Chapter 14. Infectious Diseases: II. Diagnosis of Infectious Diseases

The aims of diagnosis in infectious diseases are (1) to recognize that a sick patient is ill with an infectious disease and (2) to identify the specific etiologic agent in order to determine the most appropriate treatment, as the susceptibility of most pathogens to selected antimicrobial agents is known.

Identification of the infectious agent may be achieved in several ways.

Clinical History

Prevalence of Infectious Diseases

Hospital-Acquired (Nosocomial) Infections

Of the approximately 5 million cases of infectious diseases seen in hospitals annually in the United States, about 40% are acquired in hospitals (nosocomial infections). Hospital-acquired infections are different from those acquired in the community outside the hospital (Table 14-1). The genitourinary tract, surgical wounds, and lungs are the most common sites of nosocomial infection. Most nosocomial infections are caused by bacteria and fungi; viruses, protozoa, and metazoa rarely cause such infections. Hospital-acquired pneumonia is the most serious such infection, with a mortality rate of 20%. Disseminated infections caused by bacteria and fungi, mainly in immunocompromised patients, also account for a significant number of nosocomial infections. In newborn nurseries, hospital-acquired epidemic diarrhea is a common problem.

The high incidence of hospital-acquired infections is due to the following factors:

Increased Susceptibility

Hospitalized patients demonstrate increased susceptibility to infection as a consequence of debilitation associated with concurrent illness and in some cases the administration of immunosuppressive drugs.

Use of Invasive Procedures

Invasive surgical, diagnostic (eg, lumbar puncture, phlebotomy), and therapeutic procedures (eg, bladder catheterization, indwelling intravascular catheters) provide infectious agents with a portal of entry despite precautions to ensure sterility. The materials used in these procedures are themselves sometimes fomites (eg, contaminated intravenous fluids, tubing, respirators).

Numerous Sources of Infection

Hospitals harbor numerous sources of infection—mainly other patients with infectious diseases and hospital staff that may be carriers (eg, S aureus). Organisms or spores in the environment (eg, dust, hospital linens, and ventilation systems) are less important sources.

Use of Antibiotics

Widespread use of antibiotics promotes overgrowth of antibiotic-resistant strains of gram-negative enteric bacilli (eg, Escherichia coli, Pseudomonas aeruginosa, Proteus species, Klebsiella species, and Serratia species) and Staphylococcus aureus. These organisms are often resistant to many antibiotics and therefore pose serious problems in treatment.

Community-Acquired Infections

In community practice, viral infections of the upper respiratory tract (eg, coryza, influenza) and the gastrointestinal tract (eg, viral gastroenteritis) are the most commonly encountered infectious diseases. These illnesses are self-limited, and patients typically do not consult a physician. Hospitalization is required only when illness is severe (eg, rare cases of influenza, especially in the elderly). Community-acquired bacterial infections have a somewhat different distribution and generally are associated with a lower mortality rate than hospital-acquired infections both because the host is usually better able to respond to the infection and because the infectious agents are usually more sensitive to antibiotic therapy. Sexually transmitted diseases (eg, gonorrhea, syphilis), urinary infections in young women, and respiratory infections (eg, streptococcal pharyngitis, sinusitis, otitis, pneumonia) represent the most common bacterial infections.

Knowledge of the types of infectious disease prevalent in the community when and where the patient acquired the disease is crucial. Careful history taking must include information about the patient's normal environment, life-style, and habits in an attempt to identify factors that make a certain type of transmission and portal of entry more likely (Table 13-3). Recent immigrants to the United States will have a pattern of infectious disease characteristic of the country of origin, which will often be very different from what is endemic in the United States (Table 13-2). Recent association with anyone suffering from an infectious disease raises the possibility of that infection. This is especially true in easily transmitted diseases such as influenza and sexually transmitted diseases.

Knowledge of an epidemic of a certain disease can be critical. The rare outbreak of hantavirus infections in the western United States, for example, brings this rare disease into the differential diagnosis of any person with an acute febrile illness with pulmonary involvement; if the patient has been exposed to rodent feces, the suspicion increases further. Most public health agencies in the United States continually update information regarding infectious disease prevalence and send out newsletters to all physicians.

