A MALDI-TOF MS procedure for clinical dermatophyte species identification in the routine laboratory

L’Ollivier, Coralie; Cassagne, Christophe; Normand, Anne‐Cécile; Bouchara, Jean-Philippe; Contet‐Audonneau, N.; Hendrickx, Marijke; Fourquet, Patrick; Coulibaly, Oumar; Piarroux, Renaud; Ranque, Stéphane

doi:10.3109/13693786.2013.781691

Cited by 84 publications

(93 citation statements)

References 28 publications

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“…Prior studies have evaluated the accuracy of MALDI-TOF MS for the identification of only a few genera or groups of organisms, such as Aspergillus spp. or the dermatophytes (12,13,(19)(20)(21)(22)(23)(24)(25)(26). In our study, which examined 319 isolates from 43 different genera, the Vitek MS version 3.0 library was able to correctly identify 66.8% of isolates and 76.8% of the isolates after additional SARAMIS analysis.…”

Section: Discussionmentioning

confidence: 76%

Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Clinically Relevant Filamentous Fungi

et al. 2016

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bInvasive fungal infections have a high rate of morbidity and mortality, and accurate identification is necessary to guide appropriate antifungal therapy. With the increasing incidence of invasive disease attributed to filamentous fungi, rapid and accurate species-level identification of these pathogens is necessary. Traditional methods for identification of filamentous fungi can be slow and may lack resolution. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and accurate method for identification of bacteria and yeasts, but a paucity of data exists on the performance characteristics of this method for identification of filamentous fungi. The objective of our study was to evaluate the accuracy of the Vitek MS for mold identification. A total of 319 mold isolates representing 43 genera recovered from clinical specimens were evaluated. Of these isolates, 213 (66.8%) were correctly identified using the Vitek MS Knowledge Base, version 3.0 database. When a modified SARAMIS (Spectral Archive and Microbial Identification System) database was used to augment the version 3.0 Knowledge Base, 245 (76.8%) isolates were correctly identified. Unidentified isolates were subcultured for repeat testing; 71/ 319 (22.3%) remained unidentified. Of the unidentified isolates, 69 were not in the database. Only 3 (0.9%) isolates were misidentified by MALDI-TOF MS (including Aspergillus amoenus [n ‫؍‬ 2] and Aspergillus calidoustus [n ‫؍‬ 1]) although 10 (3.1%) of the original phenotypic identifications were not correct. In addition, this methodology was able to accurately identify 133/144 (93.6%) Aspergillus sp. isolates to the species level. MALDI-TOF MS has the potential to expedite mold identification, and misidentifications are rare. Filamentous fungi are ubiquitous environmental microorganisms that have become increasingly important pathogens, especially in immunocompromised patients. Invasive fungal diseases have a high rate of morbidity and mortality, and accurate identification is necessary to guide appropriate antifungal therapy. Traditionally, the identification of filamentous fungi has required the use of different phenotypic methods in conjunction with macro-and microscopic assessment of the organism (1). This process requires highly trained mycologists, and, in some cases, turnaround time may be prolonged due to a requirement for extended incubation periods, potentially delaying appropriate therapy. Molecular methods, which can provide accurate identification to the species level, can be expensive, require specialized equipment or expertise, and are not commonly available in clinical laboratories.Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been utilized in the clinical microbiology laboratory for rapid and accurate identification of bacteria, mycobacteria, and yeasts (2-9). For filamentous fungi, databases have been limited, and unlike bacteria, filamentous fungi require additional processing steps to dis...

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Section: Discussionmentioning

confidence: 76%

Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Clinically Relevant Filamentous Fungi

et al. 2016

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“…Nenoff et al (20) reported a very high percentage (99.3%) of correct dermatophyte identifications, the only two strains that could not be identified belonging to T. violaceum. L'Ollivier et al (21) reported that half of the T. violaceum strains they studied were misidentified as T. soudanense. The close relationship of taxa within the T. rubrum complex is confirmed by our results, and the high similarity between T. violaceum and African T. rubrum observed with MALDI-TOF MS is in accordance with the ITS sequence data (29,35,36).…”

Section: Discussionmentioning

confidence: 99%

“…Recent studies confirm that this technique may be very attractive for dermatophyte identification (18)(19)(20)(21)(22). In one study, the rate of correct identification of isolates belonging to the T. mentagrophytes complex was 89% (19), and in others, the overall rates of successful identification of dermatophyte species reached 95.8% (18), 97.8% (21), and 99.3% (20), demonstrating the potential of MALDI-TOF MS to replace classical identification methods. The technique has now also been used for the direct identification of dermatophytes in clinical samples (23).…”

mentioning

confidence: 91%

“…Sample preparation consisted of a combination of organism inactivation and protein extraction. It was based on a previously published method (9,19,21), with minor modifications. Fungal material containing all growth phases of the colony was scraped from a surface of approximately 1 cm 2 using a wet swab and suspended in 300 l of sterile deionized water.…”

