CHA P T E R
69  
Infections of the Lower Respiratory System
OBJECTIVES
1. Define the trachea, bronchi, bronchioles, and alveoli, and explain
the anatomic structure of the lower respiratory system.
2. List the most common etiologic agents responsible for lower
respiratory disease and pneumonia in patients of various ages and
categories: children <5 years of age, school-age children, young
adults, older adults, and immunocompromised patients.
3. Describe the virulence factors found in bacteria and viruses
associated with infection of the lower respiratory tract.
4. List the four possible routes of transmission or dissemination within
the body that allow organisms to cause an infection in the lungs.
5. Name the most important decision for physicians regarding the
treatment of pneumonia in older individuals, and list the three-step
process used to guide them in this decision.
6. List the most prevalent cause of community-acquired pneumonia in
adults.
7. Differentiate between community-acquired and hospital-acquired
pneumonia.
8. State the factors anaerobic bacteria possess that enhance their
ability to produce disease; explain how these anaerobes gain
entrance to the lungs.
9. Define Lukens trap, and explain the type of patient or specimen
associated with the method.
10. Describe the difference between early-onset or late-onset
hospital- or ventilator-associated pneumonia.
11. List the etiologic agent of lung infections identified in cystic fibrosis
patients.
12. Name the organisms most often associated with pneumo-
opportunistic infection in HIV-positive individuals.
13. Explain the mechanisms that, because of the bacterial production
of toxins, enable microorganisms to produce respiratory-associated
disease.
14. Explain how the host immune system can contribute to
microorganism growth in the respiratory disease process.
15. Explain why Mycobacterium tuberculosis is a classic representative
of an intracellular pathogen.
16. Describe specimens collected for respiratory infections including
determination of specimen quality and rejection criteria for the
following: sputum, induced sputum, endotracheal suction, pleural
fluid, bronchoalveolar lavage, bronchial washing, and bronchial
brush sample.
17. Explain how the microbiologist would test for the less common
causes of respiratory infection, including Pneumocystis jiroveci,
Legionella spp., Chlamydophila pneumonia, Bordetella pertussis,
Mycoplasma pneumonia, and Norcardia.
GENERAL CONSIDERATIONS
ANATOMY
The respiratory tract can be divided into two major areas:
the upper respiratory tract consists of all structures above
878
the larynx, whereas the lower respiratory tract follows
airflow below the larynx through the trachea to the
bronchi and bronchioles and then into the alveolar
spaces where gas exchange occurs (Figure 69-1). The
respiratory and gastrointestinal tracts are the two major
connections between the interior of the body and the
outside environment. The respiratory tract is the pathway
through which the body acquires fresh oxygen and
removes unneeded carbon dioxide. It begins with the
nasal and oral passages, which humidify inspired air, and
extends past the nasopharynx and oropharynx to the
trachea and then into the lungs. The trachea divides into
bronchi, which subdivide into bronchioles, the smallest
branches that terminate in the alveoli. Some 300 million
alveoli are estimated to be present in the lungs; these are
the primary microscopic gas exchange structures of the
respiratory tract.
Familiarization with the anatomic structure of the tho-
racic cavity ensures proper specimen collection from
various sites in the lower respiratory tract for processing
by the laboratory. The thoracic cavity, which contains the
heart and lungs, has three partitions separated from one
another by pleura (see Figure 69-1). The lungs occupy
the right and left pleural cavities, whereas the mediasti-
num (space between the lungs) is occupied mainly by the
esophagus, trachea, large blood vessels, and heart.
PATHOGENESIS OF THE RESPIRATORY TRACT:
BASIC CONCEPTS
Microorganisms primarily cause disease by a limited
number of pathogenic mechanisms (see Chapter 3).
Because these mechanisms relate to respiratory tract
infections, they are discussed briefly. Encounters between
the human body and microorganisms occur many times
each day. However, establishment of infection after such
contact tends to be the exception rather than the rule.
Whether an organism is successful in establishing an
infection depends not only on the organism’s ability to
cause disease (pathogenicity) but also on the human
host’s ability to prevent the infection.
Host Factors
The human host has several mechanisms that nonspecifi-
cally protect the respiratory tract from infection: the
nasal hairs, convoluted passages, and the mucous lining
of the nasal turbinates; secretory IgA and nonspecific
antibacterial substances (lysozyme) in respiratory secre-
tions; the cilia and mucous lining of the trachea; and
reflexes such as coughing, sneezing, and swallowing.
These mechanisms prevent foreign objects or organisms
from entering the bronchi and gaining access to the
lungs, which remain sterile in the healthy host.
 Infections of the Lower Respiratory System  CHAPTER 69 879

Nasal cavity
Pharynx: BOX 69-1  Organisms Present in the Nasopharynx and
Nasopharynx Oropharynx of Healthy Humans
Oropharynx
Laryngopharynx Possible Pathogens
Larynx Acinetobacter spp.
Upper
Trachea Viridans streptococci, including Streptococcus anginosus
respiratory
tract Left and right group
primary bronchi Beta-hemolytic streptococci
Streptococcus pneumoniae
Staphylococcus aureus
Neisseria meningitidis
Mycoplasma spp.
Haemophilus influenzae
Lower Haemophilus parainfluenzae
respiratory
tract
Moraxella catarrhalis
Left
Right pleural
Candida albicans
pleural cavity Herpes simplex virus
cavity Enterobacteriaceae
Mediastinum Mycobacterium spp.
Pleural
Bronchioles Pseudomonas spp.
Diaphragm space
Burkholderia cepacia
Figure 69-1  Anatomy of the respiratory tract, including upper and Filamentous fungi
lower respiratory tract regions. Klebsiella ozaenae
Eikenella corrodens
Bacteroides spp.
Peptostreptococcus spp.
Aspiration of minor amounts of oropharyngeal material, Actinomyces spp.
as occurs often during sleep, plays an important role in Capnocytophaga spp.
the pathogenesis of many types of pneumonia. Once Actinobacillus spp., A. actinomycetemcomitans
particles escape the mucociliary sweeping activity and Haemophilus aphrophilus
enter the alveoli, alveolar macrophages ingest them and Entamoeba gingivalis
carry them to the lymphatics. Trichomonas tenax
In addition to these nonspecific host defenses, normal
Rarely Pathogens
flora of the nasopharynx and oropharynx help prevent
Nonhemolytic streptococci
colonization by pathogenic organisms of the upper respi-
Staphylococci
ratory tract. Normal bacterial flora prevent the coloniza- Micrococci
tion by pathogens by competing for the same space and Corynebacterium spp.
nutrients as well as production of bacteriocins and meta- Coagulase-negative staphylococci
bolic products that are toxic to invading organisms. Neisseria spp., other than N. gonorrhoeae and
Some of the bacteria that can be isolated as part of the N. meningitidis
indigenous flora of healthy hosts, as well as many species Lactobacillus spp.
that may cause disease under certain circumstances and Veillonella spp.
are often isolated from the respiratory tracts of healthy Spirochetes
persons, are listed in Box 69-1. Under certain circum- Rothia dentocariosa
stances and for unknown reasons, these colonizing Leptotrichia buccalis
organisms can cause disease—perhaps because of previ- Selenomonas
ous damage by a viral infection, loss of some host immu- Wolinella
nity, or physical damage to the respiratory epithelium Stomatococcus mucilaginosus
(e.g., from smoking). Differentiation of normal flora of Campylobacter spp.
the respiratory tract is important for determining the
importance of an isolate in the clinical laboratory. Colo-
nization does not always represent an infection. It is
important to differentiate colonization from infection host. The virulence, or disease-producing capability of an
based on the specimen source, number of organisms organism, depends on several factors including adher-
present, and presence or quantity of white blood cells. ence, production of toxins, amount of growth or prolif-
(Organisms isolated from normally sterile sites in the eration, tissue damage, avoiding the host immune
respiratory tract by sterile methods that avoid contamina- response, and ability to disseminate.
tion with normal flora should be definitively identified Adherence.  For any organism to cause disease, it must
and reported to the clinician.) first gain a foothold within the respiratory tract to grow
to sufficient numbers to produce symptoms. Therefore,
Microorganism Factors most etiologic agents of respiratory tract disease must
Organisms possess traits or produce products that first adhere to the mucosa of the respiratory tract. The
promote colonization and subsequent infection in the presence of normal flora and the overall state of the host
880 PART VII  Diagnosis by Organ System
BOX 69-2  Respiratory Tract Pathogens
Definite Respiratory Tract Pathogens
Corynebacterium diphtheriae (toxin producing)
Mycobacterium tuberculosis
Mycoplasma pneumoniae
Chlamydia trachomatis
Chlamydia pneumoniae
Bordetella pertussis
Legionella spp.
Pneumocystis jiroveci (Pneumocystis carinii)
Nocardia spp.
Histoplasma capsulatum
Coccidioides immitis
Cryptococcus neoformans (may also be recovered from
patients without disease)
Blastomyces dermatitidis
Viruses (respiratory syncytial virus, human metapneumovirus,
adenoviruses, enteroviruses, hantavirus, herpes simplex
virus, influenza and parainfluenza virus, rhinoviruses,
severe acute respiratory syndrome)
Rare Respiratory Tract Pathogens
Francisella tularensis
Bacillus anthracis
Yersinia pestis
Burkholderia pseudomallei
Coxiella burnetii
Chlamydia psittaci
Brucella spp.
Salmonella spp.
Pasteurella multocida
Klebsiella rhinoscleromatis
Varicella-zoster virus (VZV)
Parasites
affect the ability of microorganisms to adhere. Surviving
or growing on host tissue without causing overt harmful
effects is termed colonization. Except for those microor-
ganisms inhaled directly into the lungs, all etiologic
agents of disease must first colonize the respiratory tract
before they can cause harm.
Streptococcus pyogenes possess specific adherence factors
such as fimbriae comprised of molecules such as lipotei-
choic acids and M proteins. These molecules appear as
a thin layer of fuzz surrounding the bacteria. Staphylococ-
cus aureus and certain viridans streptococci are other
bacteria that posses these lipoteichoic acid adherence
complexes. Many gram-negative bacteria (which do not
have lipoteichoic acids), including Enterobacteriaceae,
Legionella spp., Pseudomonas spp., Bordetella pertussis, and
Haemophilus spp., also adhere by means of proteinaceous
finger-like surface fimbriae. Viruses possess either a hem-
agglutinin (influenza and parainfluenza viruses) or other
proteins that mediate their epithelial attachment.
Toxins.  Certain microorganisms are almost always con-
sidered to be etiologic agents of disease if they are present
in any numbers in the respiratory tract because they
possess virulence factors that are expressed in every host.
These organisms are listed in Box 69-2. The production
of extracellular toxin was one of the first pathogenic
mechanisms discovered among bacteria. Corynebacterium
diphtheriae is a classic example of a bacterium that pro-
duces disease through the action of an extracellular
toxin. Once the organism colonizes the upper respira-
tory epithelium, it produces a toxin that is disseminated
systemically, adhering preferentially to central nervous
system cells and muscle cells of the heart. Systemic
disease is characterized by myocarditis, peripheral neuri-
tis, and local disease that can lead to respiratory distress.
Growth of C. diphtheriae causes necrosis and sloughing of
the epithelial mucosa, producing a “diphtheritic (pseudo)
membrane,” which may extend from the anterior nasal
mucosa to the bronchi or may be limited to any area
between—most often the tonsillar and peritonsillar
areas. The membrane may cause sore throat and inter-
fere with respiration and swallowing. Although nontoxic
strains of C. diphtheriae can cause local disease, it is much
milder than disease associated with toxigenic strains.
Some strains of Pseudomonas aeruginosa produce a
toxin similar to diphtheria toxin. Whether this toxin
actually contributes to the pathogenesis of respiratory
tract infection with P. aeruginosa has not been established.
Bordetella pertussis, the agent of whooping cough, also
produces toxins. The role of these toxins in production
of disease is not clear. They may act to inhibit the activity
of phagocytic cells or to damage cells of the respiratory
tract. Staphylococcus aureus and beta-hemolytic strepto-
cocci produce extracellular enzymes capable of damag-
ing host cells or tissues. Extracellular products of
staphylococci aid in the production of tissue necrosis and
the destruction of phagocytic cells and contribute to the
abscess formation associated with infection caused by this
organism. Although S. aureus can be recovered from
throat specimens, it has not been proved to cause phar-
yngitis. Enzymes of streptococci, including hyaluroni-
dase, allow rapid dissemination of the bacteria. Many
other etiologic agents of respiratory tract infection also
produce extracellular enzymes and toxins.
Microorganism Growth.  In addition to adherence and
toxin production, pathogens cause disease by merely
growing in host tissue, interfering with normal tissue
function, and attracting host immune effectors, such as
neutrophils and macrophages. Once these cells begin to
attack the invading pathogens and repair the damaged
host tissue, an expanding reaction ensues with more non-
specific and immunologic factors being attracted to the
area, increasing the amount of host tissue damage. Respi-
ratory viral infections usually progress in this manner, as
do many types of pneumonias, such as those caused by
Streptococcus pneumoniae, S. pyogenes, Staphylococcus aureus,
Haemophilus influenzae, Neisseria meningitidis, Moraxella
catarrhalis, Mycoplasma pneumoniae, Mycobacterium tubercu-
losis, and most gram-negative bacilli.
Avoiding the Host Response.  Another virulence mecha-
nism present in various respiratory tract pathogens is the
ability to evade host defense mechanisms. S. pneumoniae,
N. meningitidis, H. influenzae, Klebsiella pneumoniae, mucoid
P. aeruginosa, Cryptococcus neoformans, and others possess
polysaccharide capsules that serve both to prevent
engulfment by phagocytic host cells and to protect
somatic antigens from being exposed to host immuno-
globulins. The capsular material is produced in such
abundance by certain bacteria, such as pneumococci,