Assessment of Immune Status

The immune status of an individual determines the susceptibility to infection. In children, the history of immunizations given is crucial because, in the absence of routine immunization, diseases such as poliomyelitis, measles, mumps, rubella, whooping cough, and diphtheria enter the differential diagnosis. Risk factors for infection with human immunodeficiency virus (HIV) (Chapter 7: Deficiencies of the Host Response) are important because of its high prevalence and the enhanced susceptibility of infected persons to unusual opportunistic infections. These same opportunistic pathogens cause infection in all types of immunodeficiency, including that produced by immunosuppressive drugs.

Exposure to Animals

Exposure to animals may be important because many diseases have animal reservoirs that increase the likelihood of human infection (Table 14-2). Unusual exposure to arthropods may provide clues to diseases that are transmitted by arthropod vectors (Table 14-3), eg, recent travel to areas infested by ixodid ticks may be the clue to diagnosing Lyme disease.

Travel History

It is essential to elicit a history of travel both within the United States and to foreign countries in the recent past because the geographic variation of infectious disease is greater than that of any other type of disease. Information regarding diseases prevalent in other countries and different regions in the United States is available through the Centers for Disease Control and Prevention. With most infectious diseases, the incubation period is short (within 3 weeks for malaria and typhoid fever), and travel undertaken a long time ago is rarely relevant.

Physical Examination

Clinically Specific Infectious Diseases

A few infectious agents produce highly characteristic clinical illnesses, eg, herpes zoster (Figure 14-1); malaria (which sometimes has a characteristic intermittent fever corresponding to the life cycle of the parasite); and bacterial diseases that produce specific exotoxins, such as diphtheria, tetanus, and toxic shock syndrome (Table 13-8). In these cases, recognition of the specific agent may be achieved by clinical examination alone, and testing need be done only for confirmation (Figure 14-2).

Clinically Nonspecific Infectious Diseases

In most infectious diseases, however, clinical examination does not permit recognition of the specific agent responsible. In these cases, the physician must develop a logical method of analysis that culminates in the specific etiologic diagnosis, utilizing in the most efficient manner possible the various microbiologic and immunologic tests that are available (Figure 14-2). Test selection depends on developing a comprehensive and accurate “best guess” list of infectious agents that may be responsible for the patient's disease. If the maker of the list overlooks a possible etiologic agent, diagnostic failure may result; if the list includes organisms that could not have caused the patient's disease, unnecessary testing and increased cost are the result. Developing a logical method for arriving at a list of agents that can cause any given infectious disease is the concern here.

The first objective in physical examination of a patient with an infectious disease is to identify the tissue that has been infected (Figure 14-2). This is obvious when one organ is affected, as is true in the majority of cases. When an infected organ has multiple tissue components, identification of the specific tissue involved is necessary—eg, in a surface infection, one must determine whether the lesion involves the epidermis, dermis, an adnexal gland, subcutis, or deep fascia. In disseminated infectious diseases, an effort should be made—despite the difficulty—to identify the primary tissue from which dissemination occurred. Identification of the tissue infected is important because different tissues are infected by a relatively small range of organisms. Put another way, a given organism has varying affinities for different tissues (organotropism).

The next objective in examination is to identify the type of tissue response (Figure 14-2). In Chapter 13: Infectious Diseases: I. Mechanisms of Tissue Changes in Infection, it was noted that the type of inflammatory response occurring when an agent infected a tissue depended largely on whether the organism was extracellular; facultative intracellular, multiplying in macrophages; or obligate intracellular, multiplying in parenchymal cells (Tables 13-6 and 13-9). Review of these two tables is recommended at this time. Identification of the host response is not always easy and sometimes requires special tests such as examination of the peripheral blood, body fluids, and tissues obtained by biopsy.

Useful lists of organisms capable of causing infectious diseases are developed by combining information about which organisms infect which specific tissues with observation of the host response. This scheme of analysis is applied here for some selected tissues and clinical situations; more complete descriptions of specific infectious diseases are given in the relevant systemic pathology chapters in the second part of this book. It will become apparent that relevant information is derived in different ways when different tissues are affected.

