Background: In clinical microbiology, MALDI-TOF MS based identification of cultivated microorganisms is an integral part of routine diagnostics. The selection of a system for routine laboratory use should consider factors beyond result accuracy, such as the time to (valid) results, hand-on time, and consumable costs. Literature on these aspects is limited, and to our knowledge there is no such study comparing three devices. Our study aims to compare the suitability of three MALDI-TOF systems, namely bioMérieux"s MS Prime, Bruker"s Biotyper sirius and Zybio"s EXS2600, for use in a high-throughput setting in a diagnostic laboratory.

Methods: During the study period, all isolates that were identified using MALDI-TOF in routine diagnostics were prospectively collected and measured in parallel on the three devices. All days of the week are represented twice. Times for sample preparation and analysis were documented. Samples without valid results were subjected to repeated testing. Validity and agreement between all instruments were assessed.

Results: A total of 2,433 samples was tested. The initial runs yielded valid results for 92 % (Biotyper sirius), 88 % (EXS2600) and 86 % (MS Prime) of the samples. In the repeat measurements carried out with formic acid, valid results were obtained in 49 %, 59 % and 38 % respectively. Mean measuring times per sample varied largely between the test systems (4 – 30 seconds). Average hands-on time varied between 22 and 24 seconds per sample. For 1,862 samples all three systems yielded identical species results. 14 samples were measured as "no ID" by all devices. For 114 samples no overlaps of results at species level were observed for any of the three devices in the initial runs. Of those 58 displayed an overlap at genus level for at least two devices and 13 for all three.

Conclusion: This study provides the first comprehensive overview comparing performance and handling of these three MALDI-TOF systems in a high-throughput setting as it is encountered in routine microbiology laboratories. Depending on the laboratory's specific needs, the selection of a device may prioritize rapid measurement time or cost-effective consumables.