that soluble polysaccharide antigen particles can bind
host antibodies, blocking them from serving as opsonins.
Vaccine consisting of capsular antigens provides host
protection to infection, indicating that the capsular poly-
saccharide is a major virulence mechanism of H. influen-
zae, S. pneumoniae, and N. meningitidis.
Some respiratory pathogens evade the host immune
system by multiplying within host cells. Chlamydia tracho-
matis, Chlamydia psittaci, Chlamydia pneumoniae, and all
viruses replicate within host cells. They have evolved
methods for being taken in by the “nonprofessional”
phagocytic cells of the host to where they thrive within
the intracellular environment. Once within these cells,
the organism is protected from host humoral immune
factors and other phagocytic cells. This protection lasts
until the host cell becomes sufficiently damaged that the
organism is then recognized as foreign by the host and
is attacked. A second group of organisms that cause respi-
ratory tract disease comprises organisms capable of sur-
vival within phagocytic host cells (usually macrophages).
Once inside the phagocytic cell, these respiratory tract
pathogens are able to multiply. Legionella, Pneumocystis
jiroveci (Pneumocystis carinii), and Histoplasma capsulatum
are some of the more common intracellular pathogens.
Mycobacterium tuberculosis is the classic representative of
an intracellular pathogen. In primary tuberculosis, the
organism is carried to an alveolus in a droplet nucleus,
a tiny aerosol particle containing tubercle bacilli. Once
phagocytized by alveolar macrophages, organisms are
carried to the nearest lymph node, usually in the hilar or
other mediastinal chains. In the lymph node, the organ-
isms slowly multiply within macrophages. Ultimately,
M. tuberculosis destroys the macrophage and is subse-
quently taken up by other phagocytic cells. Tubercle
bacilli multiply to a critical mass within the protected
environment of the macrophages, which are prevented
from accomplishing phagosome-lysosome fusion capable
of destroying the bacteria. Having reached a critical
mass, the organisms spill out of the destroyed macro-
phages, through the lymphatics, and into the blood-
stream, producing mycobacteremia and carrying tubercle
bacilli to many parts of the body. In most cases, the host
immune system reacts sufficiently at this point to kill the
bacilli; however, a small reservoir of live bacteria may be
left in areas of normally high oxygen concentration, such
as the apical (top) portion of the lung. These bacilli are
walled off, and years later, an insult to the host, either
immunologic or physical, may cause breakdown of the
focus of latent tubercle bacilli, allowing active multiplica-
tion and disease (secondary tuberculosis). In certain
patients with primary immune defects, the initial bacte-
remia seeds bacteria throughout a compromised host,
leading to disseminated or miliary tuberculosis. Growth
of the bacteria within host macrophages and histiocytes
in the lung causes an influx of more effector cells, includ-
ing lymphocytes, neutrophils, and histiocytes, eventually
resulting in granuloma formation, then tissue destruc-
tion and cavity formation. The lesion consists of a semi-
solid, amorphous tissue mass resembling semisoft cheese,
from which it received the name caseating necrosis
(death of cells or tissues). The infection can extend into
bronchioles and bronchi from which bacteria are
Infections of the Lower Respiratory System  CHAPTER 69 881
disseminated via respiratory secretions and coughing.
Aerosolized droplets are produced by coughing and
contain organisms that are inhaled by the next suscep-
tible host. Other portions of the patient’s lungs may
become infected as well through aspiration (inhalation
of a fluid or solid).
DISEASES OF THE LOWER
RESPIRATORY TRACT
BRONCHITIS
Acute
Acute bronchitis is characterized by acute inflammation
of the tracheobronchial tree. This condition may be part
of, or preceded by, an upper respiratory tract infection
such as influenza (the “flu”) or the common cold. Most
infections occur during the winter when acute respira-
tory tract infections are common.
The pathogenesis of acute bronchitis has no specific
documented etiology but appears to be a mixture of viral
cytopathic events and a response by the host immune
system. Regardless of the cause, the protective functions
of the bronchial epithelium are disturbed and excessive
fluid accumulates in the bronchi. Depending on the eti-
ology, destruction of the bronchial epithelium may be
either extensive (e.g., influenza virus) or minimal (e.g.,
rhinovirus colds).
Clinically, bronchitis is characterized by cough, vari-
able fever, and sputum production. Sputum (pus from
the lungs) is often clear at the onset but may become
purulent as the illness persists. Bronchitis may manifest
as croup (a clinical condition marked by a barking cough
or hoarseness).
The value of microbiologic studies to determine the
cause of acute bronchitis in otherwise healthy individuals
has not been established. Acute bronchitis is caused by
viral agents, such as influenza and respiratory syncytial
virus (RSV). The bacterium Bordetella pertussis is often
associated with bronchitis in infants and preschool chil-
dren (Table 69-1). The best specimen for diagnosis of
pertussis is a deep nasopharyngeal specimen collected
with a calcium alginate swab (see Chapter 37).
Chronic versus Acute
Chronic bronchitis is a common condition affecting
about 10% to 25% of adults. This disease is defined by
clinical symptoms in which excessive mucus production
leads to coughing up sputum on most days during at least
3 consecutive months for more than 2 successive years.
TABLE 69-1  Major Causes of Acute Bronchitis
Bacteria Viruses
Bordetella pertussis, Influenza virus, adenovirus, rhinovirus,
B. parapertussis, coronavirus (other less common
Mycoplasma pneumoniae, viruses: respiratory syncytial virus,
Chlamydia pneumoniae human metapneumovirus,
coxsackie A21 virus)
882 PART VII  Diagnosis by Organ System
BOX 69-3  Viral Agents That Cause Bronchiolitis
Respiratory syncytial virus
Parainfluenza viruses, types 1-3
Rhinoviruses
Adenoviruses
Influenza viruses
Enteroviruses
Human metapneumovirus
Cigarette smoking, infection, and inhalation of dust or
fumes are important contributing factors. Acute bronchi-
tis is not related to long-term etiologies causing damage
to the lungs, but is typically a result of an infectious
process.
Patients with chronic bronchitis can suffer from acute
flare-ups of infection, but determination of the cause of
the infection is difficult. Potentially pathogenic bacteria,
such as nonencapsulated strains of Haemophilus influen-
zae, Streptococcus pneumoniae, and Moraxella catarrhalis, are
frequently cultured from the bronchi of these patients.
Because of chronic colonization, it is difficult to incrimi-
nate one of these organisms as the specific cause of an
acute infection in patients with chronic bronchitis.
Although the role of bacteria in acute infections in these
patients is questionable, viruses are frequent causes.
BRONCHIOLITIS
Bronchiolitis, the inflammation of the smaller diameter
bronchiolar epithelial surfaces, is an acute viral lower
respiratory tract infection that primarily occurs during
the first 2 years of life. Characteristic clinical manifesta-
tions include an acute onset of wheezing and hyperinfla-
tion as well as cough, rhinorrhea (runny nose), tachypnea
(rapid breathing), and respiratory distress. The disease
is primarily caused by viruses including a recently discov-
ered virus, human metapneumovirus. RSV accounts for
40% to 80% of cases of bronchiolitis and demonstrates
a marked seasonality; the etiologic agents of bronchiolitis
are listed in Box 69-3. Like other viral infections, bron-
chiolitis shows a marked seasonality in temperate cli-
mates with a yearly increase in cases during winter to
early spring.
Initially, the virus replicates in the epithelium of the
upper respiratory tract, but in the infant it rapidly spreads
to the lower tract airways. Early inflammation of the
bronchial epithelium progresses to necrosis. Symptoms
such as wheezing may be related to the type of inflam-
matory response to the virus as well as other host factors.
For the most part, patients are managed based on clinical
parameters, with the laboratory having a role in cases
that require hospitalization; a specific viral etiology can
be identified in a large number of infants by viral isola-
tion from respiratory secretions, preferably from a nasal
wash (see Chapter 65).
PNEUMONIA
Pneumonia (inflammation of the lower respiratory tract
involving the lung’s airways and supporting structures) is
a major cause of illness and death. There are two major
categories of pneumonias: those considered community-
acquired pneumonia (patients are believed to have
acquired their infection outside the hospital setting) and
those including hospital- or ventilator-associated (patients
are believed to have acquired their infection within the
hospital setting, usually at least 2 days following admis-
sion) or health care–associated pneumonia (affects only
patients hospitalized in an acute care hospital for 2 or
more days within 90 days of infection from a long-term
care facility, or patients who have received recent intra-
venous antibiotic therapy, chemotherapy, or wound care
within 30 days of the current infection, or who have
attended a hospital or hemolysis clinic). Nevertheless,
once a microorganism has successfully invaded the lung,
disease can follow affecting the alveolar spaces and their
supporting structure, the interstitium, and the terminal
bronchioles.
Pathogenesis
Organisms can cause infection of the lung by four pos-
sible routes: by upper airway colonization or infection
that subsequently extends into the lung, by aspiration of
organisms (thereby avoiding the upper airway defenses),
by inhalation of airborne droplets containing the organ-
ism, or by seeding of the lung via the blood from a distant
site of infection. Viruses cause primary infections of the
respiratory tract, as well as inhibit host defenses that, in
turn, can lead to a secondary bacterial infection. For
example, viruses may destroy respiratory epithelium and
disrupt normal ciliary activity. Presumably, the growth of
viruses in host cells disrupts the function of the latter and
encourages the influx of nonspecific immune effector
cells exacerbating the damage. Damage to host epithelial
tissue by virus infection is known to predispose patients
to secondary bacterial infection.
Aspiration of oropharyngeal contents is important in
the pathogenesis of many types of pneumonia. Aspira-
tion may occur during a loss of consciousness such as
during anesthesia or a seizure, or after alcohol or drug
abuse, but other individuals, particularly geriatric
patients, may also develop aspiration pneumonia. Neu-
rologic disease or esophageal pathology and periodontal
disease or gingivitis are other important risk factors.
Aided by gravity and often by loss of some host nonspe-
cific protective mechanisms, organisms reach lung tissue,
where they multiply and attract host inflammatory cells.
Other mechanisms include inhalation of aerosolized
material and hematogenous seeding. The buildup of cell
debris and fluid contributes to the loss of lung function
and thus to the pathology.
Furthermore, regarding the pathogenesis of hospital-
associated, health care–associated, and ventilator-
associated pneumonias, health care devices, the
environment, and the transfer between the patient and
staff or other patients can serve as sources of pathogens
causing pneumonia. The primary routes for bacterial
entry into the lower respiratory tract are by aspiration of
oropharyngeal organisms or leakage of secretions con-
taining bacteria around an endotracheal tube. For these
reasons, intubation and mechanical ventilation signifi-
cantly increase the risk of pneumonia (6- to 21-fold). In

