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  1. Determine if an organism of interest is a bacterium, fungus, parasite, or virus and learn how it is further classified among related organisms.

  2. Learn the organisms that produce the commonly encountered and better characterized infectious diseases.

  3. Distinguish pathogenic organisms from those found in normal flora.

  4. Learn the laboratory test results associated with the individual infectious diseases and how they are used in establishing the diagnosis.


Humans live in a world of microbes. Many types of microbes are part of the normal human flora and rarely cause disease. Others have a greater potential for virulence and can cause disease depending on complex interactions between the host and the microbe. A small group of organisms are highly virulent and usually cause disease whenever they infect humans. This chapter on infectious diseases and clinical microbiology focuses on common pathogens and frequently encountered clinical syndromes. Infectious agents include a daunting array of viruses, bacteria, fungi, protozoans, and helminths. Table 5–1 provides information on the basic microbiology and clinical significance of common pathogens. The organisms are grouped based on shared properties because these are often relevant to the diagnostic process. Microbial taxonomy is constantly evolving as we learn more about organisms, partly as a result of more complete knowledge of microbial genomes. These changes can be confusing to clinicians as organisms are moved from one species to another (Streptococcus bovis type I is now S. gallolyticus), species are subdivided (some organisms formerly known as Coccidioides immitis are now classified as C. posadasii), and the fungal phylum zygomycota is replaced by the subphylum mucorales [PMC4382724].

TABLE 5–1Selected Clinically Significant Microorganisms

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