scholarly journals Evaluation of Microsatellite Typing, ITS Sequencing, AFLP Fingerprinting, MALDI-TOF MS, and Fourier-Transform Infrared Spectroscopy Analysis of Candida auris

2020 ◽  
Vol 6 (3) ◽  
pp. 146
Author(s):  
Mansoureh Vatanshenassan ◽  
Teun Boekhout ◽  
Norman Mauder ◽  
Vincent Robert ◽  
Thomas Maier ◽  
...  
Keyword(s):  
Fourier Transform ◽  
Ftir Spectroscopy ◽  
Fourier Transform Infrared ◽  
Its Sequencing ◽  
Candida Auris ◽  
Epidemiological Typing ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Microsatellite Typing ◽  
Tof Ms

Candida auris is an emerging opportunistic yeast species causing nosocomial outbreaks at a global scale. A few studies have focused on the C. auris genotypic structure. Here, we compared five epidemiological typing tools using a set of 96 C. auris isolates from 14 geographical areas. Isolates were analyzed by microsatellite typing, ITS sequencing, amplified fragment length polymorphism (AFLP) fingerprint analysis, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and Fourier-transform infrared (FTIR) spectroscopy methods. Microsatellite typing grouped the isolates into four main clusters, corresponding to the four known clades in concordance with whole genome sequencing studies. The other investigated typing tools showed poor performance compared with microsatellite typing. A comparison between the five methods showed the highest agreement between microsatellite typing and ITS sequencing with 45% similarity, followed by microsatellite typing and the FTIR method with 33% similarity. The lowest agreement was observed between FTIR spectroscopy, MALDI-TOF MS, and ITS sequencing. This study indicates that microsatellite typing is the tool of choice for C. auris outbreak investigations. Additionally, FTIR spectroscopy requires further optimization and evaluation before it can be used as an epidemiological typing method, comparable with microsatellite typing, as a rapid method for tracing nosocomial fungal outbreaks.

scholarly journals Reagent-Free Identification of Clinical Yeasts by Use of Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy

2019 ◽  
Vol 57 (5) ◽  
Author(s):  
Lisa M. T. Lam ◽  
Philippe J. Dufresne ◽  
Jean Longtin ◽  
Jacqueline Sedman ◽  
Ashraf A. Ismail
Keyword(s):  
Fourier Transform ◽  
Ftir Spectroscopy ◽  
Fourier Transform Infrared ◽  
Attenuated Total Reflectance ◽  
Reference Database ◽  
Accurate Identification ◽  
Total Reflectance ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

ABSTRACT Invasive fungal infections by opportunistic yeasts have increased concomitantly with the growth of an immunocompromised patient population. Misidentification of yeasts can lead to inappropriate antifungal treatment and complications. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy is a promising method for rapid and accurate identification of microorganisms. ATR-FTIR spectroscopy is a standalone, inexpensive, reagent-free technique that provides results within minutes after initial culture. In this study, a comprehensive spectral reference database of 65 clinically relevant yeast species was constructed and tested prospectively on spectra recorded (from colonies taken from culture plates) for 318 routine yeasts isolated from various body fluids and specimens received from 38 microbiology laboratories over a 4-month period in our clinical laboratory. ATR-FTIR spectroscopy attained comparable identification performance with matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). In a preliminary validation of the ATR-FTIR method, correct identification rates of 100% and 95.6% at the genus and species levels, respectively, were achieved, with 3.5% unidentified and 0.9% misidentified. By expanding the number of spectra in the spectral reference database for species for which isolates could not be identified or had been misidentified, we were able to improve identification at the species level to 99.7%. Thus, ATR-FTIR spectroscopy provides a new standalone method that can rival MALDI-TOF MS for the accurate identification of a broad range of medically important yeasts. The simplicity of the ATR-FTIR spectroscopy workflow favors its use in clinical laboratories for timely and low-cost identification of life-threatening yeast strains for appropriate treatment.

Dermatophytic mycetoma of the scalp due to an atypical strain of Microsporum audouinii identified by MALDI-TOF MS and ITS sequencing

2019 ◽  
Vol 29 (2) ◽  
pp. 185-188 ◽  
Author(s):  
K. Diongue ◽  
A. Boye ◽  
L. Bréchard ◽  
M.A. Diallo ◽  
H. Dione ◽  
...  
Keyword(s):  
Its Sequencing ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Microsporum Audouinii ◽  
Tof Ms

scholarly journals Development and Validation of an in-House Library of Colombian Candida auris Strains with MALDI-TOF MS to Improve Yeast Identification

2020 ◽  
Vol 6 (2) ◽  
pp. 72 ◽  
Author(s):  
Andrés Ceballos-Garzon ◽  
Daniela Amado ◽  
Norida Vélez ◽  
María José Jiménez-A ◽  
Crescencio Rodríguez ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Candida Auris ◽  
Yeast Identification ◽  
Great Opportunity ◽  
Maldi Tof Ms ◽  
Identification Process ◽  
Clinical Strains ◽  
Maldi Tof ◽  
Development And Validation ◽  
Tof Ms

