Report of two cases and a review of the literature. Transpl Infect Dis 2019; 22:e13227. [PMID: 31785187 DOI: 10.1111/tid.13227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/10/2019] [Accepted: 11/24/2019] [Indexed: 01/14/2023]
Abstract
Cryptococcosis is the third most common invasive fungal infection following solid organ transplantation, and mortality is high. Most cases occur late and are due to reactivation of latent infection; however, very early reactivation and donor-derived transmission can occur. Routine screening pre-transplant and antifungal prophylaxis for cryptococcosis post-transplant in solid organ transplantation are not standard practice. We present two cases of very early-onset Cryptococcus neoformans disease following liver transplantation to highlight the need to consider individualized pre-transplant screening and be aware that reactivation of Cryptococcosis neoformans can occur in the immediate post-transplant period.
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Affiliation(s)
- Tina Marinelli
- Department of Infectious Diseases, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Nicholas Anagnostou
- Department of Infectious Diseases, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Santhosh Daniel
- Department of Infectious Diseases, Flinders Medical Centre, Bedford Park, South Australia, Australia.,College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Alan J Wigg
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia.,Hepatology and Transplantation Unit, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Joanne Teh
- Department of Infectious Diseases, Flinders Medical Centre, Bedford Park, South Australia, Australia
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5
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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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Paul S, Singh P, Rudramurthy SM, Chakrabarti A, Ghosh AK. Matrix-assisted laser desorption/ionization–time of flight mass spectrometry: protocol standardization and database expansion for rapid identification of clinically important molds. Future Microbiol 2017; 12:1457-1466. [DOI: 10.2217/fmb-2017-0105] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aim: To standardize the matrix-assisted laser desorption ionization–time of flight mass spectrometry protocols and expansion of existing Bruker Biotyper database for mold identification. Materials & methods: Four different sample preparation methods (protocol A, B, C and D) were evaluated. Results: On analyzing each protein extraction method, reliable identification and best log scores were achieved through protocol D. The same protocol was used to identify 153 clinical isolates. Of these 153, 123 (80.3%) were accurately identified by using existing database and remaining 30 (19.7%) were not identified due to unavailability in database. On inclusion of missing main spectrum profile in existing database, all 153 isolates were identified. Conclusion: Matrix-assisted laser desorption ionization–time of flight mass spectrometry can be used for routine identification of clinically important molds.
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Affiliation(s)
- Saikat Paul
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh-160012, India
| | - Pankaj Singh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh-160012, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh-160012, India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh-160012, India
| | - Anup K Ghosh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh-160012, India
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Zuza-Alves DL, Silva-Rocha WP, Chaves GM. An Update on Candida tropicalis Based on Basic and Clinical Approaches. Front Microbiol 2017; 8:1927. [PMID: 29081766 PMCID: PMC5645804 DOI: 10.3389/fmicb.2017.01927] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/21/2017] [Indexed: 01/12/2023] Open
Abstract
Candida tropicalis has emerged as one of the most important Candida species. It has been widely considered the second most virulent Candida species, only preceded by C. albicans. Besides, this species has been recognized as a very strong biofilm producer, surpassing C. albicans in most of the studies. In addition, it produces a wide range of other virulence factors, including: adhesion to buccal epithelial and endothelial cells; the secretion of lytic enzymes, such as proteinases, phospholipases, and hemolysins, bud-to-hyphae transition (also called morphogenesis) and the phenomenon called phenotypic switching. This is a species very closely related to C. albicans and has been easily identified with both phenotypic and molecular methods. In addition, no cryptic sibling species were yet described in the literature, what is contradictory to some other medically important Candida species. C. tropicalis is a clinically relevant species and may be the second or third etiological agent of candidemia, specifically in Latin American countries and Asia. Antifungal resistance to the azoles, polyenes, and echinocandins has already been described. Apart from all these characteristics, C. tropicalis has been considered an osmotolerant microorganism and this ability to survive to high salt concentration may be important for fungal persistence in saline environments. This physiological characteristic makes this species suitable for use in biotechnology processes. Here we describe an update of C. tropicalis, focusing on all these previously mentioned subjects.
