Updates on the applications of flow cytometry in microbiology

Abstract

Flow cytometry (FCM) was first developed for medical and clinical applications such as hematology and oncology. Although these areas still account for the vast majority of publications on this technique, during the past few years it has been also introduced in other areas, such as optimization and monitoring of biotechnological and environmental processes, pharmacology, toxicology, bacteriology and virology. In the food and drinks industries, the time required for conventional microbiology tests can lead to substantial delays in product release to the market. FCM has been used in conjunction with viability markers for rapid counting of yeast, molds and bacterial cells, including foodborne pathogens and microbial contaminants, in food products as well as for monitoring and improving the final products quality. FCM is an excellent tool, still unexplored in clinical microbiology, allowing for detection of cellular and non-cellular components in different clinical specimens, the study of antimicrobial activity, allowing for rapid and direct antimicrobial susceptibility testing and for the investigation of resistance mechanisms. Recent FCM developments important for addressing questions in environmental microbiology include the study of microbial physiology under environmentally relevant conditions, the development of new methods to identify active microbial populations and to isolate previously uncultured microorganisms and of high-throughput autofluorescence bioreporter assays. Moreover, the technological advancements will make possible the miniaturisation and automation of FCM devices, allowing to revolutionize their applications in the near future. The purpose of this minireview is to update the current applications of FCM in different fields of applied microbiology, and to highlight the main advantages and pitfalls for each of them.