addition, bacterial and viral biofilm in the endotracheal
tube with subsequent spread to distal airways may be
important in the pathogenesis of ventilator-associated
pneumonia.
Clinical Manifestations
The symptoms suggestive of pneumonia include fever,
chills, chest pain, and cough. In the past, pneumonias
were classified into two major groups: (1) typical or acute
pneumonias (e.g., Streptococcus pneumoniae) and (2) atypi-
cal pneumonias, based on whether the cough was pro-
ductive or nonproductive of mucoid sputum. However,
analysis of symptoms of pneumonia caused by the atypi-
cal pneumonia pathogens (Mycoplasma pneumoniae, Legio-
nella pneumophila, and Chlamydophila pneumoniae) has
revealed no significant differences from those symptoms
of patients with typical bacterial pneumonias. Because of
this overlap in symptoms, it is important to consider all
possible etiologies associated with the patient’s clinical
presentation.
Some patients with pneumonia exhibit no signs or
symptoms related to their respiratory tract (i.e., some
only have fever). Therefore, physical examination of the
patient, chest radiograph findings, patient history, and
clinical laboratory findings are important. In addition to
respiratory symptoms, 10% to 30% of patients with pneu-
monia complain of headache, nausea, vomiting, abdomi-
nal pain, diarrhea, and myalgias.
Epidemiology/Etiologic Agents
As previously mentioned, there are two major categories
of pneumonias: those considered community-acquired
pneumonias and hospital-, ventilator-, or health care–
associated pneumonias. Because the epidemiology and
etiologies can differ, these two categories are discussed
separately. Pneumonia in the immunocompromised
patient is addressed separately in this chapter. Emerging
viral infections associated with severe acute respiratory
syndrome (SARS) and influenza outbreaks (H1N1) are
typically associated with upper respiratory infections but
may lead to serious lower respiratory infections in the
young, elderly, or immunocompromised patient. See
Chapter 66 for detailed information related to these
emerging viral infectious diseases and diagnostic
recommendations.
Community-Acquired Pneumonia.  In the United States,
pneumonia is the sixth leading cause of death and the
number one cause of death from infectious diseases. It
is estimated that as many as 2 million to 3 million cases
of community-acquired pneumonia occur annually, and
roughly one fifth of these require hospitalization; 45,000
pneumonia-related deaths occur in the United States
each year. The etiology of acute pneumonias is strongly
dependent on age. More than 80% of pneumonias in
infants and children are caused by viruses, compared to
less than 10% to 20% of pneumonias in adults.
Children.  Community-acquired pneumonia in chil-
dren is a common and potentially serious infection. The
annual incidence of pneumonia in children younger
than 5 years of age is 34 to 40 cases per 1000 in Europe
and North America. Determining the cause of pneumo-
nia is challenging because the lungs are rarely sampled
Infections of the Lower Respiratory System  CHAPTER 69 883
directly and sputum is difficult to obtain from children.
Among previously healthy patients 2 months to 5 years
old, RSV, human metapneumovirus, parainfluenza, influ-
enza, and adenoviruses are the most common etiologic
agents of lower respiratory tract disease. Children suffer
less commonly from bacterial pneumonia, usually caused
by H. influenzae, S. pneumoniae, or S. aureus. Neonates may
acquire lower respiratory tract infections with C. tracho-
matis or P. jiroveci (which likely indicates an immature
immune system or an underlying immune defect).
M. pneumoniae and C. pneumoniae are the most common
causes of bacterial pneumonia in school-age children
(5-14 years of age). The four most common causes of
community-acquired viral pneumonia in children include
influenza, RSV, parainfluenza, and adenovirus. The
agents associated with nosocomial outbreaks in children
include the influenza virus, RSV, and adenovirus. Mixed
viral and bacterial infections have been documented in
35% of patients, with the majority of these (81%) being
mixed viral-bacterial infections. In addition, the time of
onset of hospital- or ventilator-associated pneumonia is
an important epidemiologic variable and risk factor:
early-onset pneumonia (defined as occurring within the
first 4 days of hospitalization), usually carries a better
prognosis, being more likely to be caused by antibiotic-
sensitive bacteria, whereas late-onset pneumonia (5 days
or more) is more likely to be caused by multidrug-resis-
tant organisms and is associated with increased patient
morbidity and mortality.
Young Adults.  The most common etiologic agent of
lower respiratory tract infection among adults younger
than 30 years of age is Mycoplasma pneumoniae, which is
transmitted via close contact. Contact with secretions
seems to be more important than inhalation of aerosols
for transmission and infection. After contact with respira-
tory mucosa, Mycoplasma are able to adhere to and colo-
nize respiratory mucosal cells. Both a protein adherence
factor and gliding motility determine virulence. Myco-
plasma attach to the cilia of respiratory mucosal cells;
once there, they multiply and destroy ciliary function.
Attachment and cytotoxins produced by the organisms
induce cell damage. Chlamydia pneumoniae is the third
most common agent of lower respiratory tract infection
in young adults, following mycoplasmas and influenza
viruses; it also affects older individuals. Chlamydia spp.,
intracellular pathogens capable of disrupting cellular
function and causing respiratory disease, are similar to
viral pathogens.
The epidemiology and treatment of community-
acquired and hospital-acquired pneumonia have changed
dramatically as a result of improvements in diagnostics,
antimicrobial therapy, and supportive care modalities.
The changes in the organization of health care has made
the distinction between community-acquired and hospi-
tal-acquired pneumonia less clear. However, pneumonia
still remains an important cause of morbidity and mortal-
ity in elderly patients. The American Thoracic Society
and the Infectious Disease Society of America guidelines
have suggested that patients who have been hospitalized
in the last 90 days, reside in a nursing home or long-term
care facility, or have had a recent intravenous antibiotic
therapy or hemodialysis, be classified as a patient with
884 PART VII  Diagnosis by Organ System
health care-associated pneumonia (HCAP). Patients with
health care-associated pneumonia have a higher inci-
dence of cardiopulmonary and neurodegenerative dis-
eases, cancer, chronic kidney disease, chronic obstructive
pulmonary disease, and immunosuppression than elderly
patients with community-acquired pneumonia. Both
populations become infested with various organisms.
The organisms most frequently responsible for commu-
nity-acquired pneumonia include S. pneumoniae, H. influ-
enzae, M. pneumoniae, C. pneumoniae, M. catarrhalis, and
Legionella spp. Factors that contribute to the onset include
decreased mucociliary function, decreased cough reflex,
decreased level of consciousness, periodontal disease,
and decreased general mobility. Health care-associated
patients have been found to be more frequently colo-
nized with gram-negative bacilli and other multidrug
resistant pathogens, perhaps because of poor oral
hygiene, decreased saliva, or decreased epithelial
cell turnover. The microorganisms associated with
these infections, in addition to those previously men-
tioned, may include methicillin-resistant S. aureus
(MRSA), Pseudomonas aeruginosa, a variety of Enterobac-
teriaceae, Acinetobacter spp., anaerobic bacteria, carbape-
namase-resistant Klebsiella pneumonia, and extended
spectrum beta-lactamase resistant Enterobacteriaceae
(ESBLS). According to the Infectious Diseases Society of
America (IDSA), the decision to hospitalize a patient or
to treat him or her as an outpatient is possibly the single
most important clinical decision made by physicians
during the course of illness. This decision in turn impacts
the subsequent site of treatment (home, hospital, or
intensive care unit), intensity of laboratory evaluation,
antibiotic therapy, and cost. Thus, the IDSA has devel-
oped management guidelines for community-acquired
pneumonia in adults based on a three-step process: (1)
assessment of preexisting conditions that might compro-
mise safety of home care, (2) quantification of short-term
mortality (referred to as the pneumonia port severity
index [PSI] and based on a prediction rule derived from
more than 14,000 patients) with subsequent assignment
of patients to five risk classes (classes I through V), and
(3) clinical judgment usually require hospitalization.
The PSI, however, is not useful for patients in nursing
homes or other health care facilities. It is therefore essen-
tial to properly assess the severity of the disease in both
cases of community-acquired and health care associated
pneumonia in elderly patients that clearly includes the
three major management guidelines as outlined by the
IDSA.
Pneumonia secondary to aspiration of gastric or
oral sections is common and occurs in the community
setting.
Pneumonia secondary to aspiration of gastric or oral
secretions is common and occurs in the community
setting. The most common agents include the oral anaer-
obes such as black-pigmented Prevotella and Porphyromo-
nas spp., Prevotella oris, P. buccae, P. disiens, Bacteroides
gracilis, fusobacteria, and anaerobic or microaerophilic
streptococci. The anaerobic agents possess many factors,
such as extracellular enzymes and capsules enhancing
their ability to produce disease. It is their presence,
however, in an abnormal site within the host producing
lowered oxidation-reduction potential secondary to
tissue damage that contributes to their pathogenicity.
Staphylococcus aureus, various Enterobacteriaceae, and
Pseudomonas may also be acquired by aspiration; Hae-
mophilus influenzae, Legionella spp., Acinetobacter, Moraxella
catarrhalis, Chlamydia pneumoniae, meningococci, and
other agents may also be implicated. Pnuemonia is the
leading cause of death among patients with nosocomial
infections (hospital- ventilator- and health care-associ-
ated) (as high as 50%) mortality among patients in inten-
sive care units. Some of these pneumonias are secondary
to sepsis, and some are related to contaminated inhala-
tion therapy equipment, particularly for intubated
patients. Hospitalized patients or long-term care patients
may experience asymptomatic colonization of the upper
airway and result in aspiration of microorganisms into
the lower respiratory tract. In addition to those organ-
isms previously listed, these patients are more prone to
infections with the multi-drug resistant strains of bacteria
(ESBLS and MRSA) including Providencia stuartii, Mor-
ganella morganii, E. coli, Proteus mirabilis, K. pneumoniae,
Enterobacter spp., and Staphylococcus aureus.
Adults (Viral pneumonia).  Adults may suffer from an esti-
mated 100 million cases annually of community-acquired
viral pneumonia cased by influenza, adenovirus, entero-
viruses (coxsackieviruses and rhinoviruses), coronavi-
ruses, human metapneumovirus, parainfluenza, varicella,
rubeola or RSV, particularly during epidemics. Influenza
associated viral pneumonia poses an increased risk for
pregnant women of approximately 4-9 times greater than
the general public, with the greatest risk associated with
the third trimester. RSV is considered the third most
common cause of community-acquired pneumoniae with
78% of the deaths occurring in patients over the age of
65. Similarly to RSV, human metapneumovirus has been
associated with outbreaks in long-term care facilities. Fol-
lowing viral pneumonia, secondary bacterial disease
caused by beta-hemolytic streptococci, S. aureus, M.
catarrhalis, H. influenzae, and Chlamydia pneumoniae.
Other agents may be considered depending on the geo-
graphic location and clinical presentation are viruses in
the Hantavirus group, the most common of which is sin
nombre virus as well as severe acute respiratory syndrome
(SARS). (See Chapter 65.)
Of these agents, influenza virus, RSV and adenovirus
have been implicated in nosocomial outbreaks. The time
of onset of hospital- or ventilator-associated pneumonia
is an important epidemiologic variable and risk factor;
early onset pneumonia (defined as occurring within the
first 4 days of hospitalization.
Adults (Fungal pneumonia).  Unusual causes of acute
lower respiratory tract infection in adults include Actino-
myces and Nocardia spp. Other agents may rarely be
recovered from sputum and include the agents of plague,
tularemia, melioidosis (Burkholderia pseudomallei), Bru-
cella, Salmonella, Coxiella burnetii (Q fever), Bacillus
anthracis, Pasteurella multocida, and certain parasitic agents
such as Paragonimus westermani, Entamoeba histolytica,
Ascaris lumbricoides, and Strongyloides spp. (the latter may
cause fatal disease in immunosuppressed patients). A
high index of suspicion by the clinician is usually a pre-
requisite to a diagnosis of parasitic pneumonia in the
United States. Psittacosis should be ruled out as a cause
of acute lower respiratory tract infection in patients who

