Comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry methods with conventional phenotypic identification for routine identification of bacteria to the species level

Abstract

Bacterial identification relies primarily on culture-based methodologies requiring 24 h for isolation and an additional 24 to 48 h for species identification. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is an emerging technology newly applied to the problem of bacterial species identification. We evaluated two MALDI-TOF MS systems with 720 consecutively isolated bacterial colonies under routine clinical laboratory conditions. Isolates were analyzed in parallel on both devices, using the manufacturers' default recommendations. We compared MS with conventional biochemical test system identifications. Discordant results were resolved with "gold standard" 16S rRNA gene sequencing. The first MS system (Bruker) gave high-confidence identifications for 680 isolates, of which 674 (99.1%) were correct; the second MS system (Shimadzu) gave high-confidence identifications for 639 isolates, of which 635 (99.4%) were correct. Had MS been used for initial testing and biochemical identification used only in the absence of high-confidence MS identifications, the laboratory would have saved approximately US$5 per isolate in marginal costs and reduced average turnaround time by more than an 8-h shift, with no loss in accuracy. Our data suggest that implementation of MS as a first test strategy for one-step species identification would improve timeliness and reduce isolate identification costs in clinical bacteriology laboratories now.

FIG. 1.

Illustration of mass spectrum results. Measured mass spectra ranged from 2,000 to 20,000 Da. Extraction of the peaks from the generated mass spectra and their matching against the reference spectra (“main spectra”) of the integrated database was performed with the MALDI Biotyper software program (Bruker Daltonics). The score value is defined by three components, the matches of the unknown spectrum against the main spectrum, the matches of the main spectrum peaks against the unknown spectrum, and the correlation of intensities of the matched peaks. This leads to a first score from 0 (no match) to 1,000 (perfect identity), which is converted into a log score from 0 to 3.

FIG. 2.

Accuracy of MALDI-TOF MS identifications of 720 clinical isolates.