Decoding anaerobes: a comprehensive evaluation of MALDI-TOF Sirius and VITEK MS PRIME in clinical settings

The timely identification of anaerobic bacteria at the genus and species levels is critical for managing infections and guiding antimicrobial therapy. Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has emerged as a powerful tool for the identification of anaerobic bacteria, overcoming challenges associated with their special culture requirements and low growth rates. This technique has proven to be both reliable and efficient, providing accurate identification with minimal bacterial biomass. The application of MALDI-TOF MS in clinical settings has significantly improved the identification of anaerobic bacteria, facilitating appropriate treatment decisions and enhancing patient outcomes with minor costs. This study evaluates the performance of two MALDI-TOF mass spectrometry platforms: SIRIUS (Bruker Daltonics) and VITEK MS PRIME (bioMérieux), and their latest libraries, using a panel of 60 clinically relevant anaerobic strains validated in IVD databases and approved by the Food and Drug Administration. Beyond identification accuracy, we highlight the role of rapid confirmation of anaerobic pathogens in improving clinical outcomes. Results are compared against the existing literature, including performance evaluations of our group, to underscore the advancements in MALDI-TOF technology. MALDI-TOF MS has demonstrated high accuracy in identifying anaerobic bacteria, with a genus identification success rate of over 97%, combined with a precision value of 100% and an overall performance agreement of 73.3%, with some minor discrepancies, so the choice of one or the other platform will depend on the needs of each particular laboratory. IMPORTANCE Rapid and accurate identification of anaerobic bacteria is essential for guiding antimicrobial therapy and improving patient outcomes, yet it remains challenging due to the organisms' fastidious nature. Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry has transformed clinical microbiology by enabling high-throughput, cost-effective, and reliable identification of anaerobes. This study provides a head-to-head comparison of two widely used MALDI-TOF platforms-Bruker SIRIUS and VITEK MS PRIME-using a panel of clinically relevant anaerobic strains. By assessing their diagnostic accuracy, reproducibility, and database performance, our results offer practical insights for laboratories selecting a MALDI-TOF system. The findings have direct implications for improving diagnostic workflows, reducing time-to-result, and enhancing antimicrobial stewardship in clinical settings. Furthermore, this work contributes to the development of national resources and tools that support MALDI-TOF-based diagnostics in low- and middle-income settings.