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Affiliation(s)
| | | | - Guilherme M. Chaves
- Laboratory of Medical and Molecular Mycology, Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
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8
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Ostrosky-Zeichner L, Andes D. The Role of In Vitro Susceptibility Testing in the Management of Candida and Aspergillus. J Infect Dis 2017; 216:S452-S457. [PMID: 28911047 DOI: 10.1093/infdis/jix239] [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: 11/13/2022] Open
Abstract
Antifungal susceptibility testing has evolved from a research technique to a standardized and well-validated tool for the clinical management of fungal infections and for epidemiological studies. Genetic mutations and phenotypic resistance in vitro have been shown to correlate with clinical outcomes and treatment failures, and this in turn has led to the creation of clinical breakpoints and, more recently, epidemiological cutoff values for clinically relevant fungal pathogens. Resistance mechanisms for Candida and Aspergillus species have been extensively described and their corresponding genetic mutations can now be readily detected. Epidemiological studies have been able to detect the emergence of regional clonal and nonclonal resistance in several countries. The clinical microbiology laboratory is expected to transition from culture and traditional susceptibility testing to molecular methods for detection, identification, and resistance profiling over the next 5-10 years.
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Affiliation(s)
- Luis Ostrosky-Zeichner
- Division of Infectious Diseases, McGovern Medical School, University of Texas Health Science Center at Houston
| | - David Andes
- Division of Infectious Diseases, University of Wisconsin, Madison
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9
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Lackner M, Lass-Flörl C. Commercial Molecular Tests for Fungal Diagnosis from a Practical Point of View. Methods Mol Biol 2017; 1508:85-105. [PMID: 27837499 DOI: 10.1007/978-1-4939-6515-1_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The increasing interest in molecular diagnostics is a result of tremendously improved knowledge on fungal infections in the past 20 years and the rapid development of new methods, in particular polymerase chain reaction. High expectations have been placed on molecular diagnostics, and the number of laboratories now using the relevant technology is rapidly increasing-resulting in an obvious need for standardization and definition of laboratory organization. In the past 10 years, multiple new molecular tools were marketed for the detection of DNA, antibodies, cell wall components, or other antigens. In contrast to classical culture methods, molecular methods do not detect a viable organisms, but only molecules which indicate its presence; this can be nucleic acids, cell components (antigens), or antibodies (Fig. 1). In this chapter, an overview is provided on commercially available detection tools, their strength and how to use them. A main focus is laid on providing tips and tricks that make daily life easier. We try to focus and mention methodical details which are not highlighted in the manufacturer's instructions of these test kits, but are based on our personal experience in the laboratory. Important to keep in mind is that molecular tools cannot replace culture, microscopy, or a critical view on patients' clinical history, signs, and symptoms, but provide a valuable add on tool. Diagnosis should not be based solely on a molecular test, but molecular tools might deliver an important piece of information that helps matching the diagnostic puzzle to a diagnosis, in particular as few tests are in vitro diagnostic tests (IVD) or only part of the whole test carries the IVD certificate (e.g., DNA extraction is often not included). Please be aware that the authors do not claim to provide a complete overview on all commercially available diagnostic assays being currently marketed for fungal detection, as those are subject to constant change. A main focus is put on commonly used panfungal assays and pathogen-specific assays, including Aspergillus-specific, Candida-specific, Cryptococcus specific, Histoplasma-specific, and Pneumocystis-specific assays. Assays are categorized according to their underlying principle in either antigen-detecting or antibody-detecting or DNA-detecting (Fig. 1). Other non-DNA-detecting nucleic acid methods such as FISH and PNA FISH are not summarized in this chapter and an overview on test performance, common false positives, and the clinical evaluation of commercial tests in studies is provided already in a previous book series by Javier Yugueros Marcos and David H. Pincus (Marcos and Pincus, Methods Mol Biol 968:25-54, 2013).
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Affiliation(s)
- Michaela Lackner
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstrasse 41, Innsbruck, 6020, Austria.
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstrasse 41, Innsbruck, 6020, Austria
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Nalintya E, Kiggundu R, Meya D. Evolution of Cryptococcal Antigen Testing: What is new? CURRENT FUNGAL INFECTION REPORTS 2016; 10:62-67. [PMID: 27158322 PMCID: PMC4858186 DOI: 10.1007/s12281-016-0256-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Over the last decade, an upsurge in both the frequency and severity of fungal infections due to the HIV/AIDS epidemic and the use of immunosuppressive therapy has occurred. Even diagnostic methods like culture and microscopy, which have low sensitivity and longer turn-around-times are not widely available, leading to delays in timely antifungal therapy and detrimental patient outcomes. The evolution of cryptococcal antigen (CrAg) testing to develop inexpensive and more sensitive methods to detect cryptococcal antigen is significant. These newer tests employ immunoassays as part of point-of-care platforms, which do not require complex laboratory infrastructure and they have the potential to detect early disease and reduce time to diagnosis of cryptococcal infection. Advocacy for widely available and efficacious life-saving antifungal treatment should be the only remaining challenge.