Infections of the Skin

(See also Table 14-4)

(See also Chapter 61: Diseases of the Skin)

Extracellular Agents

Infection of the skin by extracellular agents usually produces acute inflammation with neutrophils. While the basic pathologic change is the same, the clinical manifestations differ greatly depending on which component of the skin is involved. Epidermal infection produces impetigo, which causes superficial pustules that break to produce a honey-colored crust (Figure 14-3). Dermal involvement produces erisypelas, manifested as an area of red, indurated, hot, swollen, tender skin, usually on the cheek. Infection of the subcutaneous tissue causes cellulitis; this is also an area of red, swollen, hot, tender skin, but it is deeper and less indurated than erysipelas. Severe infections of the subcutis and deep fascia with extensive necrosis may result from infection by anaerobes (Figure 14-4), Bacillus anthracis, and Vibrio vulnificus. Gas gangrene is a necrotizing cellulitis that complicates infection of wounds by one of several clostridia. Infections of hair follicles and skin adnexal structures usually result in abscess formation; depending on the type of gland involved and the severity of involvement, clinically distinct lesions such as furuncles (boils), carbuncles, and hidradenitis suppurativa can be recognized.

These different types of acute pyogenic inflammation are all caused by extracellular agents. The specificity of infection varies (Table 14-4). In cellulitis and necrotizing fasciitis, culture (which must include culture for anaerobic bacteria and the use of special culture media for vibrios) is essential because of the variability of agents and the severity of disease.

Chronic suppurative infections due to Actinomyces, Nocardia, and certain mycelial fungi produce large indurated masses with multiple draining sinuses called mycetomas. Culture (which must include anaerobic culture and fungal culture media) is necessary for specific diagnosis.

Obligate Intracellular Agents

Epidermal infections by viruses cause necrosis of epidermal cells and the formation of a vesicle (blister [Figure 14-5]; see also Figure 14-1). The specific virus involved can usually be identified by the clinical distribution of the lesions or by demonstrating viral inclusions (cytoplasmic in smallpox, Cowdry A intranuclear in herpesvirus vesicles), or by demonstrating specific antigens with immunologic techniques. In rare cases, viral culture and electron microscopy may be necessary.

Epidermal viral infections (with papillomaviruses and molluscum contagiosum virus) may also result in benign wart-like neoplasms.

Dermal involvement is usually perivascular and characterized by small vessel dilation; inflammation, characterized by lymphocytes and plasma cells; and thrombosis and hemorrhage in severe cases. This is manifested clinically as an erythematous or hemorrhagic rash. Diagnosis of specific infections in this group (measles, rubella, and rickettsial diseases) is based on the nature and distribution of the rash and is confirmed by serologic techniques.

Facultative Intracellular Agents

Infection by facultative intracellular agents involves dermal macrophages and usually results in chronic inflammatory processes. Formation of epithelioid granulomas occurs in tuberculosis and tuberculoid leprosy. Diffuse macrophage proliferation, which usually produces marked thickening and nodularity of the skin, occurs in leishmaniasis and lepromatous leprosy. Combined suppurative and granulomatous inflammation is typically seen in deep infection by nonmycelial fungi. In many of these diseases, biopsy of lesions permits histologic study of the inflamed tissues as well as visualization of the agent. Culture of the tissue is the best method of diagnosis for fungal infections.

Infections of the Pharynx

(See also Chapter 32: The Ear, Nose, Pharynx, & Larynx)

The pharynx is an extremely common site for acute infections by a variety of infectious agents (Table 14-5). Chronic inflammation is rare in the pharynx.

Most patients present with a sore throat and have a red, swollen pharynx with or without concomitant tonsillar inflammation. The great majority of cases of acute pharyngitis and tonsillitis are caused by viruses (influenza and parainfluenza viruses, rhinoviruses, adenoviruses, etc) that cause a self-limited infection which usually requires only symptomatic treatment. About 5% of cases of acute pharyngitis are caused by bacterial agents that must be treated. In some of these cases, examination of the patient may provide clues. Examples are exotoxic phenomena in streptococcal infection (scarlet fever) and diphtheria (neuritis, myocarditis), the presence of a membrane in diphtheria, a history of oral sex (gonorrhea), and concomitant involvement of the larynx (Haemophilus influenzae). In many patients, however, all these agents produce an illness that is very similar clinically; there is no recognizable difference between acute inflammation with neutrophils (bacterial) and that without neutrophils (viral). Identification of cases resulting from streptococcal infection is important in children because early treatment with antibiotics prevents the occurrence of immunologic sequelae of streptococcal infection (rheumatic fever and acute glomerulonephritis). Culture of a pharyngeal swab is the most reliable means of diagnosing bacterial infection; a more rapid nonculture method is also available for streptococcal infection.

