MALDI-TOF MS and currently related proteomic technologies in reconciling bacterial systematics.

Abstract This book chapter presents an overview and discussion of the use of MALDI-TOF MS for fungal identification. The major known limitations of the technique for fungal taxonomy, and how to overcome these, are also discussed. Moreover, this should guarantee that spectra deposited in such MALDI-TOF MS database would remain public, preferably in open free access. To avoid misidentification, these stored spectra must be curated and based on well-established standard operating procedures. The number of spectra available within species needs to be increased to accommodate the diversity and geographic differences, unique strain traits and the varied culture conditions and procedures in order to establish a single public and open access MALDITOF MS database. This could then be used with metadata analysis and artificial intelligence algorithms, to provide reliable fungal identification.

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MALDI-TOF MS and its requirements for fungal identification.

Trends in the systematics of bacteria and fungi ◽

10.1079/9781789244984.0119 ◽

2021 ◽

pp. 119-140

Author(s):

Cledir Santos ◽

Paula Galeano ◽

Reginaldo Lima Neto ◽

Manoel Marques Evangelista Oliveira ◽

Nelson Lima

Keyword(s):

Sample Preparation ◽

Black Box ◽

Data Sets ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Fungal Identification ◽

Identification Of Fungi ◽

Tof Ms

Abstract Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is now used as a routine technique for the fast and reliable identification of fungi at the species level and, currently, it represents an important phenotypic methodology based on proteomic profiles. The main limitations to MALDI-TOF MS for fungal identification are related to sample quality (e.g. quality of biological material such as rigidity or pigmentation of cell walls), sample preparation (e.g. the myriad of sample preparation methodologies that deliver different data sets to different MALDI-TOF MS databases) and the databases themselves (e.g. the 'black-box' commercial databases). This chapter presents an overview and discussion of the use of MALDI-TOF MS for fungal identification. The major known limitations of the technique for fungal taxonomy, and how to overcome these, are also discussed.

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A Moldy Application of MALDI: MALDI-ToF Mass Spectrometry for Fungal Identification

Journal of Fungi ◽

10.3390/jof5010004 ◽

2019 ◽

Vol 5 (1) ◽

pp. 4 ◽

Cited By ~ 23

Author(s):

Robin Patel

Keyword(s):

Mass Spectrometry ◽

Filamentous Fungi ◽

Bacterial Identification ◽

Ionization Time ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Fungal Identification ◽

Routine Identification ◽

Tof Ms

As a result of its being inexpensive, easy to perform, fast and accurate, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF MS) is quickly becoming the standard means of bacterial identification from cultures in clinical microbiology laboratories. Its adoption for routine identification of yeasts and even dimorphic and filamentous fungi in cultures, while slower, is now being realized, with many of the same benefits as have been recognized on the bacterial side. In this review, the use of MALDI-ToF MS for identification of yeasts, and dimorphic and filamentous fungi grown in culture will be reviewed, with strengths and limitations addressed.

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MALDI-TOF MS and Filamentous Fungal Identification: A Success Story?

Current Fungal Infection Reports ◽

10.1007/s12281-017-0277-6 ◽

2017 ◽

Vol 11 (2) ◽

pp. 60-65 ◽

Cited By ~ 6

Author(s):

Marijke Hendrickx

Keyword(s):

Success Story ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Fungal Identification ◽

Tof Ms

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Development and Validation of an In-House Library for Filamentous Fungi Identification by MALDI-TOF MS in a Clinical Laboratory in Medellin (Colombia)

Microorganisms ◽

10.3390/microorganisms8091362 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1362

Author(s):

Juan C. Gómez-Velásquez ◽

Natalia Loaiza-Díaz ◽

Gilma Norela Hernández ◽

Nelson Lima ◽

Ana C. Mesa-Arango

Keyword(s):

Filamentous Fungi ◽

Clinical Laboratory ◽

Species Level ◽

Clinical Isolates ◽

Correct Identification ◽

Maldi Tof Ms ◽

Genus Level ◽

Maldi Tof ◽

Fungal Identification ◽

Tof Ms

Identification of filamentous fungi by conventional phenotypic methods are time-consuming, and a correct identification at the species level is prone to errors. Therefore, a more accurate and faster time-to-results, and cost-effective technique, is required, such as the Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). In this study, we describe the development of an in-house spectra library for the identification of filamentous fungi frequently isolated from patients with infections. An in-house spectra library was constructed using 14 reference strains grown in solid medium. Clinical isolates were identified either by the in-house spectra library or the Biotyper commercial library from Bruker Daltonics. Fungal identification was carried following the Biotyper’s established scores: ≤1.699: not reliably identified (NRI); 1.700–1.999: genus-level; ≥2.000: species-level. Clinical isolates were identified, with the in-house library, at species- and genus-level at 88.70% (55) and 3.22% (2), respectively. While 4.80% (3) was NRI and 3.22% (2) was discrepant concerning sequencing. On the contrary, identification up to species and genus-level with the commercial library was 44.44% (16) and 22.22% (8), respectively. NRI and the discrepancy was 30.55% (11) and 2.77% (1), respectively. For the reaming 26 isolates, 16 from Neoscytalidium dimidiatum and 10 from Sporothrix spp., respectively, the absence of spectrum and the specific spectra within the Sporothrix complex in the commercial library resulted in the inability to obtain an identification. In conclusion, the current results advocate the importance that each clinical microbiological laboratory needs to develop an ad hoc library associated with the MALDI-TOF MS fungal identification to overcome the limitations of the available commercial libraries.