Background: Candida auris is characterized for having a high genetic variability among species. MALDI-TOF MS library contains spectra from only three strains of C. auris, which makes difficult the identification process and gives low scores at the species level. Our aim was to construct and validate an internal library to improve C. auris identification with Colombian clinical strains. Methods: From 30 clinical strains, 770 mass spectra were obtained for the construction of the database. The validation was performed with 300 strains to compare the identification results in the BDAL and C. auris Colombia libraries. Results: Our library allowed a complete, 100% identification of the evaluated strains and a significant improvement in the scores obtained, showing a better performance compared to the Bruker BDAL library. Conclusions: The strengthening of the database is a great opportunity to improve the scoring and C. auris identification. Library data are available via ProteomeXchange with identifier PXD016387.

scholarly journals Candida auris Clinical Isolates from South Korea: Identification, Antifungal Susceptibility, and Genotyping

2019 ◽  
Vol 57 (4) ◽  
Author(s):  
Yong Jun Kwon ◽  
Jong Hee Shin ◽  
Seung A Byun ◽  
Min Ji Choi ◽  
Eun Jeong Won ◽  
...  
Keyword(s):  
Antifungal Susceptibility ◽  
Diagnostic Tools ◽  
Candida Auris ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Fluconazole Resistant ◽  
Vitek 2 ◽  
Vitek Ms ◽  
Tof Ms

ABSTRACT Candida auris is an emerging worldwide fungal pathogen. Over the past 20 years, 61 patient isolates of C. auris (4 blood and 57 ear) have been obtained from 13 hospitals in Korea. Here, we reanalyzed those molecularly identified isolates using two matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) systems, including Biotyper and Vitek MS, followed by antifungal susceptibility testing, sequencing of the ERG11 gene, and genotyping. With a research-use-only (RUO) library, 83.6% and 93.4% of the isolates were correctly identified by Biotyper and Vitek MS, respectively. Using an in vitro diagnostic (IVD) library of Vitek MS, 96.7% of the isolates were correctly identified. Fluconazole-resistant isolates made up 62.3% of the isolates, while echinocandin- or multidrug-resistant isolates were not found. Excellent essential (within two dilutions, 96.7%) and categorical agreements (93.4%) between the Clinical and Laboratory Standards Institute (CLSI) and Vitek 2 (AST-YS07 card) methods were observed for fluconazole. Sequencing ERG11 for all 61 isolates revealed that only 3 fluconazole-resistant isolates showed the Erg11p amino acid substitution K143R. All 61 isolates showed identical multilocus sequence typing (MLST). Pulsed-field gel electrophoresis (PFGE) analyses revealed that both blood and ear isolates had the same or similar patterns. These results show that MALDI-TOF MS and Vitek 2 antifungal susceptibility systems can be reliable diagnostic tools for testing C. auris isolates from Korean hospitals. The Erg11p mutation was seldom found among Korean isolates of C. auris, and multidrug resistance was not found. Both MLST and PFGE analyses suggest that these isolates are genetically similar.

Multicenter evaluation of three different MALDI-TOF MS systems for identification of clinically relevant filamentous fungi

2020 ◽  
Vol 59 (1) ◽  
pp. 81-86
Author(s):  
Yue Sun ◽  
Jian Guo ◽  
Rong Chen ◽  
Liang Hu ◽  
Qihang Xia ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Filamentous Fungi ◽  
Reference Method ◽  
Species Level ◽  
Its Sequencing ◽  
Maldi Tof Ms ◽  
Genus Level ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms

Abstract Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) holds promise as a potential tool for clinical identification of filamentous fungi. However, due to the lack of an appropriate extraction protocol and the difficulty of database building, the identification power of each system differs. In this study, we selected 126 clinical mould isolates comprising 28 species identified using internal transcribed spacer (ITS) sequencing as the reference method to evaluate three MALDI-TOF MS systems. When using cultures and sample preparation as recommended by the respective vendors, of the 126 strains tested, VITEK MS identified 121 (96.0%) to species-level and 124 (98.4%) to genus-level; Biotyper identified 53 (42.1%) to species-level and 54 (42.9%) to genus-level; Autof identified 74 (58.7%) to species-level and 76 (60.3%) to genus-level. For the Autof system, the tube extraction method recommended by the vendor performed better (59%) than the on-plate lysis (51%). Our study demonstrates that MALDI-TOF MS systems can successfully identify most clinically relevant fungi, while performance is still highly dependent on the database and sample preparation protocol.

scholarly journals Identificación de aislamientos de Candida auris recuperados a través de la vigilancia por laboratorio en Colombia: un reto para el diagnóstico

Infectio ◽  
2020 ◽  
Vol 24 (4) ◽  
pp. 224
Author(s):  
Silvia K. Carvajal-Valencia ◽  
Diana Lizarazo ◽  
Carolina Duarte ◽  
Patricia Escandon
Keyword(s):  
Candida Auris ◽  
Candida Spp ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Vitek 2 ◽  
Bruker Daltonics ◽  
Tof Ms

