Microbial Typing by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: Do We Need Guidance for Data Interpretation?

Abstract

eThe integration of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology has revolutionized species identification of bacteria, yeasts, and molds. However, beyond straightforward identification, the method has also been suggested to have the potential for subspecies-level or even type-level epidemiological analyses. This minireview explores MALDI-TOF MS-based typing, which has already been performed on many clinically relevant species. We discuss the limits of the method's resolution and we suggest interpretative criteria allowing valid comparison of strain-specific data. We conclude that guidelines for MALDI-TOF MS-based typing can be developed along the same lines as those used for the interpretation of data from pulsed-field gel electrophoresis (PFGE). Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been integrated into the routine diagnostic workflow of many industrial, pharmaceutical, and medical microbiology laboratories. It has already been thoroughly evaluated for the identification of clinically relevant bacterial species, including anaerobes, Gram-positive rods and cocci, Enterobacteriaceae, and miscellaneous Gram-negative (including nonfermentative) rods, with adequate to excellent results (1, 2).Species identification, however, is only a first step in the diagnostic workflow. The ability to quickly and reliably distinguish or "type" related bacterial isolates is essential for bacterial transmission studies and larger-scale epidemiological surveillance projects. "Conventional" phenotyping methods, such as multiple-susceptibility testing, phage typing, serotyping, biochemical typing, and several others, have been important contributors to our understanding of the epidemiology of community-and health careassociated infections. However, these methods all have practical limitations which render them largely unsuitable for comprehensive bacterial population analyses as well as for scientifically less ambitious but critical infection surveillance. Furthermore, most phenotypic methods have been developed for individual bacterial taxa and are not transferable to other taxa without considerable adaptation.Hence, over the past 2 decades, phenotyping has been largely replaced by "molecular" genotyping. Clonal reproduction by binary fission imprints the evolutionary history of the organism in genotypic markers amenable to analysis by nucleic acid-mediated methods. However, in practice, the ease with which recombination, transfection, and transformation can take place in bacteria necessitates that data from multiple genetic markers are analyzed in defining a "precise" genotype and even then there is no guarantee that an adequate natural taxonomy will be derived. Polyphasic taxonomy currently uses combinations of different phenotypic and/or genotypic data sets to define genera, species, and entities at or below the subspecies level. Still, all these approaches remain time-consuming and relatively...

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