Microbiology is the study of organisms too small to be seen by the naked eye. Clinical microbiology encompasses the study of pathogens such as bacteria, viruses, fungi, and parasites that cause disease or infection in humans. Issues of concern in clinical microbiology include the nature and epidemiology of etiological agents, how they interact with the immune system, rapid diagnosis, and providing information on treatment, such as antimicrobial susceptibility.

Fundamental knowledge of microorganisms, their identification, significance, and basic laboratory techniques provide the infection preventionist with an understanding of pathogenic organisms. This chapter includes an overview of microorganisms, clinical laboratory methods that are used to evaluate the presence and/or significance of microorganisms, and methods to analyze the relatedness of microorganisms for epidemiological purposes.