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Before moving on to discuss how, when, and where the previously mentioned agents cause human disease, we should note that the presence of microbes on or in humans is not, by itself, abnormal. In fact, from shortly after birth on, it is universal; we harbor 10 times the number of microbial cells than human cells. This population formerly called the normal flora is now referred to as our microbiota or microbiome. These microorganisms, which are overwhelmingly bacteria, are frequently found colonizing various body sites in healthy individuals. The constituents and numbers of the microbiota vary in different areas of the body and, sometimes, at different ages and physiologic states. Their names are mostly unfamiliar because they have not (yet) been associated with disease. They comprise microorganisms whose morphologic, physiologic, and genetic properties allow them to colonize and multiply under the conditions that exist in particular sites, to coexist with other colonizing organisms, and to inhibit competing intruders. Thus, each accessible area of the body presents a particular ecologic niche, colonization of which requires a particular set of properties of the colonizing microbe.
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Organisms of the microbiota may have a symbiotic relationship that benefits the host or may simply live as commensals with a neutral relationship to the host. A parasitic relationship that injures the host would not be considered “normal,” but, in most instances, not enough is known about the organism–host interactions to make such distinctions. Like houseguests, the members of the normal flora may stay for highly variable periods. Residents are strains that have an established niche at one of the many body sites, which they occupy indefinitely. Transients are acquired from the environment and establish themselves briefly, but they tend to be excluded by competition from residents or by the host’s innate or immune defense mechanisms. The term carrier state is used when organisms known to be potentially pathogenic are involved, although its implication of risk is not always justified. For example, Streptococcus pneumoniae, a cause of pneumonia, and Neisseria meningitidis, a cause of meningitis, may be isolated from the throat of 5% to 40% of healthy people. Whether these bacteria represent transient flora, resident flora, or carrier state is largely semantic. The possibility that their presence could be the prelude to disease is presently impossible to determine in advance.
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Flora may stay for short or extended periods
If pathogens are involved, the relationship is called the carrier state
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It is important for students of medical microbiology and infectious disease to understand the role of the microbiota because of its significance both as a defense mechanism against infection and as a source of potentially pathogenic organisms. In addition, it is important for physicians to know the typical composition of the microbiota at various sites to avoid confusion when interpreting laboratory culture results. The following excerpt indicates that the English poet W.H. Auden understood the need for balance between the microbiota and its host. He was influenced by an article in Scientific American about the flora of the skin.
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On this day tradition allots to taking stock of our lives, my greetings to all of you, Yeasts, Bacteria, Viruses, Aerobics and Anaerobics: A Very Happy New Year to all for whom my ectoderm is as Middle Earth to me.
For creatures your size I offer a free choice of habitat, so settle yourselves in the zone that suits you best, in the pools of my pores or the tropical forests of arm-pit and crotch, in the deserts of my fore-arms, or the cool woods of my scalp.
Build colonies: I will supply adequate warmth and moisture, the sebum and lipids you need, on condition you never do me annoy with your presence, but behave as good guests should, not rioting into acne or athlete’s-foot or a boil.
—W.H. Auden, “A New Year Greeting”
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The healthy fetus is sterile until the birth membranes rupture. During and after birth, the infant is exposed to the flora of the mother’s vagina and to other organisms in the environment. During the infant’s first few days of life, the microbiota reflects chance exposure to organisms that can colonize particular sites in the absence of competitors. Subsequently, as the infant is exposed to a broader range of organisms, those best adapted to colonize particular sites become predominant. Thereafter, the flora generally resembles that of other individuals in the same age group and cultural milieu.
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Initial flora is acquired during and immediately after birth
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Local physiologic and ecologic conditions determine the microbial makeup of the flora. These conditions are sometimes highly complex, differing from site to site, and sometimes with age. Conditions include the amounts and types of nutrients available, pH, oxidation–reduction potentials, and resistance to
local antibacterial substances such as bile and lysozyme. Many bacteria have adhesin-mediated affinity for receptors on specific types of epithelial cells; this facilitates colonization and multiplication and prevents removal by the flushing effects of surface fluids and peristalsis. Various microbial interactions also determine their relative prevalence in the flora. These interactions include competition for nutrients and inhibition by the metabolic products of other organisms.
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Physiologic conditions such as local pH influence colonization
Adherence factors counteract mechanical flushing
Ability to compete for nutrients is an advantage
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MICROBIOTA AT DIFFERENT SITES
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At any one time, the microbiota of a single person contains hundreds if not thousands of species of microorganisms, mostly bacteria. The major members known to be important in preventing or causing disease, as well as those that may be confused with etiologic agents of local infections, are summarized in Table 1–3 and are described in greater detail in subsequent chapters. The Human Microbiome Project is an ongoing effort to bring this information together.
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Blood, Body Fluids, and Tissues
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In health, the blood, body fluids, and tissues are sterile. Occasional organisms may be displaced across epithelial barriers as a result of trauma or during childbirth; they may be briefly recoverable from the bloodstream before they are filtered out in the pulmonary capillaries or removed by cells of the reticuloendothelial system. Such transient bacteremia may be the source of infection when structures such as damaged heart valves and foreign bodies (prostheses) are in the bloodstream.