Section: Isolates Studied (I) Isolates Used To Build Up the Fungal Kmentioning

confidence: 99%

“…The sample preparation method, based on previously described protocols for yeasts (9) and filamentous fungi (19,21), combines organism inactivation and protein extraction and allows working with material taken directly from agar plates, thus avoiding any environmental or instrument contamination. We first established a spectrum database using 134 reference strains belonging to 17 species in the three anamorphic genera Epidermophyton, Microsporum, and Trichophyton.…”

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confidence: 99%

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Matrix-Assisted Laser Desorption Ionization–Time of Flight (MALDI-TOF) Mass Spectrometry Using the Vitek MS System for Rapid and Accurate Identification of Dermatophytes on Solid Cultures

et al. 2014

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d; POLE Pharma Consulting, Breganzona, Switzerland e The objective of this research was to extend the Vitek MS fungal knowledge base version 2.0.0 to allow the robust identification of clinically relevant dermatophytes, using a variety of strains, incubation times, and growth conditions. First, we established a quick and reliable method for sample preparation to obtain a reliable and reproducible identification independently of the growth conditions. The Vitek MS V2.0.0 fungal knowledge base was then expanded using 134 well-characterized strains belonging to 17 species in the genera Epidermophyton, Microsporum, and Trichophyton. Cluster analysis based on mass spectrum similarity indicated good species discrimination independently of the culture conditions. We achieved a good separation of the subpopulations of the Trichophyton anamorph of Arthroderma benhamiae and of anthropophilic and zoophilic strains of Trichophyton interdigitale. Overall, the 1,130 mass spectra obtained for dermatophytes gave an estimated identification performance of 98.4%. The expanded fungal knowledge base was then validated using 131 clinical isolates of dermatophytes belonging to 13 taxa. For 8 taxa all strains were correctly identified, and for 3 the rate of successful identification was >90%; 75% (6/8) of the M. gypseum strains were correctly identified, whereas only 47% (18/38) of the African T. rubrum population (also called T. soudanense) were recognized accurately, with a large quantity of strains misidentified as T. violaceum, demonstrating the close relationship of these two taxa. The method of sample preparation was fast and efficient and the expanded Vitek MS fungal knowledge base reliable and robust, allowing reproducible dermatophyte identifications in the routine laboratory. D ermatophytes in the genera Epidermophyton, Microsporum, and Trichophyton are usually characterized and identified by cultural and morphological characters and physiological tests or, more recently, by sequencing (1). Morphological identification is time-consuming and complex, usually requiring expert mycological knowledge, while sequencing is comparatively expensive and at least 2 to 3 days elapse before sequencing results are available.Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a reliable technique for the identification and typing of microbial pathogens such as bacteria (2-7), yeasts (8-10), and filamentous fungi, including dermatophytes (7,(11)(12)(13)(14)(15)(16)(17). Recent studies confirm that this technique may be very attractive for dermatophyte identification (18-22). In one study, the rate of correct identification of isolates belonging to the T. mentagrophytes complex was 89% (19), and in others, the overall rates of successful identification of dermatophyte species reached 95.8% (18), 97.8% (21), and 99.3% (20), demonstrating the potential of MALDI-TOF MS to replace classical identification methods. The technique has now also been used for the direct identification of dermatophytes in c...

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MALDI‐TOF MS for Filamentous Fungi Identification

Hanson,

Sobczyk,

Snavely

2023

ClinMicroNow

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Identification of fungi in the clinical microbiology laboratory has traditionally relied on a combination of phenotypic characteristics, including colony morphology, microscopic examination, growth characteristics, and biochemical reactions. Sequencing‐based approaches require specialized molecular expertise, can be costly, and are relatively slow. Matrix‐assisted laser desorption ionization‐time of flight (MALDI‐TOF) mass spectrometry (MS) is a more rapid and inexpensive methodology that has been used for the identification of microorganisms, including molds, in the microbiology laboratory. Organisms are identified by using intact cells or cell protein extracts which are ionized into charged molecules using a laser. By measuring the mass to charge ratio of the ionized molecules, a spectral fingerprint is generated. These spectral fingerprints are then compared with a database of known spectra from reference organisms to generate an accurate, species‐level identification. This chapter describes protocols for application of MALDI‐TOF MS to identify filamentous fungi in the clinical microbiology laboratory.

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A MALDI-TOF MS procedure for clinical dermatophyte species identification in the routine laboratory

Cited by 84 publications

References 28 publications

Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Clinically Relevant Filamentous Fungi

Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Clinically Relevant Filamentous Fungi

Matrix-Assisted Laser Desorption Ionization–Time of Flight (MALDI-TOF) Mass Spectrometry Using the Vitek MS System for Rapid and Accurate Identification of Dermatophytes on Solid Cultures

MALDI‐TOF MS for Filamentous Fungi Identification

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