have had recent contact with birds. Among the fungal
etiologies, Histoplasma capsulatum, Blastomyces dermatitidis,
Paracoccidioides brasiliensis, Coccidioides immitis, Cryptococcus
neoformans, and, occasionally, Aspergillus fumigatus may
cause acute pneumonia. Therefore, occupational history
and history of exposure to animals are important in sug-
gesting specific potential infectious agents.
Chronic Lower Respiratory Tract Infections.  Mycobacterium
tuberculosis is the most likely etiologic agent of chronic
lower respiratory tract infection, but fungal infection and
anaerobic pleuropulmonary infection may also run a
subacute or chronic course. Mycobacteria other than
M. tuberculosis may also cause such disease, particularly
M. avium complex and M. kansasii. Although possible
causes of acute, community-acquired lower respiratory
tract infections, fungi and parasites are more commonly
isolated from patients with chronic disease. Actinomyces
and Nocardia may also be associated with gradual onset
of symptoms. Actinomyces is usually associated with an
infection of the pleura or chest wall, and Nocardia may
be isolated along with an infection caused by M. tubercu-
losis. The pathogenesis of many of the infections caused
by agents of chronic lower respiratory tract disease is
characterized by the requirement for breakdown of cell-
mediated immunity in the host or the ability of these
agents to avoid being destroyed by host cell-mediated
immune mechanisms. This may be caused by an effect
on macrophages, the ability to mask foreign antigens,
sheer size, or some other factor, allowing microbes to
grow within host tissues without eliciting an overwhelm-
ing local immune reaction.
Cystic fibrosis (CF) is a genetic disorder that leads to
persistent bacterial infection in the lung, causing airway
wall damage and chronic obstructive lung disease. Even-
tually, a combination of airway secretions and damage
leads to poor gas exchange in the lungs, cardiac malfunc-
tion, and subsequent death. Patients with CF may present
as young adults with chronic respiratory tract disease or,
more commonly, as children with gastrointestinal prob-
lems and stunted growth. Staphylococcus aureus is the most
prevalent opportunistic bacterial pathogen infecting
55% of children 0–9 years of age with CF, with Pseudomo-
nas aeruginosa the most prevalent (81%) in older chil-
dren. A very mucoid Pseudomonas, characterized by
production of copious amounts of extracellular capsular
polysaccharide, can be isolated from the sputum of
almost all patients with CF who are older than 18 years
of age, becoming more prevalent with increasing age
after 5 years. Even if CF has not been diagnosed, isolation
of a mucoid Pseudomonas aeruginosa from sputum should
alert the clinician to the possibility of underlying disease.
Microbiologists should always report this unusual mor-
phologic feature. In addition to mucoid Pseudomonas
and Staphylococcus aureus, important pathogens in patients
with CF are likely to harbor Haemophilus influenzae, Strep-
tococcus pneumoniae, Stenotrophomonas maltophilia, Achromo-
bacter xylosoxidans, Ralsotnia spp. Cupriavidus spp.,
Pandoraea spp., Escherichia coli, strains of Burkholderia
cepacia complex, fast growing mycobacteria, RSV, influ-
enza and fungi including Aspergillu, Scedosporium spp.,
and Exophiala dermatidis. In addition, due to the viscous
mucous plugs associated with CF, several anaerobic
organisms have been detected in the lungs of CF patients
Infections of the Lower Respiratory System  CHAPTER 69 885
including Prevotella, Bifidobacterium, Veillonella, Peptostrepto-
coccus and Fusobacterium. Using advanced diagnostic
molecular methods, additional organisms have also been
identified in chronic polymicrobial CF infections includ-
ing viridans streptococci, Streptococcus constellatus, Strepto-
coccus intermedius and Streptococcus anginosus.
Lung abscess is usually a complication of acute or
chronic pneumonia. In these circumstances, organisms
infecting the lung cause localized destruction of the lung
parenchyma (functional elements of the lung). Symp-
toms associated with lung abscess are similar to those of
acute and chronic pneumonia, except symptoms fail to
resolve with treatment.
Immunocompromised Patients.  Patients with Neo-
plasms.  Patients with cancer are at high risk to become
infected because of either granulocytopenia or other
defects in phagocytic defenses, cellular or humoral
immune dysfunction, damage to mucosal surfaces and
the skin, and various medical procedures such as blood
product transfusion. In these patients, the nature of the
malignancy often determines the etiology (Table 69-2)
and pneumonia is a frequent clinical manifestation.
Transplant Recipients.  For successful organ transplan-
tation, the recipient’s immune system must be sup-
pressed. As a result, these patients are predisposed to
infection. Regardless of the type of organ transplant
(heart, renal, bone marrow, heart/lung, liver, pancreas),
most infections occur within 4 months following trans-
plantation. Major infections can occur within the first
month but are usually associated with infections carried
over from the pretransplant period. Pulmonary infec-
tions are of great importance in this patient population.
Some of the most common causes of pneumonia include
S. aureus Streptococcus pneumoniae, Haemophilus influenzae,
Pneumocystis jiroveci, and cytomegalovirus. In addition,
other organisms such as Cryptococcus neoformans, Aspergil-
lus spp., Candida spp., Nocardia sp. and over, can cause
life-threatening pulmonary infection.
HIV-Infected Patients.  Patients who are infected with
human immunodeficiency virus (HIV) are at high risk
for developing pneumonia. As discussed in the previous
chapter, opportunistic infections as a result of severe
immunodeficiency are a major cause of illness and death
among these patients. In the United States, the most
common opportunistic infection among patients with
acquired immunodeficiency syndrome is Pneumocystis jir-
oveci pneumonia. Although P. jiroveci remains a major
pulmonary pathogen, other organisms must be consid-
ered in this patient population, including Mycobacterium
tuberculosis and Mycobacterium avium complex, as well as
common bacterial pathogens such as Streptococcus pneu-
moniae and Haemophilus influenzae. In addition to these
common pathogens, many other organisms can cause
lower respiratory tract infections, including Nocardia
spp., Rhodococcus equi (a gram-positive, aerobic, pleomor-
phic organism), and Legionella spp.
PLEURAL INFECTIONS
As a result of an organism infecting the lung and subse-
quently gaining access to the pleural space via an abnor-
mal passage (fistula), the patient may develop an
empyema (pus in a body cavity such as the pleural cavity).
886 PART VII  Diagnosis by Organ System
TABLE 69-4  Examples of Infectious Agents Frequently
Associated with Certain Malignancies
Malignancy (site and type
of infections) Pathogens
Acute nonlymphocytic Enterobacteriaceae
leukemia (pneumonia, Pseudomonas
oral lesions, cutaneous Staphylococci
lesions, urinary tract Corynebacterium jeikeium
infections, hepatitis, Candida
most often sepsis Aspergillus
without obvious focus) Mucor
Hepatitis C and other non-A, non-B
Acute lymphocytic leukemia Streptococci (all types)
(pneumonia, cutaneous Pneumocystis jiroveci (P. carinii)
lesions, pharyngitis, Herpes simplex virus
disseminated disease) Cytomegalovirus
Varicella zoster virus
Lymphoma (disseminated Brucella
disease, pneumonia, Candida (mucocutaneous)
urinary tract infections, Cryptococcus neoformans
sepsis, cutaneous Herpes simplex virus (cutaneous)
lesions) Varicella zoster virus
Cytomegalovirus
Pneumocystis jiroveci (P. carinii)
Toxoplasma gondii
Listeria monocytogenes
Mycobacteria
Nocardia
Salmonella
Staphylococci
Enterobacteriaceae
Pseudomonas
Strongyloides stercoralis
Multiple myeloma Haemophilus influenza
(pneumonia, cutaneous Streptococcus pneumoniae
lesions, sepsis) Neisseria meningitides
Enterobacteriaceae
Pseudomonas
Varicella zoster virus
Candida
Aspergillus
Symptoms in these patients are insidious because early
in the course of disease they are related to the primary
infection in the lung. Once enough purulent exudate is
formed, typical physical and radiographic findings indic-
ative of an empyema are produced.
LABORATORY DIAGNOSIS OF LOWER
RESPIRATORY TRACT INFECTIONS
SPECIMEN COLLECTION AND TRANSPORT
Although rapid determination of the etiologic agent is
of paramount importance in managing pneumonia,
the responsible pathogen is not identified in as many as
50% of patients, despite extensive diagnostic testing.
Unfortunately, no single test is capable of identifying all
potential lower respiratory tract pathogens. Refer to
Table 5-1 for an overview of the method used to collect,
transport, and process specimens from the lower respira-
tory tract.
Sputum
Expectorated.  The examination of expectorated sputum
has been the primary means of determining the causes
of bacterial pneumonia. However, lower respiratory tract
secretions will be contaminated with upper respiratory
tract secretions, especially saliva, unless they are collected
using an invasive technique. For this reason, sputum is
among the least clinically relevant specimens received for
culture in microbiology laboratories, even though it
is one of the most numerous and time-consuming
specimens.
Good sputum samples depend on thorough health
care worker education and patient understanding
throughout all phases of the collection process. Food
should not have been ingested for 1 to 2 hours before
expectoration and the mouth should be rinsed with
saline or water just before expectoration. Patients should
be instructed to provide a deep-coughed specimen. The
material should be expelled into a sterile container, with
an attempt to minimize contamination by saliva. Speci-
mens should be transported to the laboratory immedi-
ately. Even a moderate amount of time at room
temperature can result in the loss of viable infectious
agents and the recovery of pathogens.
Induced.  Patients unable to produce sputum may be
assisted by respiratory therapists, who use postural drain-
age and thoracic percussion to stimulate production of
acceptable sputum. Before specimen collection, patients
should brush the buccal mucosa, tongue, and gums with
a wet toothbrush. As an alternative, an aerosol-induced
specimen may be collected for the isolation of mycobac-
terial or fungal agents. Induced sputum is also recog-
nized for its high diagnostic yield in cases of Pneumocystis
jiroveci pneumonia. Aerosol-induced specimens are col-
lected by allowing the patient to breathe aerosolized
droplets, using an ultrasonic nebulizer containing 10%
0.85% NaCl or until a strong cough reflex is initiated.
Lower respiratory secretions obtained in this way appear
watery, resembling saliva, although they often contain
material directly from alveolar spaces. These specimens
are usually adequate for culture and should be accepted
in the laboratory without prescreening. Obtaining such
a specimen may obviate the need for a more invasive
procedure, such as bronchoscopy or needle aspiration.
The gastric aspirate is used exclusively for isolation of
acid-fast bacilli and may be collected from patients who
are unable to produce sputum, particularly young chil-
dren. Before the patient wakes up in the morning, a
nasogastric tube is inserted into the stomach and con-
tents are withdrawn (on the assumption that acid-fast
bacilli from the respiratory tract were swallowed during
the night and will be present in the stomach). The rela-
tive resistance of mycobacteria to acidity allows them to
remain viable for a short period. Gastric aspirate speci-
mens must be delivered to the laboratory immediately so
that the acidity can be neutralized. Specimens can be

Figure 69-2  Tracheal secretions received in the laboratory in a
Lukens trap.
neutralized and then transported if immediate delivery
is not possible.
Endotracheal or Tracheostomy Suction Specimens
Patients with tracheostomies are unable to produce
sputum in the normal fashion, but lower respiratory tract
secretions can easily be collected in a Lukens trap (Figure
69-2). Tracheostomy aspirates or tracheostomy suction
specimens should be treated as sputum by the laboratory.
Patients with tracheostomies rapidly become colonized
with gram-negative bacilli and other nosocomial patho-
gens. Such colonization per se is not clinically relevant,
but these organisms may be aspirated into the lungs and
cause pneumonia. Culture results should be correlated
with clinical signs and symptoms.
Bronchoscopy.  Bronchoscopy specimens include bron-
choalveolar lavage (BAL), bronchial washing, bronchial
brushing, and transbronchial biopsies. The diagnosis of
pneumonia, particularly in HIV-infected and other
immunocompromised patients, often necessitates the
use of more invasive procedures. Fiberoptic bronchos-
copy has dramatically affected the evaluation and man-
agement of these infections. With this method, the
bronchial mucosa can be directly visualized and collected
for biopsy, and the lung tissue can be sent for transbron-
chial biopsy for the evaluation of lung cancer and other
lung diseases. Although transbronchial biopsy is impor-
tant, the procedure is often associated with significant
complications such as bleeding. The sample should be
transported in sterile 0.85% saline.
During bronchoscopy, physicians obtain bronchial
washings or aspirates, bronchoalveolar lavage (BAL)
samples, protected bronchial brush samples, or speci-
mens for transbronchial biopsy. Bronchial washings or
aspirates are collected using a small amount of sterile
physiologic saline inserted into the bronchial tree and
withdrawing the fluid. These specimens will be contami-
nated with upper respiratory tract flora such as viridans
streptococci and Neisseria spp. Recovery of potentially
pathogenic organisms from bronchial washings should
be attempted.
Infections of the Lower Respiratory System  CHAPTER 69 887
A deep sampling of desquamated host cells and secre-
tions can be collected through bronchoscopy and BAL.
Lavages are especially suitable for detecting Pneumocys-
tis cysts and fungal elements. During this procedure, a
high volume of saline (100 to 300 mL) is infused into a
lung segment through the bronchoscope to obtain cells
and protein of the pulmonary interstitium and alveolar
spaces. It is estimated that more than 1 million alveoli
are sampled during this process. The value of this tech-
nique in conjunction with quantitative culture for the
diagnosis of most major respiratory tract pathogens,
including bacterial pneumonia, has been documented.
Scientists have found significant correlation between
acute bacterial pneumonia and greater than 103 to 104
bacterial colonies per milliliter of BAL fluid. BAL has
been shown to be a safe and practical method for diag-
nosing opportunistic pulmonary infections in immuno-
suppressed patients. At bedside, nonbronchoscopic
“mini BAL” using a Metras catheter has been introduced;
typically 20 mL or less of saline is instilled.
Another type of respiratory specimen is obtained via
a protected catheter bronchial brush as part of a bron-
choscopy examination. Specimens obtained by this
moderately invasive collection procedure are suited for
microbiologic studies, particularly in aspiration pneu-
monia. Protected specimen brush bristles collect from
0.001 to 0.01 mL of material. An overview of the collec-
tion process is shown in Figure 69-3. Upon receipt, con-
tents of the bronchial brush may be suspended in 1 mL
of broth solution with vigorous vortexing and inocu-
lated onto culture media using a 0.01-mL calibrated
inoculating loop. Some researchers have indicated that
specimens obtained via double-lumen–protected cathe-
ters are suitable for both anaerobic and aerobic cul-
tures. Colony counts of greater than or equal to 1000
organisms per milliliter in the broth diluent (or 106/
mL in the original specimen) have been considered to
correlate with infection. All facets of the bronchoscopic
procedure—such as order of sampling, use of anes-
thetic, and rapidity of plating—should be rigorously
standardized.
Transtracheal Aspirates.  Percutaneous transtracheal
aspirates (TTAs) are obtained by inserting a small plastic
catheter into the trachea via a needle previously inserted
through the skin and cricothyroid membrane. This inva-
sive procedure, although somewhat uncomfortable for
the patient and not suitable for all patients (it cannot be
used in uncooperative patients, in patients with bleeding
tendency, or in patients with poor oxygenation), reduces
the likelihood that a specimen will be contaminated by
upper respiratory tract flora and diluted by added fluids,
provided care is taken to keep the catheter from being
coughed back up into the pharynx. Although this tech-
nique is rarely used, anaerobes, such as Actinomyces and
those associated with aspiration pneumonia, can be iso-
lated from TTA specimens.
Other Invasive Procedures.  When pleural empyema is
present, thoracentesis may be used to obtain infected
fluid for direct examination and culture. This constitutes
an excellent specimen that accurately reflects the bacte-
riology of an associated pneumonia. Laboratory exami-
nation of such material is discussed in Chapter 77. Blood
888 PART VII  Diagnosis by Organ System

