Evaluation of the Zybio EXS2600 Mass Spectrometry for Accurate and Fast Identification of Filamentous Fungi Clinical Isolates

Aim: This study evaluated the performance of the new Zybio EXS2600 Ex-Accuspec database and system in identifying clinical filamentous fungal pathogens, comparing it with the existing Bruker Filamentous Fungi Library 3.0 database and system. Background: Delayed and inaccurate diagnoses can significantly increase the risk of mortality associated with invasive mold infections. Recently, the identification of mold isolates using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has progressed beyond traditional morphological identification methods. Method: A total of 180 well-characterized clinical mold isolates, representing 23 species across 11 genera, were analyzed alongside eight reference strains from three genera. This analysis was conducted using the direct extraction method on both the EXS2600 and the Biotyper. The results were evaluated using both the manufacturer-recommended cutoff scores and lower cutoff scores. Result: Among the 180 clinical isolates, the EXS2600 achieved significantly higher identification rates than the Bruker Biotyper at both the species/species-complex level (57.2% vs. 17.2%) and genus level (82.8% vs. 45.6%) using the manufacturer-recommended score thresholds (both p < 0.001). When reduced score thresholds were applied, identification rates increased to 82.8% and 91.7% at the species/species-complex and genus levels, respectively, for the EXS2600, compared with 45.6% and 66.7% for the Bruker Biotyper (both p < 0.001). The EXS2600 system achieved high species-level identification rates for Aspergillus fumigatus (80.8%), Aspergillus flavus (93.8%), and dermatophytes (85.0%). In contrast, the Bruker Biotyper showed numerically higher species/species-complex-level identification rates for the Fusarium solani species complex (28.6%) and the Fusarium fujikuroi species complex (28.6%) compared with the EXS2600. Both systems showed limited identification performance for dematiaceous molds, while Trichophyton indotineae was not represented in the Bruker Biotyper database. Additionally, the EXS2600 offered a simpler sample preparation workflow compared with the Biotyper. Conclusions: Our results highlight the Zybio EXS2600 Ex-Accuspec database and system as a promising and reliable tool for the routine identification of filamentous fungi, demonstrating high identification rates and a relatively simple sample preparation procedure. Additionally, lowering the validity cutoff levels may improve the Zybio EXS2600 system’s performance.