Objetivo: Comparar los resultados obtenidos de diferentes sistemas de identificación de C. auris.Métodos: Análisis descriptivo con datos recopilados durante 2016-19 mediante la vigilancia nacional. Se evaluaron los resultados generados por los sistemas MicroScan, Phoenix BD, VITEK 2 y MALDI-TOF MS de instituciones hospitalarias de 843 aislamientos clínicos sospechosos de C. auris remitidos al INS y se compararon con los resultados generados de confirmación a través de MALDI- TOF MS (Bruker Daltonics) o PCR. Resultados: De los 843 aislamientos clínicos remitidos al INS, el 81,7% fueron confirmados como C. auris mediante MALDI- TOF MS o PCR en el INS y el resto, 18,3%, fueron identificados como otras especies de Candida spp. Las identificaciones correctas enviadas por los laboratorios representaron el 42,4%. MicroScan identificó C. auris principalmente como C. haemulonii, C. guilliermondii, C. albicans y C. famata; Phoenix BD, VITEK 2 y MALDI-TOF MS identificó C. auris como C. haemulonii. Discusión: Estudios señalan que C. auris exhibe una estrecha relación filogenética con C. haemulonii. Las identificaciones discrepantes pueden darse debido a que las bases de datos de los sistemas de diagnóstico son limitadas para este patógeno. Las deficiencias de los sistemas comerciales para la identificación de C. auris deben ser complementados con otros sistemas como MALDI-TOF MS o pruebas moleculares.

scholarly journals Application of Spectroscopic Techniques in Early Detection of Fungal Plant Pathogens

2021 ◽  
Author(s):  
Ritesh Kumar ◽  
Shikha Pathak ◽  
Nishant Prakash ◽  
Upasna Priya ◽  
Abhijeet Ghatak
Keyword(s):  
Fluorescence Spectroscopy ◽  
Ftir Spectroscopy ◽  
Pathogen Detection ◽  
Plant Pathogens ◽  
Spectroscopic Techniques ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Fungal Phytopathogens ◽  
Tof Ms

Among the plant pathogens, around 85% of diseases in plants are caused by fungi. Rapid and accurate detection of fungal phytopathogens up to the species level is crucial for the implementation of proper disease control strategies, which were previously relied on conventional approaches. The conventional identification methods have been replaced by many rapid and accurate methods like high throughput sequencing, real-time polymerase chain reaction (PCR), serological and spectroscopic technique. Among these rapid pathogen detection techniques, spectroscopy is a rapid, cost-effective, non-destructive method and does not require sample preparation. Nowadays, visible, infrared and near-infrared rays are commonly employed for pathogen detection. Fluorescence Spectroscopy, Nuclear Magnetic Resonance (NMR) spectroscopy, Fourier Transform Infrared (FTIR) spectroscopy, Attenuated Total Reflection (ATR)-FTIR spectroscopy, Raman Spectroscopy, Matrix-assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS). Biocontrol fungus-like Trichoderma spp. can be detected with the help of MALDI-TOF MS. Fluorescence spectroscopy used fluorescence emanating from the sample and successfully used in the detection of powdery mildew (Blumeria graminis). Hyperspectral imaging is an advanced approach which uses artificial intelligence in plant disease detection. This literature discusses briefly about the features of above-mentioned spectroscopy techniques which may impel the general understanding and propel the research activities.

ATR-FTIR Spectroscopy Highlights the Problem of Distinguishing Between Exophiala dermatitidis and E. phaeomuriformis Using MALDI-TOF MS

2015 ◽  
Vol 71 (2) ◽  
pp. 339-346 ◽  
Author(s):  
Çağrı Ergin ◽  
Yaşar Gök ◽  
Yasemin Bayğu ◽  
Ramazan Gümral ◽  
Betil Özhak-Baysan ◽  
...  
Keyword(s):  
Ftir Spectroscopy ◽  
Exophiala Dermatitidis ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

scholarly journals Isolation of Candida auris from cystic fibrosis patient, Greece, April 2019

2019 ◽  
Vol 24 (29) ◽  
Author(s):  
Angeliki Stathi ◽  
Ioanna Loukou ◽  
Helen Kirikou ◽  
Argyri Petrocheilou ◽  
Maria Moustaki ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Fungal Infection ◽  
Cystic Fibrosis Patient ◽  
Species Level ◽  
Sputum Culture ◽  
Candida Auris ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Level Identification ◽  
Tof Ms

We report the first isolation of Candida auris in Greece from a sputum culture of a cystic fibrosis patient in their 20s under posaconazole treatment. The pathogen was identified as C. duobushaemulonii by VITEK2YST, but as C. auris by MALDI-TOF MS. This case underscores the need for species-level identification of all non-albicans Candida (NAC) isolates from cystic fibrosis patients and patients with predisposing factors to fungal infection.

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