Matrix Assisted Laser Desorption Ionisation/Time Of Flight (MALDI/TOF) mass spectrometry is not done revolutionizing clinical microbiology diagnostic.

The introduction of MALDI TOF mass spectrometry (MALDI TOF MS) in clinical microbiology at the end of 2010 has been a revolution for microbial identification [ [1] Seng P. Drancourt M. Gouriet F. La Scola B. Fournier P.E. Rolain J.M. et al. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis. 2009; 49: 543-551https://doi.org/10.1086/600885 Crossref PubMed Scopus (1484) Google Scholar ]. Unlike the conventional uses of MALDI TOF MS in clinical chemistry laboratories, detecting and quantifying specific peaks of known proteins, the routine use of MALDI TOF MS in clinical microbiology is based on the comparison of mass spectra (intensity of m/z values corresponding to peptides in the low m/z region) to a database of mass spectra, allowing the attribution of matching scores without any a priori on the corresponding proteins. This technique is easy-to-use, fast, requires a low amount of cells, and is cost effective for labs identifying >100 bacteria species per day. Because it is a powerful tool, many authors have attempted to use MALDI TOF MS to obtain additional data (a) direct resistance detection (e.g., methicillin-resistant Staphylococcus aureus/methicillin-susceptible Staphylococcus aureus detection): [ [2] Yu J. Tien N. Liu Y.C. Cho D.Y. Chen J.W. Tsai Y.T. et al. Rapid identification of methicillin-resistant Staphylococcus aureus using MALDI-TOF MS and machine learning from over 20,000 clinical isolates. Microbiol Spectr. 2022; 10e0048322https://doi.org/10.1128/spectrum.00483-22 Crossref Scopus (8) Google Scholar ] (b) virulence factor detection (e.g. delta toxin of S. aureus); [ [3] Gagnaire J. Dauwalder O. Boisset S. Khau D. Freydière A.M. Ader F. et al. Detection of Staphylococcus aureus delta-toxin production by whole-cell MALDI-TOF mass spectrometry. PLoS One. 2012; 7e40660https://doi.org/10.1371/journal.pone.0040660 Crossref PubMed Scopus (59) Google Scholar ]; (c) typing approaches for outbreak detection or multilocus sequence typing (e.g. S. aureus clones) [ [4] Wolters M. Rohde H. Maier T. Belmar-Campos C. Franke G. Scherpe S. et al. MALDI-TOF MS fingerprinting allows for discrimination of major methicillin-resistant Staphylococcus aureus lineages. Int J Med Microbiol. 2011; 301: 64-68https://doi.org/10.1016/j.ijmm.2010.06.002 Crossref PubMed Scopus (193) Google Scholar ]; (d) resistance mechanism detection with functional test (e.g. carbapenemase detection) [ [5] Gato E. Anantharajah A. Arroyo M.J. Artacho M.J. Caballero J.D. Candela A. et al. Multicenter performance evaluation of MALDI-TOF MS for rapid detection of carbapenemase activity in enterobacterales: the future of networking data analysis with online software. Front Microbiol. 2021; 12789731https://doi.org/10.3389/fmicb.2021.789731 Crossref PubMed Scopus (3) Google Scholar ]; and (e) resistance detection through growth/no growth detection (e.g. MALDI Biotyper antibiotic susceptibility test rapid assay [MTB-ASTRA® kit], direct-on-target microdroplet growth assay) [ [6] Idelevich E.A. Becker K. Matrix-assisted laser desorption ionization-time of flight mass spectrometry for antimicrobial susceptibility testing. J Clin Microbiol. 2021; 59e0181419https://doi.org/10.1128/JCM.01814-19 Crossref PubMed Scopus (7) Google Scholar ]. However, the use of these protocols remains very scarce in routine practice. Whereas MALDI TOF MS is widely used in isolated colonies, the main additional use of MALDI TOF MS lies in the direct identification of positive blood cultures that reduces the delay in species identification. Despite the availability of two commercial kits (SepsisType kit and VITEK® MS Blood Culture Kit), many laboratories use ‘homemade’ protocols either for better performance or to reduce the number of manual steps for sample preparation [ [7] Kayin M. Mert B. Aydemir S. Özenci V. Comparison of rapid BACpro® II, Sepsityper® kit and in-house preparation methods for direct identification of bacteria from blood cultures by MALDI-TOF MS with and without Sepsityper® module analysis. Eur J Clin Microbiol Infect Dis. 2019; 38: 2133-2143https://doi.org/10.1007/s10096-019-03654-4 Crossref PubMed Scopus (17) Google Scholar ]. Despite all applications previously described, MALDI TOF MS remains today almost exclusively used routinely for the identification of microorganisms because of the heterogeneous performance. Indeed, these applications are limited by their low practicability and reliability, partly attributable to the low accuracy (e.g. mass spectrometer calibration drift and mass peak shifts) and reproducibility (e.g. peak number, spectral resolution, non-quantitative peak intensities) of the generated spectra by the linear MALDI TOF technology. These applications are also limited by external factors, such as the protein size (over or below the m/z acquisition window) or level of expression (poorly expressed proteins can be not detected because their level of expression may be below the limit of detection of the instrument). Although they are totally embedded in identification algorithms, these varying parameters are poorly controlled for resistance and virulence detection algorithms, and they should be taken into account within these algorithms for better performance and possible use in routine practice. Quality of MALDI-TOF mass spectra in routine diagnostics: results from an international external quality assessment including 36 laboratories from 12 countries using 47 challenging bacterial strainsClinical Microbiology and InfectionVol. 29Issue 2PreviewMatrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a widely used method for bacterial species identification. Incomplete databases and mass spectral quality (MSQ) still represent major challenges. Important proxies for MSQ are the number of detected marker masses, reproducibility, and measurement precision. We aimed to assess MSQs across diagnostic laboratories and the potential of simple workflow adaptations to improve it. Full-Text PDF Open Access