1: Overview of Medical Microbiology

Microbiology can certainly be overwhelming for the student confronted with the daunting task of learning about hundreds of medically important microbes. I remember well the first day of my introductory graduate course in medical microbiology; the course instructor handed each student a 1000-page syllabus consisting of lecture outlines, notes, and literature references. That became known not so lovingly as the book of pain. Not to be limited to lecture notes, we also had an assigned 2000-page textbook to guide our studies. In retrospect, much of the information in both the notes and the textbook was very interesting from a fundamental microbiology perspective but of very little relevance for a student studying medicine. However, I have always felt that the information that is important for a student to know can be presented in a clear, organized, logical way without unnecessary digression into the minutia of this field. For example, microbiology is not so challenging if the subject matter—the microbes—is subdivided into groups and further subdivided into related units. Let me illustrate this in this introductory chapter.

Microbes are subdivided into one of the four groups:

• • Viruses
• • Bacteria
• • Fungi
• • Parasites

The structural complexity of these groups increases from viruses (the simplest structure) to parasites (the most complex). There is generally no confusion about which group a microbe should be placed in, although a few fungi were formerly classified as parasites. Each group of microbes is then further subdivided, generally based on a key feature of the group.

Viruses

Viruses are very simple microbes, consisting of nucleic acid, a few proteins, and (in some) a lipid envelope. These microbes are completely dependent on the cells they infect for their survival and replication. Medically important viruses are subdivided into 20 families defined by the structural properties of the members. The most important feature is the nucleic acid. Viruses contain either DNA or RNA but not both. The families of DNA viruses and RNA viruses are further subdivided into viruses with either single-stranded or double-stranded nucleic acids. Lastly, these viral families are further subdivided into viruses with an outer envelope and naked or nonenveloped viruses. Now the perceptive student would say that this gives us eight families of viruses and not 20. Well, the viruses are further subdivided by their shape (spherical or rodlike) and size (big or small [“pico”]). Thus, the key to understanding viruses is to place them into their respective families based on their structural features.

Bacteria

Bacteria are a bit more complex, with both RNA and DNA, metabolic machinery for self-replication, and a complex cell wall structure. Bacteria are prokaryotic organisms, i.e., simple unicellular organisms with no nuclear membrane, mitochondria, Golgi bodies, or endoplasmic reticulum, and they reproduce by asexual division. The key feature that is used to classify most bacteria is their staining property, with the Gram stain and acid-fast stain being the most important. Most bacteria are either gram-positive (retain the blue dye) or gram-negative (lose the blue stain and stain with the red dye). These bacteria are then subdivided by their shape (either spherical [cocci] or rod-shaped), whether they grow aerobically or anaerobically (many bacteria grow in both atmospheres and are called facultative anaerobes), and whether they form resilient spores or not (only gram-positive rods are spore-formers). The other important bacterial stain is the acid-fast stain that is retained only by a few bacteria that have a characteristic lipid-rich cell wall. This group is further subdivided by how difficult it is to remove the acid-fast stain (the stain is named because an acid solution removes the stain from most other bacteria). Finally, there are groups of organisms that do not stain with these procedures so they are separated by other features, such as shape (spiral-shaped bacteria) or their need to grow inside a host cell (e.g., leukocyte) or cell cultures in the laboratory.

Fungi and Parasites

Fungi and parasites are more complex eukaryotic organisms that contain a well-defined nucleus, mitochondria, Golgi bodies, and endoplasmic reticulum. Single-celled and multi-celled organisms are members of both groups. As can be seen, the line separating these two groups is not as well defined as that separating these organisms from bacteria or viruses, but the classification is still well-recognized.

Fungi

Fungi are subdivided into single-celled organisms (yeasts) or multi-celled organisms (molds), with a few medically important members existing in both forms (dimorphic fungi). Molds are complex organisms with cells organized into threadlike tubular structures (hyphae) and specialized asexual reproductive forms (conidia). The molds are then further subdivided by the structure of the hyphae (pigmented or nonpigmented, separated into individual cells [septated molds] or not) and the arrangement of the conidia.

Parasites

Parasites are also subdivided into single-celled organisms (protozoa) or multi-celled organisms (worms and bugs). Members of the family Protozoa are then further divided into amebae, flagellates (think of them as hairy protozoa), and coccidia (some are shaped like cocci but many are not). The worms (technically called helminths) are nicely classified by their shape: roundworms, flatworms, and tapeworms—pretty simple, although many have very complex lifecycles that unfortunately are important for understanding how the parasites infect humans and cause disease. The bugs are simply “bugs.” These include mosquitos, ticks, fleas, lice, mites, and flies. They are important because they are vectors of a number of viruses and bacteria (but not fungi) that are responsible for diseases. Other bugs obviously exist (such as spiders), but these generally are not vectors for other pathogenic microbes.

Good Versus Bad Microbes

Microbes, particularly the bacteria, have unjustly earned a bad reputation. Most have historically been viewed as bad and recognized only for their ability to cause diseases. We have coined the derogatory term germs, and great efforts are made to eliminate our exposure to these organisms. The reality is most microbes are not only good but critical for our health. The surfaces of the skin, nose, mouth, gut, and genitourinary tract are covered with bacteria, as well as some fungi and parasites. These organisms are critical for the maturation of our immune system, important metabolic functions such as the digestion of food products, and protection from infection with unwanted pathogens. These organisms are referred to as our normal flora or microbiome. If these organisms are maintained in their proper balance, then health can be maintained. If they are disrupted either naturally or through man-made interventions (e.g., antibiotics, skin peels, enemas), then we risk disease. Infectious diseases are also initiated when the members of the microbiome are introduced into normally sterile sites (e.g., abdominal cavity, tissues, lungs, urinary tract) through trauma or disease. This is referred to as an endogenous infection or an infection caused by the normal microbial population. Finally, infections can...