Trachea

Bronchoscope Bronchoscope

Outer cannula
Plug

A
B

21.5c/DiagnosticicrM
obiology 21.5c/DiagnosticicrM
obiology

Outer cannula
Inner cannula
Plug

Brush
Purulent exudate
C D
Figure 69-3  Overview for obtaining a protected catheter bronchial brush during a bronchoscopy examination. A, The bronchoscope is
introduced into the nose and advanced through the nasopharyngeal passage into the trachea. The bronchoscope is then inserted into the
lung area of interest. B, A small brush that holds 0.001 to 0.01 mL of secretions is placed within a double cannula. The end of the outermost
tube or cannula is closed with a displaceable plug made of absorbable gel. The cannula is inserted to the proper area. C, Once in the
correct area, the inner cannula is pushed out, dislodging the protective plug as it is extruded. D, The brush is then extended beyond the
inner cannula, and the specimen is collected by “brushing” the involved area. The brush is withdrawn into the inner cannula, which is with-
drawn into the outer cannula to prevent contamination by upper airway organisms as it is removed.

cultures, of course, should always be obtained from
patients with pneumonia.
For patients with pneumonia, a thin needle aspiration
of material from the involved area of the lung may be
performed percutaneously. If no material is withdrawn
into the syringe after the first try, approximately 3 mL
of sterile saline can be injected and then withdrawn into
the syringe. Patients with emphysema, uremia, throm­
bocytopenia, or pulmonary hypertension may be at
increased risk of complication (primarily pneumothorax
[air in the pleural space] or bleeding) from this proce-
dure. The specimens obtained are very small in volume,
and protection from aeration is usually impossible. This
technique is more frequently used in children than in
adults.
The most invasive procedure for obtaining respiratory
tract specimens is the open lung biopsy. Performed by
surgeons, this method is used to procure a wedge of lung
tissue. Biopsy specimens are extremely helpful for diag-
nosing severe viral infections, such as herpes simplex
pneumonia, for rapid diagnosis of Pneumocystis pneumo-
nia, and for other hard-to-diagnose or life-threatening
pneumonias. Ramifications of this and all other speci-
men collection techniques are discussed in Cumitech 7B,
“Laboratory Diagnosis of Lower Respiratory Tract
Infections.”

A B
Figure 69-4  Gram stain of sputum specimens. A, This specimen contains numerous polymorphonuclear leukocytes and no visible squamous
epithelial cells, indicating that the specimen is acceptable for routine bacteriologic culture. B, This specimen contains numerous squamous
epithelial cells and rare polymorphonuclear leukocytes, indicating an inadequate specimen for routine sputum culture.
SPECIMEN PROCESSING
Direct Visual Examination
Lower respiratory tract specimens can be examined by
direct wet preparation for parasites and special proce-
dures for Pneumocystis. Fungal elements can be visualized
under phase microscopy with 10% potassium hydroxide,
under ultraviolet light with calcofluor white, or using
periodic acid-Schiff–stained smears.
For most other evaluations, the specimen must be
fixed and stained. Bacteria and yeasts can be recognized
on Gram stain. One of the most important uses of the
Gram stain, however, is to evaluate the quality of expec-
torated sputum received for routine bacteriologic culture.
A portion of the specimen consisting of purulent mate-
rial is chosen for the stain. The smear can be evaluated
adequately even before it is stained, thus negating the
need for Gram stain of specimens later judged unaccept-
able. An acceptable specimen yields fewer than 10 squa-
mous epithelial cells per low-power field (100×). The
number of white blood cells may not be relevant, because
many patients are severely neutropenic and specimens
from these patients will not show white blood cells on
Gram stain examination. On the other hand, the pres-
ence of 25 or more polymorphonuclear leukocytes per
100× field, together with few squamous epithelial cells,
implies an excellent specimen (Figure 69-4). Samples
that contain predominantly upper respiratory tract mate-
rial should be rejected. Previously, only expectorated
sputa were suitable for rejection based on microscopic
screening. However, endotracheal aspirates (ETAs) from
mechanically ventilated adult patients can be screened
by Gram stain. Criteria used to reject ETAs from adult
patients include greater than 10 squamous epithelial
cells per low-power field or no organisms seen under oil
immersion (1000×). In Legionella pneumonia, sputum
may be scant and watery, with few or no host cells. Such
specimens may be positive by direct fluorescent antibody
stain and culture, and they should not be subjected to
screening procedures. Conversely, sputum from patients
with CF should be screened. A throat swab is an accept-
able specimen from patients with CF in selected clinical
settings and should be processed in a similar manner as
CF sputum. Staining of respiratory samples is useful and
Infections of the Lower Respiratory System  CHAPTER 69 889
should be compared to culture results to reveal errors in
procedures, specimen collection, and transport or speci-
men identification.
Respiratory secretions may need to be concentrated
before staining. The cytocentrifuge instrument has been
used successfully for this purpose, concentrating the cel-
lular material in an easily examined monolayer on a glass
slide. As an alternative, specimens are centrifuged, and
the sediment is used for visual examinations and cul-
tures. For screening purposes, the presence of ciliated
columnar bronchial epithelial cells, goblet cells, or pul-
monary macrophages in specimens obtained by bron-
choscopy or BAL indicates a specimen from the lower
respiratory tract.
In addition to the Gram stain, respiratory specimens
may be stained for acid-fast bacilli with either the classic
Ziehl-Neelsen or the Kinyoun carbolfuchsin stain. Aura-
mine or auramine-rhodamine is also used to detect acid-
fast organisms. Because they are fluorescent, these stains
fluorescent superior already here comment only are
more sensitive than the carbolfuchsin formulas and are
preferable for rapid screening. Slides may be restained
with the classic stains directly over the fluorochrome
stains as long as all of the immersion oil has been removed
carefully with xylene. All of the acid-fast stains will reveal
Cryptosporidium spp. if they are present in the respiratory
tract, as may occur in immunosuppressed patients. These
patients are often at risk of infection with P. jiroveci.
Although the modified Gomori methenamine silver stain
has been used traditionally to recognize Nocardia, Actino-
myces, fungi, and parasites, it takes approximately 1 hour
of the technologist’s time to perform, is technically
demanding, and is not suitable as an emergency proce-
dure. A fairly rapid stain, toluidine blue O, has been used
in many laboratories with some success. Toluidine blue
O stains Pneumocystis, Nocardia asteroides, and some fungi.
A monoclonal antibody stain is the optimum stain for
Pneumocystis (see Chapter 59) for less invasive specimens
such as BAL and induced sputa.
Direct fluorescent antibody (DFA) staining has been
used to detect Legionella spp. in lower respiratory tract
specimens. Sputum, pleural fluid, aspirated material,
and tissues are all suitable specimens. Because there are
so many different serotypes of legionellae, polyclonal
890 PART VII  Diagnosis by Organ System
antibody reagents and a monoclonal antibody directed
against all serotypes of Legionella pneumophila are used.
Because of low sensitivity (50% to 75%), DFA results
should not be relied on in lieu of culture. Rather, Legio-
nella culture, DFA or urinary antigen, and serology
should be performed for optimum sensitivity. See Chapter
35 for details regarding detection of Legionella spp.
Commercially available DFA reagents are also used to
detect antigens of numerous viruses, including herpes
simplex, cytomegalovirus, adenovirus, influenza viruses,
and RSV (see Chapter 65). Commercial suppliers of
reagents provide procedure information for each of
these tests. Monoclonal and polyclonal fluorescent stains
for Chlamydia trachomatis are available and may be useful
for staining respiratory secretions of infants with pneu-
monia. A number of molecular amplification techniques
(see Chapter 8) for the direct detection of respiratory
pathogens have been described; however, the sensitivity
and specificity of these assays vary greatly from one study
to another. Amplification assays are also available for the
direct detection of Mycobacterium tuberculosis on smear-
positive specimens (see Chapter 43).
Rapid direct detection from respiratory samples is
now available using nucleic acid-based methods. The
xTAG Respiratory Viral Panel (RVP) (Luminex Corpora-
tion, Austin, TX), can be used for the simultaneous
detection of influenza (four types), RSV, human meta-
pneumovirus, and adenovirus from nasopharyngeal
swabs. In addition, the FilmArray Respiratory Panel
(BIOFIRE Diagnostics, Salt Lake City, UT ) is capable of
detecting upper respiratory tract infections associated
with coronavirus (four types) , adenovirus, influenza
(five types), rhinovirus, parainfluenza virus (four types),
enterovirus, human metapneumovirus, RSV, Bordetella
pertussis, Mycoplasma pneumoniae, and Chlamydophila pneu-
moniae in approximately 1 hour directly from patient
samples. Smaller molecular panels are also available such
as the real-time multiplex amplification kit for influenza
A, B, and RSV (Hologic-Gen-Probe, San Diego, CA). All
of the previously mentioned methods are FDA-approved.
In addition to these, there are a variety of research-use-
only and other molecular respiratory panels in clinical
validation studies. It is important when considering the
use of a molecular assay that the laboratory consider
their patient population including severity of illness,
immune status, and transplant histories.
Routine Culture
Most of the commonly sought etiologic agents of lower
respiratory tract infection are isolated on routine media:
5% sheep blood agar, MacConkey agar for the isolation
and differentiation of gram-negative bacilli, and choco-
late agar for Haemophilus and Neisseria spp. Because of
contaminating oral flora, sputum specimens, specimens
obtained by bronchial washing and lavage, tracheal aspi-
rates, and tracheostomy or endotracheal tube aspirates
are not inoculated to enrichment broth or incubated
anaerobically. Only specimens obtained by percutaneous
aspiration (including transtracheal aspiration) and pro-
tected bronchial brush are suitable for anaerobic culture;
the latter must be done quantitatively for proper inter-
pretation (refer to prior discussion). Transtracheal and
percutaneous lung aspiration material may be inoculated
to enriched thioglycollate as well as to solid media. For
suspected cases of Legionnaires’ disease, buffered
charcoal-yeast extract (BCYE) agar and selective BCYE
should be inoculated. Plates should be streaked in four
quadrants to provide a basis for objective semiquantita-
tion to define the amount of growth. After 24 to 48 hours
of incubation, the numbers and types of colonies are
recorded. For Legionella cultures, colonies form on the
selective agar after 3 to 5 days at 35° C.
Sputum specimens from patients known to have CF
should be inoculated to selective agar, such as specific
chromagenic agar, for recovery of S. aureus and selective
horse blood–bacitracin, incubated anaerobically and
aerobically, for recovery of H. influenzae that may be
obscured by the mucoid Pseudomonas on routine media.
The use of a selective medium for B. cepacia, such as PC
or OFPBL agars, is also necessary.
For interpretation of culture results on those speci-
mens contaminated by normal oropharyngeal flora (e.g.,
expectorated and induced sputum, bronchial washings),
growth of the predominant aerobic and facultative anaer-
obic bacteria is reported. To ensure optimum culture
reporting, conditions must be well defined in terms of
an objective grading system for streaked plates. Finally,
the clinical significance of culture findings depends
not only on standardized and appropriate laboratory
methods but also on how specimens are collected and
transported, other laboratory data, and the patient’s
clinical presentation.
Numerous bacterial agents that cause lower respi­
ratory tract infections are not detected by routine bac­
teriologic culture. Mycobacteria, Chlamydia, Nocardia,
Bordetella pertussis, Legionella, and Mycoplasma pneumoniae
require special procedures for detection; this also applies
to viruses and fungi. Optimal recovery for Mycobacterium
tuberculosis requires multiple specimens for acid-fast stain-
ing culture, and at least one sample for molecular testing
as recommended by the Centers for Disease Control.
Refer to the appropriate chapter section for more infor-
mation regarding these organisms. Finally, one must
keep in mind those potential agents for bioterrorist
attack, such as Bacillus anthracis, Francisella tularensis, and
Yersinia pestis, that might be recovered from respiratory
specimens (see Chapter 80).
Visit the Evolve site to complete
the review questions.
 Infections of the Lower Respiratory System  CHAPTER 69 890.e1

10. True or False

CHAPTER REVIEW _____ An acceptable sputum specimen when visualized by Gram
stain must show significant white blood cells and fewer than
1. Which of the following lung conditions are a major cause of illness
10 squamous epithelial cells per low-power field.
and death?
_____ Respiratory specimens first stained for acid-fast bacilli, with
a. pneumonia
auramine or auramine-rhodamine, can be restained with the
b. bronchiolitis
classic stains directly over the fluorochrome stain as long as
c. acute bronchitis
all the immersion oil has been removed with xylene.
d. chronic bronchitis
_____ A single culture is able to identify all potential pathogens
2. What is the most frequent cause of community-acquired pneumonia that cause lower respiratory tract infections.
in adults? _____ Sputum is the most clinically relevant specimen received for
a. Streptococcus pyogenes culture in the microbiology laboratory for the diagnosis of
b. Streptococcus pneumonia respiratory infection.
c. Mycoplasma pneumoniae _____ A moderate amount of time at room temperature will not
d. Klebsiella pneumonia affect the quality of a sputum sample.
3. Psittacosis is a lower respiratory infection in humans caused by _____ Patients with tracheostomies are unable to produce sputum
contact with what animal? in the normal fashion.
a. swine _____ The modified Gomori methenamine silver stain has been
b. seals used traditionally to recognize Norcardia, Actinomyces, fungi,
c. cats and parasites but is technically and time demanding.
d. birds _____ Pneumonia patients that are assessed to be risk classes II
4. What organism may be recovered as a subacute illness in and III generally require hospitalization.
respiratory disease caused by M. tuberculosis? _____ The production of extracellular toxin was one of the first
a. Nocardia pathogenic mechanisms discovered in bacteria.
b. Actinomyces _____ The areas of the lungs most affected by pneumonia are the
c. M. kansasii alveolar spaces and the interstitium, the supporting structure
d. M. avium intracellulare of the alveoli, and the terminal bronchioles.