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Tissues and body fluids such as blood are sterile in health
Transient bacteremia can result from trauma
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The skin surface provides a dry, slightly acidic, aerobic environment. It plays host to an abundant flora that varies according to the presence of its appendages (hair, nails) and the activity of sebaceous and sweat glands. The flora is more abundant on moist skin areas (axillae, perineum, and between toes). Staphylococci and members of the Propionibacterium genus occur all over the skin, and facultative diphtheroids (corynebacteria) are found in moist areas. Propionibacteria are slim, anaerobic, or microaerophilic gram-positive rods that grow in subsurface sebum and break down skin lipids to fatty acids. Thus, they are most numerous in the ducts of hair follicles and of the sebaceous glands that drain into them. Even with antiseptic scrubbing, it is difficult to eliminate bacteria from skin sites, particularly those bearing pilosebaceous units. Organisms of the skin flora are resistant to the bactericidal effects of skin lipids and fatty acids, which inhibit or kill many extraneous bacteria. The conjunctivae have a very scanty flora derived from the skin flora. The low bacterial count is maintained by the high lysozyme content of lachrymal secretions and by the flushing effect of tears.
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Propionibacteria and staphylococci are dominant bacteria
Skin flora is not easily removed
Conjunctiva resembles skin
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The mouth and pharynx contain large numbers of facultative and anaerobic bacteria. Different species of streptococci predominate on the buccal and tongue mucosa because of different specific adherence characteristics. Gram-negative diplococci of the genus Neisseria and coccobacillary Moraxella make up the balance of the most commonly isolated organisms. Strict anaerobes and microaerophilic organisms of the oral cavity have their niches in the depths of the gingival crevices surrounding the teeth and in sites such as tonsillar crypts, where anaerobic conditions can develop readily.
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Oropharynx has streptococci and Neisseria
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The total number of organisms in the oral cavity is very high, and it varies from site to site. Saliva usually contains a mixed flora of about 108 organisms per milliliter, derived mostly from the various epithelial colonization sites. The genera include Actinomyces, Bacteroides, Prevotella, Streptococcus, and others. The stomach contains few, if any, resident organisms in health because of the lethal action of gastric hydrochloric acid and peptic enzymes on bacteria. One species, H pylori, long thought to be a common resident is now known to be the primary cause of ulcers. The small intestine has a scanty resident flora, except in the lower ileum, where it begins to resemble that of the colon.
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H pylori turned out to be a stomach pathogen
Small intestinal flora is scanty but increases toward lower ileum
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The colon carries the most abundant and diverse microbiota in the body. In the adult, feces are 25% or more bacteria by weight (about 1010 organisms per gram). More than 90% are anaerobes, predominantly members of the genera Bacteroides, Fusobacterium, Eubacterium, and Clostridium. The remainder of the flora is composed of facultative organisms such as Escherichia coli, enterococci, yeasts, and numerous other species. There are considerable differences in adult flora depending on the diet of the host. Those whose diets include substantial amounts of meat have more Bacteroides and other anaerobic gram-negative rods in their stools than those on a predominantly vegetable or fish diet. Recent studies have suggested the composition of the colonic microbiota could play a role in obesity.
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Adult colonic flora is abundant and predominantly anaerobic
Diet affects species composition
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The external 1 cm of the anterior nares has a flora similar to that of the skin. This is the primary site of carriage of a major pathogen, Staphylococcus aureus. Approximately 25% to 30% of healthy people carry this organism as either resident or transient flora at any given time. The nasopharynx has a flora similar to that of the mouth; however, it is often the site of carriage of potentially pathogenic organisms such as pneumococci, meningococci, and Haemophilus species.
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S aureus is carried in anterior nares
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The respiratory tract below the level of the larynx is protected in health by the action of the epithelial cilia and by the movement of the mucociliary blanket; thus, only transient inhaled organisms are encountered in the trachea and larger bronchi. The accessory sinuses are normally sterile and are protected in a similar fashion, as is the middle ear by the epithelium of the eustachian tubes.
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Lower tract is protected by mucociliary action
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The urinary tract is sterile in health above the distal 1 cm of the urethra, which has a scanty flora derived from the perineum. Thus, in health, the urine in the bladder, ureters, and renal pelvis is sterile. The vagina has a flora that varies according to hormonal influences at different ages. Before puberty and after menopause, it is mixed, nonspecific, and relatively scanty, and it contains organisms derived from the flora of the skin and colon. During the childbearing years, it is composed predominantly of anaerobic and microaerophilic members of the genus Lactobacillus, with smaller numbers of anaerobic gram-negative rods, gram-positive cocci, and yeasts (Figure 1–4) that can survive under the acidic conditions produced by the lactobacilli. These conditions develop because glycogen is deposited in vaginal epithelial cells under the influence of estrogenic hormones and metabolized to lactic acid by lactobacilli. This process results in a vaginal pH of 4 to 5, which is optimal for growth and survival of the lactobacilli, but inhibits many other organisms.
