Because microorganisms are found everywhere, human encounters are inevitable, but the means of encounter vary widely. Which microbial population a human is exposed to and the mechanism of exposure are often direct consequences of a person’s activity or behaviors. Certain activities carry different risks for an encounter, and there is a wide spectrum of activities or situations over which a person may or may not have absolute control. For example, acquiring salmonellosis because one fails to cook the holiday turkey thoroughly is avoidable, whereas contracting tuberculosis as a consequence of living in conditions of extreme poverty and overcrowding may be unavoidable. The role that human activities play in the encounter between humans and microorganisms cannot be overstated, because most of the crises associated with infectious disease could be avoided or greatly reduced if human behavior and living conditions could be altered.

Microbial Reservoirs and Transmission

Humans encounter microorganisms when they enter or are exposed to the same environment in which the microbial agents live or when the infectious agents are brought to the human host by indirect means. The environment, or place of origin, of the infecting agent is referred to as the reservoir. As shown in Figure 3-2, microbial reservoirs include humans, animals, water, food, air, and soil. The human host may acquire microbial agents by various means referred to as the modes of transmission. The mode of transmission is direct when the host directly contacts the microbial reservoir and is indirect when the host encounters the microorganism by an intervening agent of transmission.

The agents of transmission that bring the microorganism from the reservoir to the host may be a living entity, such as an insect, in which case they are called vectors, or they may be a nonliving entity, referred to as a vehicle or fomite. Additionally, some microorganisms may have a single mode of transmission, whereas others may spread by various methods. From a diagnostic microbiology perspective, knowledge about an infectious agent’s mode of transmission is often important for determining optimum specimens for isolation of the organism and for implementing precautions that minimize the risk of laboratory-acquired infections (see Chapters 4 and 80 for more information regarding laboratory safety).

Once a microbe and the human host are brought into contact, the outcome of the encounter depends on what happens during each step of interaction (see Figure 3-1), beginning with colonization. The human host’s role in microbial colonization, defined as the persistent survival of microorganisms on a surface of the human body, is dictated by the defenses that protect vital internal tissues and organs against microbial invasion. The first defenses are the external and internal body surfaces that are in direct contact with the external environment and are the anatomical regions where the microorganisms will initially come in contact with the human host. These surfaces include:

Because body surfaces are always present and provide protection against all microorganisms, skin and mucous membranes are considered constant and nonspecific protective mechanisms. As is discussed later in this text, other protective mechanisms are produced in response to the presence of microbial agents (inducible defenses), and some are directed specifically at particular microorganisms or (specific defense mechanisms).

Mucous Membranes

Because cells that line the respiratory tract, gastrointestinal tract, and genitourinary tract are involved in numerous functions besides protection, they are not covered with a hardened, acellular layer as is the skin surface. However, the cells that compose these membranes still exhibit various protective characteristics (Table 3-2 and Figure 3-4).

General Protective Characteristics.

Mucus is a major protective component of the membranes. This substance serves to trap bacteria before they can reach the outer surface of the cells, lubricates the cells to prevent damage that promotes microbial invasion, and contains specific chemical (i.e., antibodies) and nonspecific antibacterial substances. In addition to the chemical properties and physical movement of the mucus and trapped microorganisms mediated by ciliary action, rapid cellular shedding and tight intercellular connections provide effective barriers to infection. As is the case with the skin, specific cell clusters, known as mucosa-associated lymphoid tissue, exist below the outer cell layer and mediate specific protective mechanisms against microbial invasion.

Specific Protective Characteristics.

Besides the general protective properties of mucosal cells, the mucosal linings throughout the body have characteristics specific to each anatomic site (Figure 3-5).

The mouth, or oral cavity, is protected by the flow of saliva that physically carries microorganisms away from cell surfaces and also contains antibacterial substances, such as antibodies (IgA) and lysozyme that participate in the destruction of bacterial cells. The mouth is also heavily colonized with protective microorganisms that produce substances that hinder successful invasion by harmful organisms.

In the gastrointestinal tract, the low pH and proteolytic (protein-digesting) enzymes of the stomach prevent the growth of many microorganisms. In the small intestine, protection is provided through the presence of bile salts, which disrupt bacterial membranes, and by peristaltic movement and the fast flow of intestinal contents, which hinder microbial attachment to mucosal cells. Although the large intestine also contains bile salts, the movement of bowel contents is slower, permitting a higher concentration of microbial agents the opportunity to attach to the mucosal cells and inhabit the gastrointestinal tract. As in the oral cavity, the high concentration of normal microbial inhabitants in the large bowel also contributes significantly to protection.

In the upper respiratory tract, nasal hairs keep out large airborne particles that may contain microorganisms. The cough-sneeze reflex significantly contributes to the removal of potentially infective agents. The cells lining the trachea contain cilia (hairlike cellular projections) that move microorganisms trapped in mucus upward and away from the delicate cells of the lungs (see Figure 3-4); this is referred to as the mucociliary escalator. These barriers are so effective that only inhalation of particles smaller than 2 to 3 µm have a chance of reaching the lungs.

In the female urogenital tract, the vaginal lining and the cervix are protected by heavy colonization with normal microbial inhabitants and a low pH. A thick mucus plug in the cervical opening is a substantial barrier that keeps microorganisms from ascending and invading the more delicate tissues of the uterus, fallopian tubes, and ovaries. The anterior urethra of males and females is naturally colonized with microorganisms, and a stricture at the urethral opening provides a physical barrier that, combined with a low urine pH and the flushing action of urination, protects against bacterial invasion of the bladder, ureters, and kidneys.

The Microorganism’s Perspective

As previously discussed, microorganisms that inhabit many surfaces of the human body (see Figure 3-5) are referred to as colonizers, or normal flora (also referred to as normal microbiota). Some are transient colonizers, because they are able to survive, but do not multiply, on the surface and are frequently shed with the host cells. Others, called resident flora, not only survive but also thrive and multiply; their presence is more persistent.

The body’s normal flora varies considerably with anatomic location. For example, environmental conditions, such as temperature and oxygen availability, differ considerably between the nasal cavity and the small bowel. Only microorganisms with the metabolic capability to survive under the physiologic conditions of the anatomic location are inhabitants of those particular body surfaces.

Knowledge of the normal flora of the human body is extremely important in diagnostic microbiology, especially for determining the clinical significance of microorganisms isolated from patient specimens. Organisms considered normal flora are frequently found in clinical specimens. This may be a result of contamination of normally sterile specimens during the collection process or because the colonizing organism is actually involved in the infection. Microorganisms considered as normal colonizers of the human body and the anatomic locations they colonize are addressed in Part VII.