5. All of the acid-fast stains will reveal which of the following 11. Matching:
organisms from respiratory specimens? Match the term with the appropriate definition.
a. Mycobacterium tuberculosis _____ bronchioalveolar lavage a. needle puncture of the pleural
b. Mycobacterium avium complex (BAL) cavity used to obtain pleural fluid
c. Cryptosporidium _____ catheter bronchial for direct examination and culture
d. All of the above brush in patients with pleural empyema
_____ percutaneous b. used exclusively for isolation of
6. Which of the following stains is used to detect Legionella in lower
transtracheal aspirates acid-fast bacilli and particularly
respiratory specimens?
(TTAs) used for young children
a. DFA staining
_____ aerosol-induced sputum c. used to obtain a wedge of lung
b. Gram stain
_____ gastric aspirate tissue to diagnose severe viral
c. Kinyoun carbol fuchsin
_____ thoracentesis infection or other hard-to-
d. Ziehl-Neelsen
_____ open lung biopsy diagnose or life-threatening
7. Which of the following media is used in addition to normal pneumonia
respiratory culture media in suspected cases of Legionnaires’ d. good method for detecting
disease? Pneumocystis cysts and fungal
a. buffered charcoal-yeast extract agar (BCYE) elements
b. Regan-Lowe agar e. useful for detecting anaerobes
c. Bordet-Gengou agar such as Actinomyces but rarely
d. cystine-tellurite agar still used
8. Which of the following organisms could potentially be isolated from f. useful for isolating agents of
a respiratory specimen and is not also considered a potential agent mycobacterial or fungal disease;
for bioterrorism? provides a high diagnostic yield in
a. Bacillus anthracis cases of Pneumocystis jiroveci
b. Bordetella pertussis pneumonia
c. Francisella tularensis g. good for microbiology studies,
d. Yersinia pestis particularly in aspiration
9. Which of the following procedures has dramatically affected the pneumonia
evaluation and management of pneumonia, particularly in HIV-
infected and immunocompromised patients?
a. tracheostomy suction
b. fiberoptic bronchoscopy
c. thoracic percussion
d. catheter bronchial brush
890.e2 PART VII  Diagnosis by Organ System

12. Matching: Key Terms 13. Short Answer

Match the term with the appropriate definition. 1. Explain the benefits of using the Binax NOW S. pneumoniae
_____ empyema a. runny nose urinary antigen test for presumptive diagnosis of pneumococcal
_____ fistula b. rapid breathing pneumonia.
_____ HAP c. abnormal passage 2. Why are enrichment broths or anaerobe plates not used in the
_____ VAP d. proteinaceous finger-like surface culture of routine sputum specimens, specimens obtained by
_____ fimbriae structures that help bacteria adhere bronchial washing, and lavage tracheal aspirates?
_____ caseating necrosis to host tissue 3. What specimens are suited for anaerobic culture with regard to
_____ miliary tuberculosis e. mass of dead tissue resembling respiratory culture?
_____ expectorated soft cheese 4. What characteristics do the following bacteria share that enable
_____ alveoli f. inhalation of a fluid or solid the organisms to resist engulfment by phagocytic host cells:
_____ tachypnea g. hospital-acquired pneumonia S. pneumoniae, N. meningitides, H. influenzae, K. pneumoniae,
_____ rhinorrhea h. microscopic structures for gas P. aeruginosa, and Cryptococcus neoformans.
_____ aspiration exchange 5. Define the pathogenesis of acute bronchitis.
_____ thoracic cavity i. body space that contains the heart 6. When is thoracentesis used to obtain a sample for direct
_____ mediastinum and lungs examination and culture?
_____ nosocomial j. ventilator-acquired pneumonia 7. What is an important epidemiologic variable and risk factor in
k. pus in a body cavity hospital- or ventilator-associated pneumonia?
l. space between the lungs 8. What virus infection effect may predispose patients to a
m. disseminated disease secondary bacterial infection?
n. infection acquired while in the 9. What hinders diagnosing the causative agent in pediatric
hospital pneumonia in children younger than 5 years of age?
o. cough up, spit out

CASE STUDY  69-1 
A 16-month-old boy was admitted with fever, lethargy, and
trouble breathing. A diagnosis of pneumonia was made by
physical examination. The child had recently been to Panama
and was treated with ceftriaxone for cough and fever. His fever
continued, despite treatment. On admission, he was given
erythromycin therapy. Tracheal aspirate and blood cultures
were obtained, but the respiratory specimen contained numer-
ous epithelial cells and yielded normal respiratory flora on
culture. A pleural aspirate and blood cultures were positive for
Streptococcus pneumoniae, which was resistant to erythromy-
cin and penicillin and intermediate in susceptibility to ceftriax-
one. The patient was given high doses of ceftriaxone and
vancomycin and responded to this therapy.
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Infections of the Lower Respiratory System  CHAPTER 69 891
QUESTIONS
1. What criteria are used in laboratories to reject sputum and tracheal
aspirates for culture?
2. If greater than 10 squamous epithelial cells per low-power field are
seen in a Gram stain but the smear also has numerous white blood
cells (greater than 25 per low-power field), should the specimen be
rejected for culture?
3. In cases of pneumococcal pneumonia, what percentage of blood
and sputum cultures is positive for S. pneumoniae?
4. The organism was reported as resistant to penicillin (MIC of
4 µg/mL) and intermediate in susceptibility to third-generation
cephalosporins (minimum inhibitory concentration to ceftriaxone of
2 µg/mL). How does the laboratory test for this organism?
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diagnosis of pneumonia, Clin Microbiol Newsletter 9:70, 1987.
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nocompetent adults, Clin Infect Dis 37:1405, 2003.
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McIntosh K: Community-acquired pneumonia in children, N Engl J Med
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Salemi C, Morgan J, Padilla S, et al: Association between severity of
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CHA P T E R
70  
Upper Respiratory Tract Infections and
Other Infections of the Oral Cavity and Neck
OBJECTIVES
1. Explain the anatomy and structures of the upper respiratory tract,
including the three parts of the pharynx.
2. Identify the principal causative organism of pharyngitis; name other
organisms capable of causing pharyngitis.
3. Define the following conditions: laryngitis, epiglottis, and parotitis.
List the etiologic organisms associated with these conditions.
4. Explain the pathogenic mechanisms (virulence factors) associated
with Streptococcus pyogenes pharyngitis.
5. Define Vincent’s angina and peritonsillar abscesses. What organism
do they share as the causative agent of disease?
6. Describe the disease process caused by pharyngeal infection with
Corynebacterium diphtheriae; name the hallmark symptom of this
infection and list the complications associated with infection.
7. Differentiate between stomatitis and thrush, and explain the testing
process for each disease.
8. Outline the steps used in the culture of specimens for the isolation
of Streptococcus pyogenes.
9. Explain the signs and symptoms and pathogenic mechanisms
associated with disease caused by Bordetella pertussis. What
special requirements are needed to detect this organism in Acute laryngitis is usually associated with the common
culture?
10. List three types of periodontal infections that require culture to
identify the causative agent of infection; name the bacteria
associated with these infections.
11. Explain the unique characteristics of C and G streptococcus, and
explain how they contribute to their pathogenesis.
GENERAL CONSIDERATIONS
ANATOMY
The respiratory tract is generally divided into two regions,
the upper and the lower.
The upper respiratory tract includes all the structures
down to the larynx: the sinuses, throat, nasal cavity, epi-
glottis, and larynx; the throat is also called the pharynx.
These anatomic structures are shown in Figure 70-1.
The pharynx is a tubelike structure that extends from
the base of the skull to the esophagus (see Figure 70-1).
Made of muscle, this structure is divided into three
parts:
• Nasopharynx (portion of the pharynx above the soft
palate)
• Oropharynx (portion of the pharynx between the soft
palate and epiglottis)
• Laryngopharynx (portion of the pharynx below the
epiglottis that opens into the larynx)
The oropharynx and nasopharynx are lined with strat-
ified squamous epithelial cells that are teeming with
microbial flora. The tonsils are contained within the oro-
pharynx; the larynx is located between the root of the
tongue and the upper end of the trachea.
892
PATHOGENESIS
An overview of the pathogenesis of respiratory tract
infections is presented in Chapter 69. It is important to
keep in mind that upper respiratory tract infections may
spread and become more serious because the mucosa
(mucous membrane) of the upper tract is continuous
with the mucosal lining of the sinuses, eustachian tube,
middle ear, and lower respiratory tract.
DISEASES OF THE UPPER RESPIRATORY
TRACT, ORAL CAVITY, AND NECK
UPPER RESPIRATORY TRACT
Diseases of the upper respiratory tract are named accord-
ing to the anatomic sites involved. Most of these infec-
tions are self-limiting, and the majority of infections are
of viral origin.
Laryngitis
cold or influenza syndromes. Characteristically, patients
complain of hoarseness and lowering or deepening of
the voice. Acute laryngitis is generally a benign illness.
Acute laryngitis is almost exclusively associated with
viral infection. Although numerous viruses can cause lar-
yngitis, influenza and parainfluenza viruses, rhinoviruses,
adenoviruses, coronavirus, and human metapneumovi-
rus are the most common etiologic agents. If examina-
tion of the larynx reveals an exudate or membrane on
the pharyngeal or laryngeal mucosa, streptococcal infec-
tion, mononucleosis, or diphtheria should be suspected
(see the discussion about miscellaneous infections caused
by other agents, presented later in this chapter). Chronic
laryngitis, although less frequently associated with infec-
tious agents, may be caused by bacteria or fungal isolates.
Infections have been identified that are associated with
methicillin-resistant Staphylococcus aureus (MRSA) and
Candida spp.
Laryngotracheobronchitis
Another clinical syndrome closely related to laryngitis is
acute laryngotracheobronchitis, or croup. Croup is a
relatively common illness in young children, primarily
those younger than 3 years of age. Of significance, croup
can represent a potentially more serious disease if the
infection extends downward from the larynx to involve
the trachea or even the bronchi. Illness is characterized
by variable fever, inspiratory stridor (difficulty in moving
enough air through the larynx), hoarseness, and a harsh,
barking, nonproductive cough. These symptoms last for
3 to 4 days, although the cough may persist for a longer
period. In young infants, severe respiratory distress and
fever are common symptoms.
 Upper Respiratory Tract Infections and Other Infections of the Oral Cavity and Neck   CHAPTER 70 893
Pharyngeal tonsil
(adenoids)
Nasopharynx
Palatine tonsil
Oropharynx
Soft
palate Epiglottis
Laryngopharynx
Lingual
tonsil
Vocal cords
Esophagus
Figure 70-1  The pharynx, including its three divisions and nearby
structures.
Similar to the etiologic agents of laryngitis, viruses are
a primary cause of croup; parainfluenza viruses are
the major etiologic agents. In addition to parainfluenza
viruses, influenza viruses, respiratory syncytial virus, and
adenoviruses can also cause croup.
Also capable of causing croup, though not as fre-
quently, are Mycoplasma pneumoniae, rhinoviruses, and
enteroviruses.
Epiglottitis
Epiglottitis is an infection of the epiglottis and other soft
tissues above the vocal cords. Infection of the epiglottis
can lead to significant edema (swelling) and inflamma-
tion. Most commonly, children between the ages of 2 and
6 years of age are infected. These children typically
present with fever, difficulty in swallowing because of
pain, drooling, and respiratory obstruction with inspira-
tory stridor. Epiglottitis is a potentially life-threatening
disease because the patient’s airway can become com-
pletely obstructed (blocked) if not treated.
In contrast to laryngitis, epiglottitis is usually associ-
ated with bacterial infections. In the past, 2- to 4-year-old
children were typically infected with Haemophilus influen-
zae type b as the primary cause of epiglottitis. However,
due to the common use of Haemophilus influenzae type b
conjugated vaccine, the typical patient is an adult with a
sore throat. Other organisms occasionally implicated are
streptococci and staphylococci. Diagnosis is established
on clinical grounds, including the visualization of the
epiglottis, which appears swollen and bright red in color.
Bacteriologic culture of the epiglottis is contraindicated
because swabbing of the epiglottis may lead to respira-
tory obstruction. Of importance, H. influenzae bactere-
mia usually occurs in children with epiglottitis caused by
this organism.
Pharyngitis, Tonsillitis, and Peritonsillar Abscesses
Pharyngitis and Tonsillitis.  Pharyngitis (sore throat) and ton-
sillitis are common upper respiratory tract infections
affecting both children and adults. Acute pharyngitis is an
illness that frequently causes people to seek medical care.
Clinical Manifestations.  Infection of the pharynx is
associated with pharyngeal pain. Visualization of the
pharynx reveals erythematous (red) and swollen tissue.
Depending on the causative microorganism, either
inflammatory exudate (fluid with protein, inflammatory
cells, and cellular debris), vesicles (small blister-like sacs
containing liquid) and mucosal ulceration, or nasopha-
ryngeal lymphoid hyperplasia (swollen lymph nodes)
may be observed.
Pathogenesis.  Pathogenic mechanisms differ and
depend on the organism causing the pharyngitis. For
example, some organisms directly invade the pharyngeal
mucosa (e.g., Arcanobacterium haemolyticum), others elabo-
rate toxins and other virulence factors at the site (e.g.,
Corynebacterium diphtheriae), and still others invade the
pharyngeal mucosa and elaborate toxins and other viru-
lence factors (e.g., group A streptococci [Streptococcus
pyogenes]). Pathogenic mechanisms are reviewed in Part
III according to various organism groups.
Epidemiology/Etiologic Agents.  Most cases of pharyn-
gitis occur during the colder months and often accom-
pany other infections, primarily those caused by viruses.
Patients with respiratory tract infections caused by influ-
enza types A and B, parainfluenza, coxsackie A, rhinovi-
ruses, or coronaviruses frequently complain of a sore
throat. Pharyngitis, often with ulceration, is also com-
monly found in patients with infectious mononucleosis
caused by either Epstein-Barr virus or cytomegalovirus.
Although less common, pharyngitis caused by adenovirus
or herpes simplex virus is clinically severe. Finally, acute
retroviral syndrome caused by human immunodeficiency
virus 1 (HIV-1) is associated with acute pharyngitis.
Although different bacteria can cause pharyngitis or
tonsillitis, the primary cause of bacterial pharyngitis is
Streptococcus pyogenes (or group A beta-hemolytic strepto-
cocci). Viral pharyngitis or other causes of pharyngitis/
tonsillitis must be differentiated from that caused by
S. pyogenes, because pharyngitis resulting from S. pyogenes
is treatable with penicillin and a variety of other anti-
microbials, whereas viral infections are not. In addition,
treatment is of particular importance because infection
with S. pyogenes can lead to complications such as acute
rheumatic fever and glomerulonephritis. These compli-
cations are referred to as poststreptococcal sequelae (dis-
eases that follow a streptococcal infection) and are
primarily immunologically mediated; these sequelae are
discussed in greater detail in Chapter 15. S. pyogenes may
also cause pyogenic infections (suppurations) of the
tonsils, sinuses, and middle ear, or cellulitis as secondary
pyogenic sequelae after an episode of pharyngitis. Accord-
ingly, streptococcal pharyngitis is usually treated to
prevent both the suppurative and nonsuppurative
sequelae, as well as to decrease morbidity.
Although bacteria other than group A streptococci
may cause pharyngitis, this occurs less often. Large
colony isolates of groups C and G streptococci (classified
as Streptococcus dysgalactiae subsp. equisimilis) are pyogenic
streptococci with similar virulence traits as S. pyogenes;
symptoms of pharyngitis caused by these agents are also
similar to S. pyogenes. In contrast to S. pyogenes, these
agents are rarely associated with poststreptococcal
sequelae, namely glomerulonephritis and possibly
894 PART VII  Diagnosis by Organ System