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Bladder and upper urinary tract are sterile
Hormonal changes affect the vaginal flora
Use of epithelial glycogen by lactobacilli produces low pH
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Bacterial vaginosis (BV) is a long known and unfortunately common syndrome which is still poorly understood. Its dominant feature is an uncomfortable vaginal discharge with a “fishy” odor which contains epithelial cells coated with bacteria (clue cells). This change is associated with a shift in the vaginal microbiota away from the acidic Lactobacillus flora to one with a higher pH and a greater mixture of species including more anaerobes. Over the years several of these newcomers have been tagged as the cause of BV, particularly Gardnerella vaginalis and Mobiluncus. The BV situation appears to be more complex than this, involving complex interactions of the vaginal microbiota.
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BV is associated with a shift in vaginal microbiota
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ROLES IN HEALTH AND DISEASE
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Opportunistic Infection
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Many species among the microbiota are opportunists in that they can cause infection when they reach protected areas of the body in sufficient numbers. For example, certain strains of E coli can reach the urinary bladder by ascending the urethra and cause acute urinary tract infection. Perforation of the colon from a ruptured diverticulum or a penetrating abdominal wound releases feces into the peritoneal cavity; this contamination may be followed by peritonitis or intraabdominal abscesses caused by members of the flora which have virulence factors allowing them to exploit this situation. There are now examples of the microbiota supplying a step in the pathogenesis of a classic pathogen. Attachment of Neisseria gonorrhoeae to the cervix has been shown to be enhanced when an enzyme produced by the cervicovaginal microbiota unmasks a crucial receptor (see Chapter 30). Caries and periodontal disease are caused by organisms that are members of the oral microbiota (see Chapter 41).
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Flora that reach sterile sites may cause disease
Virulence factors increase the opportunity for invasion
Mouth flora plays a major role in dental caries
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Balancing the prospect of opportunistic infection is the tendency of the resident microbiota to produce conditions that compete with extraneous newcomers who happen to be pathogens and thus reduce their ability to establish a niche in the host. The microbiota in the colon of the breastfed infant produces an environment inimical to colonization by enteric pathogens, as does a vaginal flora dominated by lactobacilli. The benefit of this exclusionary effect has been demonstrated by what happens when it is removed. Antibiotic therapy, particularly with broad-spectrum agents, may so alter the microbiota of the gastrointestinal tract that antibiotic-resistant organisms multiply in the ecologic vacuum. Under these conditions, the spore-forming Clostridium difficile has a selective advantage that allows it to survive, proliferate, and produce a toxic colitis.
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Competing with pathogens has a protective effect
Antibiotic therapy may provide a competitive advantage for pathogens
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Priming of Immune System
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Organisms of the microbiota play an important role in the development of immunologic competence. Animals delivered and raised under completely aseptic conditions (“sterile” or gnotobiotic animals) have a poorly developed reticuloendothelial system, low serum levels of immunoglobulins, and lack antibodies to antigens that often confer a degree of protection against pathogens. There is evidence of immunologic differences between children who are raised under usual conditions and those whose exposure to diverse flora is minimized. Some studies have found a higher incidence of immunopathologic states, such as asthma in the more isolated children.
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Sterile animals have little immunity to microbial infection
Low exposure correlates with asthma risk
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PROMOTING A GOOD MICROBIOTA
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The field of probiotics is based on the notion that we can manipulate the microbiota by promoting colonization with “good” bacteria. Elie Metchnikoff originally suggested this in his observation that the longevity of Bulgarian peasants was attributable to their consumption of large amounts of yogurt; the live lactobacilli in the yogurt presumably replaced the colonic flora to the general benefit of their health. This notion persists today in capsules containing freeze-dried lactobacilli sold by the sizable probiotics industry and by promotion of the health benefit of natural (unpasteurized) yogurt, which contains live lactobacilli. Because these lactobacilli are adapted to food and not the intestine, they are unlikely to persist, much less replace, the typical microbiota of the adult colon. In some clinical studies, administration of preparations containing a particular strain of Lactobacillus (Lactobacillus rhamnosus strain GG, LGG) has been shown to reduce the duration of rotavirus diarrhea in children. The use of similar preparations to prevent relapses of antibiotic-associated diarrhea caused by C difficile has shown little success but fecal transplant (a whole new microbiota) has blocked recurrences of pseudomembranous colitis, the most serious form of this disease.
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Intestinal lactobacilli may protect against diarrheal agents
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Research into the role of the microbiota in health and disease is one of the most exciting topics in science. This is by no means limited to topics related to infectious disease. Currently the most active areas involve mechanisms of obesity, autoimmune disorders (arthritis, asthma) and more subjective subjects like human cravings. Much of the work involves the interactions between multiple species many of which can only be detected by genomic methods. Obviously, it is going to take considerable time to sort these relationships out.