Factors Associated With MALDI-TOF Mass Spectral Quality of Species Identification in Clinical Routine Diagnostics

Abstract

BackgroundAn accurate and timely identification of bacterial species is critical in clinical diagnostics. Species identification allows a potential first adaptation of empiric antibiotic treatments before the resistance profile is available. Matrix assisted Laser Desorption Ionization Time of Flight mass spectrometry (MALDI-TOF MS) is a widely used method for bacterial species identification. However, important challenges in species identification remain. These arise from (i) incomplete databases, (ii) close relatedness of species of interest, and (iii) spectral quality, which is currently vaguely defined.MethodsWe selected 47 clinically relevant bacterial isolates from 39 species, which can be challenging to identify by MALDI-TOF MS. We measured these isolates under various analytical conditions on two MALDI-TOF MS systems. First, we identified spectral features, which were associated with correct species identification in three different databases. Considering these features, we then systematically compared spectra produced with three different sample preparation protocols. In addition, we varied quantities of bacterial colony material applied and bacterial colony age.ResultsWe identified (i) the number of ribosomal marker peaks detected, (ii) the median relative intensity of ribosomal marker peaks, (iii) the sum of the intensity of all detected peaks, (iv) a high measurement precision, and (v) reproducibility of peaks to act as good proxies of spectral quality. We found that using formic acid, measuring bacterial colonies at a young age, and frequently calibrating the MALDI-TOF MS device increase mass spectral quality. We further observed significant differences in spectral quality between different bacterial taxa and optimal measurement conditions vary per taxon.ConclusionWe identified and applied quality measures for MALDI-TOF MS and optimized spectral quality in routine settings. Phylogenetic marker peaks can be reproducibly detected and provide an increased resolution and the ability to distinguish between challenging species such as those within the Enterobacter cloacae complex, Burkholderia cepacia complex, or viridans streptococci.

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

“…These are some strains of complex bacterial groups, including A. calcoaceticus-A. baumannii complex, Enterobacter cloacae complex, Burkholderia cepacia complex, and S. mitis complex [ 15 , 108 , 109 , 110 ]. In addition, Shigella and Escherichia coli cannot be accurately identified by MALDI-TOF MS because they have similar mass spectra [ 111 ].…”

“…MALDI-TOF MS has good identification outcomes for common, clinically isolated bacteria [ 14 , 15 ]. In fungi, the identification of Candida spp.…”

Application and Perspectives of MALDI–TOF Mass Spectrometry in Clinical Microbiology Laboratories

“…The proper proportion between sample and matrix, and therefore the crystallization of the mixture, is an essential if massive fragmentation or even destruction of the sample is to be avoided. Moreover, bacterial age, the agar medium, bacteria culture atmosphere, the number of laser shots applied and the averaged spectra per measurement could interfere with the quality of the results and therefore to the proper identification of the sample [ 16 ]. The second disadvantage of MALDI–TOF MS is that the identification of new species relies strongly on a complete database [ 9 ].…”

Identification and Antifungal Susceptibility Analysis of Stephanoascus ciferrii Complex Species Isolated From Patients With Chronic Suppurative Otitis Media

“…However, as for a rare kind of opportunistic pathogenic fungus, identifying S. ciferrii complex at species level is of great importance in epidemiological studies and the management of empirical antifungal therapy. Recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized microbial diagnostics ( Cuenod et al, 2021 ). Because of its minimal hands-on and turnaround time, low costs, and high accuracy, MALDI-TOF MS has been widely used in the identification of bacterial and fungi species clinically ( Angeletti and Ciccozzi, 2019 ; Cuenod et al, 2021 ).…”

“…Recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized microbial diagnostics ( Cuenod et al, 2021 ). Because of its minimal hands-on and turnaround time, low costs, and high accuracy, MALDI-TOF MS has been widely used in the identification of bacterial and fungi species clinically ( Angeletti and Ciccozzi, 2019 ; Cuenod et al, 2021 ).…”