TABLE 70-1  Examples of Bacteria That Can Cause Acute

Pharyngitis and/or Tonsillitis BOX 70-1  Viral Agents That Can Cause Rhinitis

Organism Disease Relative Frequency Rhinoviruses

Coronaviruses
Streptococcus Pharyngitis/tonsillitis/ 15% to 35% Adenoviruses
pyogenes rheumatic fever/ Parainfluenza and influenza viruses
scarlet fever Respiratory syncytial virus
Enterovirus
Group C and G Pharyngitis/tonsillitis <3% to 11%
beta-hemolytic
streptococci
Peritonsillar Abscesses.  Peritonsillar abscesses are gen-
Arcanobacterium Pharyngitis/tonsillitis/ <1% to 10% erally considered a complication of tonsillitis. This infec-
(Corynebacterium) rash tion is most common in children older than 5 years of
haemolyticum age and in young adults. It is important to treat these
Neisseria Pharyngitis/ Rare* infections because they can spread to adjacent tissues, as
gonorrhoeae disseminated well as erode into the carotid artery to cause an acute
disease hemorrhage. The predominant organisms isolated in
Corynebacterium Pharyngitis Rare peritonsillar abscesses include non–spore-forming anaer-
ulcerans obes, such as Fusobacterium (especially F. necrophorum),
Bacteroides (including the B. fragilis group), and anaero-
Mycoplasma Pneumonia/ Rare bic cocci. Streptococcus pyogenes and viridans streptococci
pneumoniae bronchitis/ may also be involved.
pharyngitis
Yersinia Pharyngitis/ Rare Rhinitis
enterocolitica enterocolitis Rhinitis (common cold) is an inflammation of the nasal
Human Pharyngitis/acute Rare mucous membrane or lining. Depending on the host
immunodeficiency retroviral disease response and the etiologic agent, rhinitis is characterized
virus-1 by variable fever, increased mucous secretions, inflamma-
tory edema of the nasal mucosa, sneezing, and watery
*Less than 1%. eyes. With rare exceptions, rhinitis is typically associated
with viral infections (20%-25%); some of these agents are
rheumatic fever. Recent studies have demonstrated that listed in Box 70-1. Rhinitis is common because of the
these streptococci can exchange genetic information large number of different causative viruses, and reinfec-
with S. pyogenes and thus potentially obtain virulence tions may occur. Bacterial agents associated with rhinitis
factors usually associated with S. pyogenes such as M pro- (10%-15%) include Chlamydia pneumoniae, Mycoplasma
teins, streptolysin O, and superantigen genes. Arcanobac- pneumoniae, and Group A streptococci.
terium haemolyticum is also a cause of pharyngitis among
adolescents. Examples of agents that can cause pharyn- Miscellaneous Infections Caused by Other Agents.
gitis or tonsillitis are listed in Table 70-1. Corynebacterium diphtheriae.  Pharyngitis caused by Coryne-
Although H. influenzae, S. aureus, and S. pneumoniae are bacterium diphtheriae is less common than streptococcal
frequently isolated from nasopharyngeal and throat cul- pharyngitis. After an incubation period of 2 to 4 days,
tures, they have not been shown to cause pharyngitis. diphtheria usually presents as pharyngitis or tonsillitis.
Carriage of any of these organisms, as well as Neisseria Patients are often febrile and complain of sore throat
meningitidis, may have clinical importance for some and malaise (body discomfort). The hallmark for diph-
patients. Cultures of specimens obtained from the ante- theria is the presence of an exudate or membrane that
rior nares often yield S. aureus. The carriage rate for this is usually on the tonsils or pharyngeal wall. The gray-
organism is especially high among health care workers, white membrane is a result of the action of diphtheria
and 10%-30% of the general population can be colo- toxin on the epithelium at the site of infection. Compli-
nized with this microbe, depending on the population cations occur frequently with diphtheria and are usually
characteristics. seen during the last stage of the disease (paroxysmal
Vincent’s angina, also called acute necrotizing ulcer- stage). The most feared complications are those involv-
ative gingivitis, or trench mouth, is a mixed bacterial- ing the central nervous system such as seizures, coma, or
spirochetal infection of the gingival edge. The infection blindness. Information as to how this organism causes
is relatively rare today, but it is considered a serious disease disease is discussed in Chapter 69. Additional specifics
because it is often complicated by septic jugular thrombo- regarding this organism are provided in Chapter 17.
phlebitis, bacteremia, and widespread metastatic infec- Bordetella pertussis.  Although mass immunization pro-
tion. Adults are more often affected than children; poor grams have greatly reduced the incidence of pertussis,
oral hygiene is a predisposing factor. Multiple anaerobes, enough cases (because of outbreaks and regional epi-
especially Fusobacterium necrophorum, are implicated in this demics) still occur. In 2010, the CDC reported 27,500
syndrome. Although Gram stain of a throat specimen is cases of pertussis. This increased number of identifiable
usually not predictive, in those patients with symptoms cases may be due to improved awareness and improved
suggestive of Vincent’s angina, Gram stain reveals numer- diagnostic methods, such as nucleic acid-based testing. It
ous fusiform, gram-negative bacilli, and spirochetes. is important that laboratories are capable of detecting,
 Upper Respiratory Tract Infections and Other Infections of the Oral Cavity and Neck   CHAPTER 70 895
isolating, and identifying the organism, or the specimen
should be referred to a reference laboratory.
Characteristically, pertussis, or whooping cough, is a
prolonged disease (lasting as long as 6 to 8 weeks)
marked by paroxysmal (sudden or intense) coughing.
Following an incubation period of 7 to 13 days, the
patient with symptomatic infection develops upper respi-
ratory symptoms, including a dry cough, fever, runny
nose, and sneezing. After about 2 weeks, this may pro­
gress to spells of paroxysmal coughing. As these episodes
worsen, the characteristic whoop, caused by attempted
inspiration through an epiglottis undergoing spasm,
begins. Vomiting may occur, and usually a lymphocytosis
is present. This phase of the illness may last as long as 6
weeks. Bacterial culture for B. pertussis is effective using
nasopharyngeal specimens during the first 2 weeks when
symptoms are evident. Amplification and polymerase
chain reaction may demonstrate positive results within
0-4 weeks of the onset of symptoms. However, positive
results should be interpreted with caution and in correla-
tion with patient signs and symptoms. More information
regarding B. pertussis is provided in Chapter 37.
Klebsiella spp.  Rhinoscleroma is a rare form of chronic,
granulomatous infection of the nasal passages, including
the sinuses and occasionally the pharynx and larynx.
Associated with Klebsiella rhinoscleromatis and Klebsiella
ozaenae, the disease is characterized by nasal obstruction
appearing over a long period, caused by tumor-like
growth with local extension. K. ozaenae may contribute to
another infrequent condition called ozena, character-
ized by a chronic, mucopurulent nasal discharge that is
often foul smelling. It is caused by secondary, low-grade
anaerobic infection.
ORAL CAVITY
Stomatitis
Stomatitis is an inflammation of the mucous membranes
of the oral cavity. Herpes simplex virus is the primary
agent of this disease, in which multiple ulcerative lesions
are seen on the oral mucosa. These lesions are painful
and can be found in the mouth and in the oropharynx.
Herpetic infections of the oral cavity are prevalent among
immunosuppressed patients.
Thrush
Candida spp. can also invade the oral mucosa. Immuno-
suppressed patients, including very young infants, may
develop oral candidiasis, called thrush. Oral thrush can
extend to produce pharyngitis or esophagitis, a common
finding in patients with acquired immunodeficiency syn-
drome and in other immunosuppressed patients. Thrush
is suspected if whitish patches of exudate on an area of
inflammation are observed on the buccal (cheek)
mucosa, tongue, or oropharynx. Oral mucositis or phar-
yngitis in the granulocytopenic patient may be caused by
Enterobacteriaceae, S. aureus, or Candida spp. and is
manifested by erythema, sore throat, and possibly exudate
or ulceration.
Periodontal Infections
Types.  The three dental problems that may require
culture and identification in a clinical laboratory include
(1) root canal infections, with or without periapical
abscess; (2) orofacial odontogenic infections, with or
without osteomyelitis (inflammation of a bone) in the
jaw; and (3) perimandibular space infections. Oral bac-
teria are clearly important in other dental processes,
such as caries (destruction of the mineralized tissues of
the tooth; a cavity), periodontal (tissues in, around, and
supporting the tooth) disease, and localized juvenile
periodontitis, but clinical laboratories are not involved
in culturing in such cases.
Etiologic Agents.  The bacteriology is similar in all of
these infections and involves primarily anaerobic bacte-
ria and streptococci except for perimandibular space
infections, which may also involve staphylococci and
Eikenella corrodens in about 15% of patients. The strepto-
cocci are microaerobic or facultative and are usually
alpha-hemolytic (particularly the Streptococcus anginosus
group—see Chapter 15); they are usually found in 20%
to 30% of dental infections.
Members of the Bacteroides fragilis group are found in
root canal infections, orofacial odontogenic infections,
and bacteremia secondary to dental extraction in 5% to
10% of patients. Anaerobic cocci (both Peptostreptococcus
and Veillonella), pigmented Prevotella and Porphyromonas,
the Prevotella oralis group, and Fusobacterium are found in
about 20% to 50% of the three conditions mentioned,
as well as in postextraction bacteremia. Infection with
Actinomyces israelii may complicate oral surgery.
Salivary Gland Infections
Acute suppurative parotitis (inflammation of the salivary
glands located under the cheek in front of and below the
external ear) is seen in very ill patients, especially those
who are dehydrated, malnourished, elderly, or recover-
ing from surgery. It is associated with painful, tender
swelling of the parotid gland; purulent drainage may be
evident at the opening of the duct of the gland in the
mouth. Staphylococcus aureus is the major pathogen but
on occasion Enterobacteriaceae, other gram-negative
bacilli, and oral anaerobes may play a role in infection.
A chronic bacterial parotitis has been described involving
Staphylococcus aureus. Less often, other salivary glands may
be involved with a bacterial infection, usually because of
ductal obstruction.
The mumps virus is traditionally the major viral agent
involved in parotitis; however, since the advent of child-
hood vaccination, infection with mumps virus is rarely
diagnosed. Influenza virus and enteroviruses may also
cause this syndrome. Viral parotitis is typically diagnosed
using serology. Infrequently, Mycobacterium tuberculosis
may involve the parotid gland in conjunction with pul-
monary tuberculosis.
NECK
Infections of the deep spaces of the neck are potentially
serious because they may spread to critical structures such
as major vessels of the neck or to the mediastinum,
leading to mediastinitis, purulent pericarditis, and pleural
empyema. Oral flora is responsible for these infections.
Accordingly, the predominant organisms are anaerobes,
primarily Peptostreptococcus, various Bacteroides, Prevotella,
Porphyromonas, Fusobacterium spp., and Actinomyces.
896 PART VII  Diagnosis by Organ System
Streptococci, chiefly of the viridans variety, are also impor-
