Progress in proteomics for clinical microbiology: MALDI-TOF MS for microbial species identification and more

Abstract

Although classical proteomic approaches are still used regularly in routine clinical diagnostic procedures, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) MS has recently moved into diagnostic microbiology laboratories. MALDI-TOF MS is currently replacing phenotypic microbial identification. Many laboratories now use MALDI-TOF MS for its high efficiency, both from a diagnostic and a cost-per-analysis point of view. The US FDA has now cleared two of the commercially available systems for in vitro diagnostics. This will further spark development of MS applications in antimicrobial susceptibility testing and epidemiology. This review summarizes the state of affairs of MALDI-TOF MS in clinical microbiology; however, this is an active field of research subject to rapid evolution. We emphasize assessment of the clinical relevance and studies focusing on data obtained through comparative analyses of different MALDI-TOF MS instrumentation and multicenter validation studies. The future of MALDI-TOF MS, including antimicrobial susceptibility testing and epidemiological typing, is also highlighted.

Keywords:

• antimicrobial susceptibility testing
• clinical microbiology
• epidemiology
• identification
• MALDI-TOF MS
• matrix-assisted laser-desorption ionization time of flight mass spectrometry

Acknowledgements

We apologize for not having been able to include all currently published papers on MALDI-TOF MS that appeared over the past years. We included examples of the key type of publications and given the huge acceleration of the MALDI-TOF MS technology in clinical microbiology refrained from trying to include all data in the public domain. We gratefully acknowledge all of the colleagues who were involved in the development of the bioMérieux VITEK MS. Dedicated work of a big and multi-disciplinary team has resulted in an innovative and successful new addition to our product portfolio. VITEK MS is a brand in the bioMérieux range of infectious disease diagnostics.

Financial & competing interests disclosure

All authors are employees of bioMérieux, a company developing and selling diagnostic tools for the clinical microbiology laboratory. bioMérieux is offering VITEK MS as a mass spectrometry based solution for bacterial and fungal identification. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

Key issues

• Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) MS and associated, simple sample processing methods have been successfully introduced into clinical microbiology laboratories over the past decade.

• Databases development and database management are central to the development of reliable MALDI-TOF MS applications.

• The MALDI-TOF MS microbiology market is currently dominated by two major players, bioMérieux (France) and Bruker (Germany), and their commercial offers have been FDA approved after extensive and successful clinical trials.

• Beyond microbe identification, the first experimental MALDI-TOF MS applications for antimicrobial susceptibility testing and epidemiological typing have been presented in the literature.

• MALDI-TOF MS technology can also be used to identify other organisms, including, for instance, flies and ticks, and be used in other medical fields including oncology and surgery.

• MALDI-TOF MS has an obvious clinical impact and rapid diagnostics has an important effect on infection control and antibiotic stewardship.

• Next-generation mass spectrometry technologies are currently explored to define their clinical potential.

• Next-generation sequencing will be challenging MALDI-TOF MS in the scientific and commercial microbial identification arena over the years to come.