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Performance of MALDI-TOF MS platforms for fungal identification

Mycoses ◽

10.1111/myc.12506 ◽

2016 ◽

Vol 59 (11) ◽

pp. 678-690 ◽

Cited By ~ 68

Author(s):

Carole Cassagne ◽

Anne-Cécile Normand ◽

Coralie L'Ollivier ◽

Stéphane Ranque ◽

Renaud Piarroux

Keyword(s):

Maldi Tof Ms ◽

Maldi Tof ◽

Fungal Identification ◽

Tof Ms

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Maximizing the Taxonomic Resolution of MALDI-TOF-MS-Based Approaches to Bacterial Characterization: From Culture Conditions Through Data Analysis

Applications of Mass Spectrometry in Microbiology ◽

10.1007/978-3-319-26070-9_6 ◽

2016 ◽

pp. 147-181 ◽

Cited By ~ 2

Author(s):

Lin Zhang ◽

Todd R. Sandrin

Keyword(s):

Data Analysis ◽

Culture Conditions ◽

Taxonomic Resolution ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Bacterial Characterization ◽

Tof Ms

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Performance of the new ID-fungi plate using two types of reference libraries (Bruker and MSI) to identify fungi with the Bruker MALDI Biotyper

Medical Mycology ◽

10.1093/mmy/myz138 ◽

2020 ◽

Vol 58 (7) ◽

pp. 946-957 ◽

Cited By ~ 1

Author(s):

Laura Heireman ◽

Sofie Patteet ◽

Sophia Steyaert

Keyword(s):

Growth Medium ◽

Web Application ◽

Fungal Infections ◽

Species Level ◽

Promising Alternative ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Fungal Identification ◽

Significant Difference ◽

Tof Ms

Abstract During the last decade, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the diagnosis of fungal infections. Recently, a new Conidia ID-fungi plate (IDFP) medium was introduced to facilitate growth and sampling of fungi. This study aimed to evaluate the IDFP for fungal MALDI-TOF MS identification by comparison with a standard fungal growth medium using two reference libraries. A total of 75 filamentous fungal isolates (including 32 dermatophytes) were inoculated on IDFP and Sabouraud-gentamicin-chloramphenicol (SGC) agar and identified by MALDI-TOF MS using formic acid/acetonitrile extraction. Both the commercially available Bruker library (version 2.0) and the public available MSI web application (version 2018) were applied. For 15% of the isolates, a faster growth was noticed on IDFP compared to SGC. IDFP enhanced the performance of fungal identification compared to SGC for both MSI (increase of 16% identifications to genus and 5% to species level) and Bruker library (increase of 22% identifications to genus and 8% to species level). In total, only 73% of the tested isolates were present in the Bruker library compared to 92% for MSI library. No significant difference (P = 0.46) in MALDI score between IDFP and SGC was observed for the MSI library, but scores were significantly (P = 0.03) higher for IDFP when using Bruker library, potentially explained by the prevention of agar contamination by using IDFP since the Bruker database was created from liquid media. IDFP is a promising alternative growth medium for MALDI-TOF MS fungal identification which would strongly benefit from optimizing the Bruker reference library.

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Study on Molecular Profiles of Staphylococcus aureus Strains: Spectrometric Approach

Molecules ◽

10.3390/molecules25214894 ◽

2020 ◽

Vol 25 (21) ◽

pp. 4894

Author(s):

Michał Złoch ◽

Paweł Pomastowski ◽

Ewelina Maślak ◽

Fernanda Monedeiro ◽

Bogusław Buszewski

Keyword(s):

Staphylococcus Aureus ◽

Culture Conditions ◽

Strain Typing ◽

Major Health Problem ◽

Matrix Type ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Molecular Profiles ◽

The Impact ◽

Tof Ms

Staphylococcus aureus remains a major health problem responsible for many epidemic outbreaks. Therefore, the development of efficient and rapid methods for studying molecular profiles of S. aureus strains for its further typing is in high demand. Among many techniques, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI TOF MS) represents a timely, cost-effective, and reliable strain typing approach, which is still rarely used due to insufficient knowledge about the impact of sample preparation and analysis conditions on the molecular profiles and strain classification efficiency of S. aureus. The aim of this study was to evaluate the effect of the culture conditions and matrix type on the differentiation of molecular profiles of various S. aureus strains via the MALDI TOF MS analysis and different computational methods. The analysis revealed that by changing the culture conditions, matrix type, as well as a statistical method, the differentiation of S. aureus strains can be significantly improved. Therefore, to accelerate the incorporation of the MALDI-based strain typing in routine laboratories, further studies on the standardization and searching of optimal conditions on a larger number of isolates and bacterial species are of great need.

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