Transcriptomic Techniques in Diagnostic Microbiology
Traditional pathogen detection methods have long been the standard diagnostic approach to infectious diseases. While undoubtedly useful, pathogen detection is hampered by low sensitivity and specificity or prolonged turnaround times. A novel concept that addresses these limitations involves focusing on the host’s response to infection rather than presence or absence of an invading pathogen. Specifically, gene expression in host peripheral blood cells responds in a robust and reproducible way that is pathogen class specific, allowing for quantification to diagnose infection. New techniques for RNA stabilization and amplification, coupled with breakthroughs in computational and statistical analysis of massive datasets, have set the stage for transcriptomic analysis of the host immune response. Transcriptomic techniques have the potential to revolutionize the diagnostic approach to certain infectious diseases, with the utility of gene expression diagnostics already being demonstrated in the fields of oncology and transplant medicine. This chapter highlights the process of developing novel host-based biomarker disease classifiers, examines the performance of previously published classifiers across various disease states, and provides insight into the potential clinical uses of gene expression-based diagnostic tests in the field of infectious diseases. The advantages of adding host-based biomarker tests to our diagnostic toolbox, as well as barriers faced in translating these tests into clinical practice, are discussed here as well.
