Mass Spectrometry for Species or Strain Identification after Culture or without Culture: Past, Present, and Future

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Abstract
This minireview discusses the use of mass spectrometry in biomarker discovery, the current utility of these markers for bacterial identification after culture, and the potential for non- culture-based diagnosis of infectious diseases. The bases of these thoughts are the independent revolutions that have oc- curred in the fields of molecular biology and analytical chem- istry, leading to the current interrelatedness of genomics, pro- teomics, and bioinformatics. The particular focus is on protein markers and proteomics, which are today essentially synonymous with biomedical mass spectrometry. The methods and approaches, while discussed here in the context of bacterial identification, are equally ap- plicable to viruses, fungi, and parasites. To gain a better un- derstanding of the current state of the art, it is important to understand what mass spectrometry has achieved, what are its current capabilities, and what might be expected in the not- too-distant future. The molecular biology revolution included the development of the PCR and use of restriction enzymes for recognition of sequence differences among organisms by employing "known" genetic markers. The process of marker discovery has been greatly aided in recent years by whole-genome sequencing. In turn, there has been a revolution in mass spectrometry, leading to sequencing of the expressed protein products of these ge- nomes (proteomics). Matrix-assisted laser desorption ioniza- tion-time-of-flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry (MS) and tandem mass spectrometry (MS-MS) have been at the core of these developments. Microbiologists, whose research does not focus on mass spectrometers, are often thinking of an older technology (gas chromatography-mass spectrometry (GC-MS)). In the clinical microbiology field GC is now routinely used for whole-cell fatty acid profiling after prior growth in culture medium (10, 19); included in reference 10 is a nice chapter by Wayne Moss (one of the pioneers of this technique, now known as GC analysis of FAMEs (fatty acid methyl esters)). GC-MS provides additional structure information on these profiles. Therefore, a short section on small-molecule profiling using GC-MS has been included here to provide some perspective ("past devel- opments"). The genomic revolution has given us a vast array of molecular biology tools for discrimination of well-known pathogens as well as emerging infections by the presence or absence of genes or, for closely related organisms, small changes in DNA sequence. It is anticipated that protein se- quence-based discrimination will be as important for the next generation of clinical microbiologists. Thus, a section on large- molecule analysis for bacterial identification after culture is presented (8, 20) ("the present"). Finally, the potential for rapid diagnosis of diseases without culture is briefly discussed ("the future").

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