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

Abstract

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.

Contaminated fungi in dried salted fishes: Isolation, identification, and their inhibition by chitooligosaccharide‐gallic acid conjugate

“…No. 5027071) with the pattern‐matching process, they were reported as an average for five independent samples established scores as follows: <1.699 not identified, 1.700–1.990 genera level identification, and ≥2.000 species level identification (Gómez‐Velásquez et al., 2020).…”

“…Molecular identification based on specific genes such as ITS1‐5.8s‐ITS2 region is usually used to identify the species, but some genera cannot be identified by only a single gene (Siqueira et al., 2018). Nowadays, MALDI‐TOF MS analysis is extensively used to identify microorganisms because it is a more accurate, faster, and cost‐effective technique (Gómez‐Velásquez et al., 2020). Aspergillus spp.…”

Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review

“…Currently, the identification protocol for filamentous fungi uses the home-brew method in the laboratory [ 11 , 51 ]. The conventional matrix-assisted dissociation effect of formic acid and acetonitrile and a matrix in the laboratory is imperfect, and the extraction effect must be improved by physical or enzymatic lysis of the microbial cell wall.…”

Towards the Development of Sustainable Ground Improvement Techniques—Biocementation Study of an Organic Soil

“…For a more reliable identification, many laboratories often extend the commercial database (e.g. [56,63]). The use of the preparatory extraction of microbes with formic acid (FA) was also reported to increase the ability of MALDI-TOF MS in identifying in particular Gram-positive species [43].…”