MALDI‐TOF mass spectrometry identification of filamentous fungi in the clinical laboratory

Ranque, Stéphane; Normand, Anne‐Cécile; Cassagne, Christophe; Murat, Jean-Benjamin; Bourgeois, Nathalie; Dalle, Frédéric; Gari-Toussaint, M.; Fourquet, Patrick; Hendrickx, Marijke; Piarroux, Renaud

doi:10.1111/myc.12115

Cited by 108 publications

(83 citation statements)

References 23 publications

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“…The majority of published studies examining large study sets of filamentous fungi utilize the Bruker Biotyper MALDI-TOF MS and the associated library and/or laboratory-developed libraries (10,11,(15)(16)(17)(18). 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.…”

Section: Discussionmentioning

confidence: 99%

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: 99%

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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“…Recently, the MALDI-TOF MS approach was also applied to mold identification and was shown to be able to accurately identify a wide array of species from various genera or groups of clinical interest, including Aspergillus spp. and dermatophytes (33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44). Species identification by MALDI-TOF MS within the Fusarium genus has not yet been thoroughly investigated.…”

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Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identification of Molds of the Fusarium Genus

et al. 2015

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eThe rates of infection with Fusarium molds are increasing, and a diverse number of Fusarium spp. belonging to different species complexes can cause infection. Conventional species identification in the clinical laboratory is time-consuming and prone to errors. We therefore evaluated whether matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a useful alternative. The 289 Fusarium strains from the Belgian Coordinated Collections of Microorganisms (BCCM)/Institute of Hygiene and Epidemiology Mycology (IHEM) culture collection with validated sequence-based identities and comprising 40 species were used in this study. An identification strategy was developed, applying a standardized MALDI-TOF MS assay and an in-house reference spectrum database. In vitro antifungal testing was performed to assess important differences in susceptibility between clinically relevant species/species complexes. We observed that no incorrect species complex identifications were made by MALDI-TOF MS, and 82.8% of the identifications were correct to the species level. This success rate was increased to 91% by lowering the cutoff for identification. Although the identification of the correct species complex member was not always guaranteed, antifungal susceptibility testing showed that discriminating between Fusarium species complexes can be important for treatment but is not necessarily required between members of a species complex. With this perspective, some Fusarium species complexes with closely related members can be considered as a whole, increasing the success rate of correct identifications to 97%. The application of our user-friendly MALDI-TOF MS identification approach resulted in a dramatic improvement in both time and accuracy compared to identification with the conventional method. A proof of principle of our MALDI-TOF MS approach in the clinical setting using recently isolated Fusarium strains demonstrated its validity.

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“…Compared to that of bacteria, the cell wall of molds is more robust and rigid, making sample preparation more labor-and time-intensive (13,14). Several studies reported the generation of in-house databases for the Bruker MALDI Biotyper (Bruker Daltonik, Bremen, Germany) covering mainly single genera, such as Aspergillus (15), Fusarium (15, 16), Lichtheimia (17), or the Pseudallescheria/Scedosporium complex (18); orders, such as the Mucorales (15); and individual groups of fungi, such as the dermatophytes (19,20) or clinically important molds (14,(21)(22)(23). However, the species coverage of most of these fungus databases is limited, and many are neither publicly nor commercially available.…”

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confidence: 99%

Use of the Bruker MALDI Biotyper for Identification of Molds in the Clinical Mycology Laboratory

et al. 2014

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Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is increasingly used for the identification of bacteria and fungi in the diagnostic laboratory. We evaluated the mold database of Bruker Daltonik (Bremen, Germany), the Filamentous Fungi Library 1.0. First, we studied 83 phenotypically and molecularly well-characterized, nondermatophyte, nondematiaceous molds from a clinical strain collection. Using the manufacturer-recommended interpretation criteria, genus and species identification rates were 78.3% and 54.2%, respectively. Reducing the species cutoff from 2.0 to 1.7 significantly increased species identification to 71.1% without increasing misidentifications. In a subsequent prospective study, 200 consecutive clinical mold isolates were identified by the MALDI Biotyper and our conventional identification algorithm. Discrepancies were resolved by ribosomal DNA (rDNA) internal transcribed spacer region sequence analysis. For the MALDI Biotyper, genus and species identification rates were 83.5% and 79.0%, respectively, when using a species cutoff of 1.7. Not identified were 16.5% of the isolates. Concordant genus and species assignments of MALDI-TOF MS and the conventional identification algorithm were observed for 98.2% and 64.2% of the isolates, respectively. Four erroneous species assignments were observed using the MALDI Biotyper. The MALDI Biotyper seems highly reliable for the identification of molds when using the Filamentous Fungi Library 1.0 and a species cutoff of 1.7. However, expansion of the database is required to reduce the number of nonidentified isolates. Molds are an important cause of morbidity and mortality among hospitalized patients, particularly among those who are immunocompromised or suffer from serious underlying disease (1-3). Traditionally, identification of molds in the diagnostic mycology laboratory is based on phenotypic traits (4-6). Sufficient growth and sporulation are required to assess macromorphological criteria, including growth on different media and at different temperatures, as well as micromorphological criteria, such as shape of conidia, spores, and mycelial structures. Conventional identification methods have important drawbacks: (i) conventional identification of molds requires a comparably long time to result, (ii) the enormous morphological variability of molds asks for extensive individual expertise of the laboratory personnel, and (iii) some mold isolates do not develop their characteristic structural features under laboratory conditions, preventing identification or even leading to misidentifications. Nucleic acid sequence analysis of the internal transcribed spacer (ITS) regions between the 18S and 28S rRNA genes has emerged as an alternative to conventional identification, especially for isolates with unusual phenotypic profiles and rare molds, including environmental contaminants (4, 7-9).Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is increasingly used in diagnostic bacter...

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MALDI‐TOF mass spectrometry identification of filamentous fungi in the clinical laboratory

Cited by 108 publications

References 23 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

Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identification of Molds of the Fusarium Genus

Use of the Bruker MALDI Biotyper for Identification of Molds in the Clinical Mycology Laboratory

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