In the 1860s, the Golden Age of Microbiology dawned with major centers in Berlin and Paris. Under the tutelage of Pasteur and Koch, waves of new insights and understanding spread with world-renowned centers for research and education attracting the best and brightest students from Europe and eventually the United States. For more than 100 years, our understanding of bacteria, fungi and parasites grew exponentially as the complexities of these organisms were described, cataloged and compared. This phenotypic foundation built upon Pasteur, Koch, Linnaeus, Klebs, Gram, Salmon, Shiga, Ehrlich, Neisser and so many more provided the basis of our understanding of a tremendous amount of the world around us and revolutionized our fundamental thoughts about many disease processes.
With the revolution brought by Watson and Crick in 1953, for the DNA code that drove how all micro-organisms looked and behaved provided the possibility of new insights into the world of microbiology. By the 1990s, clinical microbiology began to apply the understanding of nucleic acids to the identification of more and more infectious microbes and, by the beginning of the 21st century, a true revolution had arrived in the world of diagnostic and clinical microbiology. In 2014, Mortensen declared that, “We are on the cusp of the biggest change in clinical microbiology since Louis Pasteur declared that life does not arise spontaneously!”
Clearly the research and innovation engines associated with the diagnostic laboratories had shifted their interests and emphasis to molecular methods of detection and identification of pathogenic organisms, but had the educational institutions upheld their role of innovation and adaptation that had started in Berlin and Paris 150 years ago?
Matrix-assisted Laser Desorption/Ionization Time of Flight (MALDI- TOF) is an ionization technique used in mass spectrometry that allows for the analysis of a number of biological molecules, including proteins. MALDI-TOF is a multistep process. First, the sample is mixed with a matrix material and applied to a plate. Second, a pulsed laser irradiates the sample, triggering desorption and ionization by being protonated or deprotonated in the hot plume of ablated gases. Finally, these molecules are then accelerated into a time of flight tube onto a mass detector.
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In the last several years, this methodology has been applied to the identification of routine bacteria, mycobacteria and fungi. Despite the relatively new status of this diagnostic technique, its rapid turnaround time (15 minutes to identification), low cost ($0.50 per identification) and high specificity and sensitivity has proven useful in addressing the complexities associated with the identification of these organisms. Many laboratories rely on this method as the major platform for bacterial identification, replacing biochemical testing to determine organism phenotypes.
Polymerase Chain Reaction (PCR)
Although PCR has been used in research laboratories since the 1980s, the movement of this revolutionary technology in the routine clinical laboratory has been steady, but slow. In the last several years, a number of PCR platforms that are considered “closed” systems have been reviewed and cleared by the FDA for use in routine clinical laboratories. These systems employ a variety of technologies to limit or eliminate open tubes, pipettes and other steps that risk release of amplified DNA. The platforms also allow laboratories to run PCR assays without the need for multiple separated rooms. Therefore, many clinical microbiology laboratories have one or more PCR platforms for routine testing for infectious agents, such as Chlamydia sp. and Neisseria gonorrheae, Clostridium difficile toxin, Streptococcus pyogenes (group A strep) and others.
The human genome project and other major research initiatives has spilled over into pathology and, more recently, microbiology. There are a number of methods and platforms in use for determining the sequence of DNA samples, including classic Sanger sequencing as well as a number of newer technologies. The cost and complexity of isolating DNA and sequencing samples has brought these methods within reasonable reach of a routine clinical laboratory-whether that be as a core facility or in the pathology or microbiology department.