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Affiliation(s)
- Elizabeth Nalintya
- Infectious Diseases Institute, Mulago Hill Road, Makerere University, Uganda
| | - Reuben Kiggundu
- Infectious Diseases Institute, Mulago Hill Road, Makerere University, Uganda
| | - David Meya
- Infectious Diseases Institute, Mulago Hill Road, Makerere University, Uganda.; Department of Medicine, Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, USA.; School of Medicine, College of Health Sciences, Makerere University
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11
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Molecular Detection and Identification of Fungal Pathogens. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and Bayesian phylogenetic analysis to characterize Candida clinical isolates. J Microbiol Methods 2015; 119:214-22. [PMID: 26551247 DOI: 10.1016/j.mimet.2015.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 11/01/2015] [Accepted: 11/05/2015] [Indexed: 11/23/2022]
Abstract
Clinical Candida isolates from two different hospitals in Rome were identified and clustered by MALDI-TOF MS system and their origin and evolution estimated by Bayesian phylogenetic analysis. The different species of Candida were correctly identified and clustered separately, confirming the ability of these techniques to discriminate between different Candida species. Focusing MALDI-TOF analysis on a single Candida species, Candida albicans and Candida parapsilosis strains clustered differently for hospital setting as well as for period of isolation than Candida glabrata and Candida tropicalis isolates. The evolutionary rates of C. albicans and C. parapsilosis (1.93×10(-2) and 1.17×10(-2)substitutions/site/year, respectively) were in agreement with a higher rate of mutation of these species, even in a narrow period, than what was observed in C. glabrata and C. tropicalis strains (6.99×10(-4) and 7.52×10(-3)substitutions/site/year, respectively). C. albicans resulted as the species with the highest between and within clades genetic distance values in agreement with the temporal-related clustering found by MALDI-TOF and the high evolutionary rate 1.93×10(-2)substitutions/site/year.
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Pfaller MA, Castanheira M. Nosocomial Candidiasis: Antifungal Stewardship and the Importance of Rapid Diagnosis. Med Mycol 2015; 54:1-22. [PMID: 26385381 DOI: 10.1093/mmy/myv076] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 07/20/2015] [Indexed: 01/12/2023] Open
Abstract
Candidemia and other forms of candidiasis are associated with considerable excess mortality and costs. Despite the addition of several new antifungal agents with improved spectrum and potency, the frequency of Candida infection and associated mortality have not decreased in the past two decades. The lack of rapid and sensitive diagnostic tests has led to considerable overuse of antifungal agents resulting in increased costs, selection pressure for resistance, unnecessary drug toxicity, and adverse drug interactions. Both the lack of timely diagnostic tests and emergence of antifungal resistance pose considerable problems for antifungal stewardship. Whereas antifungal stewardship with a focus on nosocomial candidiasis should be able to improve the administration of antifungal therapy in terms of drug selection, proper dose and duration, source control and de-escalation therapy, an important parameter, timeliness of antifungal therapy, remains a victim of slow and insensitive diagnostic tests. Fortunately, new proteomic and molecular diagnostic tools are improving the time to species identification and detection. In this review we will describe the potential impact that rapid diagnostic testing and antifungal stewardship can have on the management of nosocomial candidiasis.
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Affiliation(s)
- Michael A Pfaller
- T2Biosystems, Lexington, Massachusetts JMI Laboratories, North Liberty, Iowa University of Iowa College of Medicine College of Public Health, Iowa City, Iowa
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Application of Culture-Independent Rapid Diagnostic Tests in the Management of Invasive Candidiasis and Cryptococcosis. J Fungi (Basel) 2015; 1:217-251. [PMID: 29376910 PMCID: PMC5753112 DOI: 10.3390/jof1020217] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/17/2015] [Accepted: 08/17/2015] [Indexed: 12/26/2022] Open
Abstract
The diagnosis of invasive candidiasis (IC) and cryptococcosis is often complicated by slow and insensitive culture-based methods. Such delay results in poor outcomes due to the lack of timely therapeutic interventions. Advances in serological, biochemical, molecular and proteomic approaches have made a favorable impact on this process, improving the timeliness and accuracy of diagnosis with resultant improvements in outcome. This paper will serve as an overview of recent developments in the diagnostic approaches to infections due to these important yeast-fungi.