Infections of the Lung

(See also Table 14-6)

(See also Chapter 34: The Lung: I. Structure & Function; Infections)

Extracellular Agents

Extracellular agents infecting the lung multiply in the alveoli and evoke an acute inflammation in which the alveoli become filled with exudate and numerous neutrophils. Spread to contiguous alveoli results in a tissue abnormality known as consolidation because the normally air-filled lung becomes solid with alveolar exudate. Consolidation produces typical changes in clinical examination and radiology that permit characterization of this type of process as being caused by extracellular agents (usually bacteria). By far the most common agent responsible is Streptococcus pneumoniae, which causes over 80% of cases of bacterial pneumonia. Rare bacteria (Yersinia pestis and Bacillus anthracis) cause a highly virulent rapidly progressive necrotizing pneumonia; others such as Staphylococcus aureus and gram-negative bacilli tend to produce abscesses. Chronic lung abscess is usually caused by a polymicrobial infection that includes anaerobes. Specific diagnosis of bacterial lung infections requires culture of sputum or of exudate aspirated from abscesses.

Obligate Intracellular Agents

When obligate intracellular agents (viruses, chlamydiae, and rickettsiae) infect the lung, they produce a very different type of tissue reaction. The organisms infect the alveolar epithelial cells and cause acute inflammation in the interstitium characterized by numerous lymphocytes and plasma cells (acute interstitial pneumonitis). This produces clinical and radiologic features that are very different from bacterial pneumonia and permit characterization of the infection as being due to obligate intracellular agents. One exception to this general rule is Mycoplasma pneumoniae, which, although an extracellular organism, produces an acute interstitial pneumonitis indistinguishable from that produced by obligate intracellular agents. The specific diagnosis of viral infection can be made by biopsy (inclusions in cytomegalovirus or herpesvirus infection and giant cells in measles) or serologic testing.

Facultative Intracellular Agents

Facultative intracellular agents usually cause chronic granulomatous inflammation of the lung, resulting in large areas of destruction, fibrosis, and cavitation. The lesions can resemble neoplasms. The diagnosis can often be suspected by clinical and radiologic studies but requires biopsy and culture (of sputum and tissue samples) for definitive diagnosis. When tissue is resected surgically in a lesion that may be granulomatous, it is very important to send a sample for mycobacterial and fungal culture before that tissue is fixed; failure to do so may lead to a failure of specific diagnosis because in approximately 30% of cases of granulomatous lung disease, microscopic examination fails to reveal the causative agent.

Infections of the Nervous System

(See also Table 14-7)

(See also Chapter 63: The Central Nervous System: II. Infections)

Infections of the Meninges

(Table 14-8.) Acute inflammation of the meninges may result from infection with all three classes of organisms: extracellular, bacterial meningitis; obligate intracellular, viral meningitis; and facultative intracellular, tuberculous meningitis. In all cases, the clinical presentation is with acute onset of fever, headache, and neck stiffness. Meningitis is confirmed by the finding of inflammatory cells in the cerebrospinal fluid because the exudation associated with the meningeal inflammation becomes admixed with the fluid. Differentiation of the three groups can be made by the nature of the inflammatory cells in the cerebrospinal fluid: with bacterial meningitis, neutrophils dominate; with viral meningitis, lymphocytes dominate; and with tuberculous meningitis, there is a mixture of neutrophils and lymphocytes. Specific diagnosis within these groups requires demonstration of the agent in smears or culture of cerebrospinal fluid (Table 14-8).

Chronic meningitis is much less common and usually results from infection by facultative intracellular agents: tubercle bacilli, fungi, and Treponema pallidum. Cerebrospinal fluid culture and serologic testing are necessary to identify the causative agent.

Infection of the Brain Parenchyma (Encephalitis)

Encephalitis, either alone or associated with meningitis, is usually the result of viral infection. The most common cause of sporadic encephalitis in adults is herpes simplex virus; herpes simplex encephalitis may also occur in neonates delivered vaginally when the mother has an active herpes genital infection. In epidemics, arboviruses are the most common causes of encephalitis. In most cases of viral encephalitis, there is diffuse infection of the entire brain. More specific types of viral infection of the central nervous system occur in rabies (hippocampal infection) and poliomyelitis (infection of lower motor neurons of the brain stem and spinal cord).

Bacterial (suppurative) encephalitis is usually the result of spread of an infection from an infected middle ear or paranasal sinus or secondary to trauma, both situations that are clinically obvious. Very rare cases of infection of the brain by free-living amebas (amebic meningoencephalitis) have been reported.

