Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for the rapid identification of yeasts causing bloodstream infections

Abstract

Few studies have systematically standardised and evaluated matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identification of yeasts from bloodstream infections. This is rapidly becoming pertinent for early identification of yeasts and appropriate antifungal therapy. We used 354 yeast strains identified by polymerase chain reaction (PCR) sequencing for standardisation and 367 blind clinical strains for validation of our MALDI-TOF MS protocols. We also evaluated different sample preparation methods and found the on-plate formic acid extraction method as most cost- and time-efficient. The MALDI-TOF assay correctly identified 98.9% of PCR-sequenced yeasts. Novel main spectrum projections (MSP) were developed for Candida auris, C. viswanathii and Kodamaea ohmeri, which were missing from the Bruker MALDI-TOF MS database. Spectral cut-offs computed by receiver operating characteristics (ROC) analysis showed 99.4% to 100% accuracy at a log score of ≥ 1.70 for C. tropicalis, C. parapsilosis, C. pelliculosa, C. orthopsilosis, C. albicans, C. rugosa, C. guilliermondii, C. lipolytica, C. metapsilosis, C. nivariensis. The differences in the species-specific scores of our standardisation and blind validation strains were not statistically significant, implying the optimal performance of our test protocol. The MSPs of the three new species also were validated. We conclude that MALDI-TOF MS is a rapid, accurate and reliable tool for identification of bloodstream yeasts. With proper standardisation, validation and regular database expansion, its efficiency can be further enhanced.

Misidentification of a Rare Species, Cryptococcus laurentii, by Commonly Used Commercial Biochemical Methods and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Systems: Challenges for Clinical Mycology Laboratories

“…However, its application in China (Table 1) and other resource-poor countries has been limited by the initial high equipment cost (18). Unfortunately, the MALDI-TOF MS systems did not show a markedly better performance in this study, mainly owing to deficiencies in their mass fingerprint databases for rare yeast species (see Table S1 in the supplemental material) (12,18). Therefore, ITS rDNA sequencing is still necessary as a supplementary confirmatory test for these rare yeasts (12,20).…”

“…The present study further confirms these findings, as the Vitek 2 system was highly unreliable in the identification of C. laurentii. Moreover, discrepant identification results were noted between local hospitals and the central laboratory using (12,(18)(19)(20). However, its application in China (Table 1) and other resource-poor countries has been limited by the initial high equipment cost (18).…”

“…Unfortunately, the MALDI-TOF MS systems did not show a markedly better performance in this study, mainly owing to deficiencies in their mass fingerprint databases for rare yeast species (see Table S1 in the supplemental material) (12,18). Therefore, ITS rDNA sequencing is still necessary as a supplementary confirmatory test for these rare yeasts (12,20). Remarkably, due to notable differences between the spectra of the two clinical isolates and reference spectra in the current database, both systems failed to identify the two genuine C. laurentii isolates, although the organism is within the systems' identification databases (Fig.…”

“…1). Therefore, it is important for MALDI-TOF MS databases to have spectra representing different strains of the same species for wide identification coverage (12,18).…”

“…Mass spectral profiles of the two C. laurentii clinical isolates confirmed by ITS sequencing were used to construct a main spectrum profile (MSP) dendrogram along with reference spectra of C. laurentii and other Cryptococcus species provided in the Bruker database, for fingerprint relatedness analysis. These data were subsequently used to expand the Bruker MALDI-TOF MS database following the manufacturer's instructions (12).…”