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15
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Bourassa L, Butler-Wu SM. MALDI-TOF Mass Spectrometry for Microorganism Identification. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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16
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Chao QT, Lee TF, Teng SH, Peng LY, Chen PH, Teng LJ, Hsueh PR. Comparison of the accuracy of two conventional phenotypic methods and two MALDI-TOF MS systems with that of DNA sequencing analysis for correctly identifying clinically encountered yeasts. PLoS One 2014; 9:e109376. [PMID: 25330370 PMCID: PMC4199611 DOI: 10.1371/journal.pone.0109376] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 09/03/2014] [Indexed: 01/21/2023] Open
Abstract
We assessed the accuracy of species-level identification of two commercially available matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems (Bruker Biotyper and Vitek MS) and two conventional phenotypic methods (Phoenix 100 YBC and Vitek 2 Yeast ID) with that of rDNA gene sequencing analysis among 200 clinical isolates of commonly encountered yeasts. The correct identification rates of the 200 yeast isolates to species or complex (Candida parapsilosis complex, C. guilliermondii complex and C. rugosa complex) levels by the Bruker Biotyper, Vitek MS (using in vitro devices [IVD] database), Phoenix 100 YBC and Vitek 2 Yeast ID (Sabouraud's dextrose agar) systems were 92.5%, 79.5%, 89%, and 74%, respectively. An additional 72 isolates of C. parapsilosis complex and 18 from the above 200 isolates (30 in each of C. parapsilosis, C. metapsilosis, and C. orthopsilosis) were also evaluated separately. Bruker Biotyper system could accurately identify all C. parapsilosis complex to species level. Using Vitek 2 MS (IVD) system, all C. parapsilosis but none of C. metapsilosis, or C. orthopsilosis could be accurately identified. Among the 89 yeasts misidentified by the Vitek 2 MS (IVD) system, 39 (43.8%), including 27 C. orthopsilosis isolates, could be correctly identified Using the Vitek MS Plus SARAMIS database for research use only. This resulted in an increase in the rate of correct identification of all yeast isolates (87.5%) by Vitek 2 MS. The two species in C. guilliermondii complex (C. guilliermondii and C. fermentati) isolates were correctly identified by cluster analysis of spectra generated by the Bruker Biotyper system. Based on the results obtained in the current study, MALDI-TOF MS systems present a promising alternative for the routine identification of yeast species, including clinically commonly and rarely encountered yeast species and several species belonging to C. parapsilosis complex, C. guilliermondii complex, and C. rugosa complex.
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Affiliation(s)
- Qiao-Ting Chao
- Departments of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tai-Fen Lee
- Departments of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Shih-Hua Teng
- Department of Graduate Institute of Biomedical Sciences, Chang Gung University, Tao-Yuan, Taiwan; Bruker Taiwan Co., Ltd., Taipei, Taiwan
| | - Li-Yun Peng
- Departments of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ping-Hung Chen
- Departments of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Lee-Jene Teng
- Departments of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Departments of and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
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State-of-the-Art Procedures and Quality Management in Diagnostic Medical Mycology. CURRENT FUNGAL INFECTION REPORTS 2013. [DOI: 10.1007/s12281-013-0145-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Multicenter study evaluating the Vitek MS system for identification of medically important yeasts. J Clin Microbiol 2013; 51:2267-72. [PMID: 23658267 DOI: 10.1128/jcm.00680-13] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The optimal management of fungal infections is correlated with timely organism identification. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is revolutionizing the identification of yeasts isolated from clinical specimens. We present a multicenter study assessing the performance of the Vitek MS system (bioMérieux) in identifying medically important yeasts. A collection of 852 isolates was tested, including 20 Candida species (626 isolates, including 58 C. albicans, 62 C. glabrata, and 53 C. krusei isolates), 35 Cryptococcus neoformans isolates, and 191 other clinically relevant yeast isolates; in total, 31 different species were evaluated. Isolates were directly applied to a target plate, followed by a formic acid overlay. Mass spectra were acquired using the Vitek MS system and were analyzed using the Vitek MS v2.0 database. The gold standard for identification was sequence analysis of the D2 region of the 26S rRNA gene. In total, 823 isolates (96.6%) were identified to the genus level and 819 isolates (96.1%) were identified to the species level. Twenty-four isolates (2.8%) were not identified, and five isolates (0.6%) were misidentified. Misidentified isolates included one isolate of C. albicans (n = 58) identified as Candida dubliniensis, one isolate of Candida parapsilosis (n = 73) identified as Candida pelliculosa, and three isolates of Geotrichum klebahnii (n = 6) identified as Geotrichum candidum. The identification of clinically relevant yeasts using MS is superior to the phenotypic identification systems currently employed in clinical microbiology laboratories.
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