Demonstration of the agent—either by microscopic examination or culture of tissues and fluids removed from the patient—is the most common means of providing an etiologic diagnosis of infectious disease. Physicians must know what specimens to collect; how to collect, store, and transport them to the laboratory; what clinical information to send to the laboratory; and how to interpret the microbiology report (Table 14-9). The actual identification of the infectious agent from the specimen in the laboratory is the function of the pathologist, who is used in some centers as a consultant in infectious diseases.

With few exceptions (eg, T pallidum, Mycobacterium leprae), microorganisms can be isolated in culture. Living cell systems are necessary for growth of obligate intracellular agents; artificial culture media usually suffice for extracellular and facultative intracellular agents. Larger parasites, including protozoa and metazoa, are not usually cultured, but because of their large size they or their larvae or ova are usually recognizable on microscopic examination of tissues and smears of infected material.

Culture of an organism is also important when antimicrobial sensitivity of that agent varies, eg, in many bacterial infections. Although antibiotics are often chosen on the basis of existing clinical findings and treatment is started empirically after specimens have been obtained for culture, in vitro antibiotic sensitivity of the cultured organism is used to guide appropriate antibiotic therapy.

Microorganisms have different growth requirements, and many special techniques are used to isolate organisms. The physician should tell the laboratory what organisms need to be looked for. This is of greater importance when special cultures are needed, eg for anaerobic bacteria, mycobacteria, fungi, or viruses. Failure to request these specific cultures may lead to diagnostic failure.

A sharp (fourfold) increase in serum antibody titers against a specific agent is diagnostic of acute infection by that agent. In general, immunologic diagnosis requires paired serum samples, one obtained early in the disease and one during convalescence 2–3 weeks later. High antibody titers in a single specimen are of less significance than high levels in multiple samples. In general, IgM levels rise first, peak in 2–3 months, and then fall progressively; IgG levels rise after IgM in a primary immune response. A nonspecific (anamnestic) rise in IgG antibodies of a wide range of specificities may occur in many infections. Such nonspecific responses do not involve IgM antibodies. An increased IgM level of a specific antibody is therefore of greater diagnostic value than an increased IgG level.

Serologic tests are generally quite specific for one infectious agent, and a vast number of such tests are available, many of them very expensive. Careful selection of appropriate tests based on the list of possible agents is essential.

Immunologic markers—specific antibodies labeled with fluorescent dyes—are being employed more frequently to detect infectious agents in tissues and smears; eg, fluorescent-labeled antibody against Legionella pneumophila is used to demonstrate the organisms in sputum samples and thus permit specific diagnosis of Legionnaires' disease in patients with pneumonia. Development of deoxyribonucleic acid (DNA) probes with high levels of specificity against cytomegalovirus and Epstein-Barr virus has provided a means of identifying these viral genomes in infected cells.

Infectious diseases are frequently encountered in tissue biopsy specimens and resected tissues; in some cases, histologic examination provides the first evidence that the patient is suffering from an infectious disease. For example, in a patient presenting with diarrhea, the finding of Entamoeba histolytica in a colonoscopic biopsy is a common method of diagnosis of amebic colitis.

Larger infectious agents such as fungi, protozoa, and metazoal parasites can often be identified in tissue sections on the basis of distinctive structures such as ova, cysts, yeasts, spherules, or hyphae. In the case of larger parasites that cannot be routinely cultured, their identification in the tissues represents the main method of specific diagnosis, eg, identification of Toxoplasma gondii in a brain biopsy (Figure 14-6).

A few bacteria can be identified or at least partially characterized in tissues. Silver stains permit identification of spirochetes and L pneumophila; acid-fast stains demonstrate mycobacteria; and the morphologic features of Actinomyces (Figure 14-7) and Nocardia on tissue Gram stains are fairly typical. Some viruses (eg, cytomegalovirus, herpes simplex virus, and measles virus) may be specifically identified by the changes produced in cells, eg, inclusions or giant cells (Chapter 13: Infectious Diseases: I. Mechanisms of Tissue Changes in Infection). Immunohistologic techniques provide the most specific means of recognizing pathogens in tissue sections and are becoming available for a growing list of microbial agents (Figure 14-8). Also becoming available are newer molecular biology techniques such as in situ hybridization and polymerase chain reaction, which also permit identification of increasing numbers of infectious agents in tissue sections.