tant. Staphylococcus aureus and various aerobic, gram-
negative bacilli may be recovered, particularly from
patients developing these problems in the hospital.
Scrofula is a tuberculous infection in the lymph nodes
of the neck that may be associated with Mycobacterium tuber-
culosis, Mycobacterium scrofulaceum, or Mycobacterium avium.
The characteristic signs and symptoms include painless
swelling of the lymph nodes with the rare appearance of
fever or ulcerations. Diagnosis may require bacterial
culture of the lymph nodes, computed tomography (CT)
of the neck, biopsy, and chest x-ray or PPD (purified
protein derivative) testing associated with M. tuberculosis.
DIAGNOSIS OF UPPER RESPIRATORY
TRACT INFECTIONS
COLLECTION AND TRANSPORT
OF SPECIMENS
Sterile, Dacron, or Rayon swabs with plastic shafts are suit-
able for collecting most upper respiratory tract microor-
ganisms. Flocked swabs may also be used when available.
If the swab remains moist, no further precautions need to
be taken for specimens cultured within 4 hours of collec-
tion. After that period, transport medium is required to
maintain viability and prevent overgrowth of contaminat-
ing organisms. Swabs for detection of group A strepto-
cocci (Streptococcus pyogenes) are the only exception. This
organism is highly resistant to desiccation and remains
viable on a dry swab for as long as 48 to 72 hours. These
throat swabs can be placed in glassine paper envelopes for
mailing or transport to a distant laboratory. Throat swabs
are also adequate for recovery of adenoviruses and herpes
viruses, Corynebacterium diphtheriae, Mycoplasma, Chlamydia,
and Candida spp. Recovery of C. diphtheriae is enhanced
by culturing both the throat and nasopharynx.
Nasopharyngeal swabs are better suited for recovery
of Bordetella pertussis, Neisseria spp., along with several
viruses including respiratory syncytial virus, parainflu-
enza virus, and the other viruses causing rhinitis.
Optimum conditions for the collection and transport of
specimens for viral detection or culture are described in
Chapter 65. Although swabs made of calcium alginate are
commonly used to collect nasopharyngeal specimens
(excluding those specimens for chlamydia or viral
culture), nasopharyngeal secretions collected by either
aspiration or washing will improve recovery for Bordetella
pertussis because a larger amount of material is obtained.
The type of swab used for collection is very important.
For example, cotton swabs should never be used for
culture because fibers contain fatty acids on the surface,
which are capable of killing Bordetella. Calcium alginate or
Dacron swabs are acceptable for obtaining nasopharyn-
geal swab specimens, with calcium alginate being optimal
for culture. However, if polymerase chain reaction (PCR)
is to be performed, Dacron or rayon swabs on plastic shafts
are preferred. Specimens for B. pertussis ideally should be
inoculated directly to fresh culture media at the patient’s
bedside. If this is not possible, transport for less than 2
hours in 1% Casamino acid medium at room temperature
is acceptable. If specimens are plated on the day of collec-
tion, Amies transport medium with charcoal is acceptable.
If specimens are plated more than 24 hours after collec-
tion, Regan-Lowe or Jones-Kendrick transport medium is
optimal; both contain charcoal, starch, and nutrients as
well as cephalexin. If lengthy delays in transport are
expected, transport of specimens in Regan-Lowe medium
at 4°C is recommended.
DIRECT VISUAL EXAMINATION OR DETECTION
A Gram stain of material obtained from upper respira-
tory secretions or lesions may not improve diagnosis.
Yeast-like cells can be identified, which are helpful in
identifying thrush, and the characteristic pattern of fusi-
form and spirochetes of Vincent’s angina may be visual-
ized. Gram’s crystal violet (allowed to remain on the slide
for 1 minute before rinsing with tap water) and the Gram
stain can be used to identify the spirilla and fusiform
bacilli of Vincent’s angina. However, if crystal violet is
used, the smear should be very thin because everything
will be intensely Gram positive, making a thick smear
difficult to read. Additionally, spirilla and bacilli may be
stained using a dilute solution of carbol fuchsin.
For causes of pharyngitis, Gram stains are unreliable.
Direct smears of exudate from membrane-like lesions
used to differentiate diphtheria from other causes are
also not reliable or recommended.
Fungal elements, including yeast cells and pseudohy-
phae, may be visualized with a 10% potassium hydroxide
(KOH) preparation, calcofluor white fluorescent stain,
or periodic acid-Schiff (PAS) stain. Direct examination
of material obtained from the nasopharynx of suspected
cases of whooping cough using a fluorescent antibody
stain (see Chapter 37) has been shown to yield some
early positive results for detection of B. pertussis. However,
direct fluorescent antibody (DFA) staining of nasopha-
ryngeal secretions often lack sensitivity and specificity
depending on the antibody used. Numerous studies have
demonstrated that PCR-based assays for B. pertussis in
nasopharyngeal secretions are superior to both DFA and
culture. Various methods, including fluorescent antibody
stain reagents, enzyme immunoassays, and nucleic acid
amplification methods are also commercially available to
detect numerous viral agents (see Chapter 65).
Improvement in the development of rapid methods for
detection of group A streptococcal antigen or nucleic acid
has obviated the need for culture of pharyngeal speci-
mens. At least 40 commercial products are available to
identify group A streptococcal antigens using membrane
enzyme immunoassays or liposomal and optical immuno-
assay techniques. Although the specific procedures vary
with the products, several generalizations can be made.
Throat swabs are incubated in an acid reagent or enzyme
to extract the group A specific carbohydrate antigen.
Dacron swabs seem to be most efficient at releasing
antigen, although other types of swabs may yield accept-
able results. In laboratory comparisons between a rapid
antigen method and conventional culture methods for
detecting the presence of group A streptococci in throat
swabs, the commercial kits have shown relatively accept-
able (62% to more than 90%) sensitivity and specificity.
 Upper Respiratory Tract Infections and Other Infections of the Oral Cavity and Neck   CHAPTER 70 897
Specimens with a negative direct antigen test for group A
streptococci should be cultured (requires collection of
specimen with two swabs) or confirmed using a nucleic
acid method. Group A streptococci can be directly detected
from pharyngeal specimens by nucleic acid testing using
different molecular assay formats. The commercially avail-
able assay (Probe Group A Strep Direct Test (GAS Direct),
Hologic-GenProbe, Inc., San Diego, California) that
employs a nonisotopic, chemiluminescent, single-stranded
DNA probe complementary to the rRNA target of the
group A Streptococcus. The assay detects organisms directly
from swab specimens by lysing the bacterial cells before
amplification. Dacron swabs are acceptable for use with
this assay. Sensitivities of the Gen-Probe Group A Strep
Direct Test range from 91.7% to 99.3% when compared
with culture. A rapid-cycle real-time PCR method, the
Light Cycler Strep-A (Roche Applied Science, Indianapo-
lis, Indiana), also detects S. pyogenes directly from throat
swabs. Using this technology, 32 samples (including con-
trols) can be tested per run in about 1.5 hours. Isothermol
DNA amplification is also available for the detection of
Group A Streptococcus from throat swabs (Illumigene
Group A Streptococcus, Meridian Bioscience, Inc., Cincin-
nati, Ohio) and demonstrates sensitivity equal to the
Group A Strep Direct test. See Chapter 8 for more infor-
mation on isothermal DNA amplification.
CULTURE
Streptococcus pyogenes (Beta-Hemolytic
Group A Streptococci)
Because the primary cause of bacterial pharyngitis in
North America is Streptococcus pyogenes, most laboratories
routinely screen throat cultures for this organism. Group
A streptococci are usually beta-hemolytic, with less than
1% being nonhemolytic. Three variables must be taken
into consideration regarding successful culture of group
A streptococci from pharyngeal specimens: medium,
atmosphere, and duration of incubation. Kellogg recom-
mended four combinations of media and atmosphere of
incubation for throat specimens; these are listed in Table
70-2. Regardless of the medium and atmosphere of incu-
bation employed, culture plates should be incubated for
at least 48 hours before reporting as negative for group A
streptococci. In addition, the incubation of sheep blood
agar in 5% to 10% CO2 was strongly discouraged.
Drawbacks to culture include an extended incubation
time of 24 to 48 hours for visible colony formation with
TABLE 70-2  Medium and Atmosphere for Incubation of Cultures
to Recover Group A Streptococci from Pharyngeal Specimens
Media Atmosphere of Incubation
Sheep blood agar Anaerobic
Sheep blood agar with coverslip Aerobic
over the primary area of
inoculation
Sheep blood agar with 5%-10% CO2 or anaerobic
trimethoprim-sulfamethoxazole
additional manipulations of the beta-hemolytic organ-
isms for definitive identification (see Chapter 15). If suf-
ficient numbers of pure colonies are not available for
identification, a subculture requiring additional incuba-
tion is necessary. By placing a 0.04-unit differential baci-
tracin filter paper disk, available commercially directly
on the area of initial inoculation, presumptive identifica-
tion of S. pyogenes can be made after overnight incubation
(all of group A and a very small percentage of group B
streptococci are susceptible). However, use of the baci-
tracin disk in the primary area of inoculation reduces the
sensitivity and specificity of culture and identification of
S. pyogenes. Sometimes growth of too few beta-hemolytic
colonies or overgrowth of other organisms makes inter-
pretation difficult. Therefore, using the bacitracin disk
as the only method of identification of S. pyogenes is not
recommended. New selective agars, such as streptococcal
selective agar, have been developed that suppress the
growth of almost all normal flora and beta-hemolytic
streptococci except for groups A and B and Arcanobacte-
rium haemolyticum. Direct antigen or nucleic detection
tests or the PYR test (see Chapter 15) can also be carried
out on isolated beta-hemolytic colonies.
Corynebacterium diphtheriae
If diphtheria is suspected, the physician must communi-
cate this information to the clinical laboratory. Because
streptococcal pharyngitis is included in the differential
diagnosis of diphtheria and because dual infections do
occur, cultures for Corynebacterium diphtheriae should be
plated onto sheep blood agar or streptococcal selective
agar, as well as onto special media for recovery of this
agent. These special media include a Loeffler’s agar slant
and a cystine-tellurite agar plate. Chapter 17 discusses
the identification of the organism. Recovery of this
organism is improved when culturing specimens from
the throat and nasopharynx of potentially infected
patients. In addition to culture, rapid toxigenicity assays,
including immunoassays and polymerase chain reaction,
may be used to assist in the diagnosis. Caution should be
used when interpreting molecular assays, because posi-
tive results have been associated with related species of
Corynebacteria.
Bordetella pertussis
Freshly prepared Bordet-Gengou agar was the first
medium developed for isolation of Bordetella pertussis.
However, because it was inconvenient to use, other media
were subsequently developed (see Chapter 37). Today,
Regan-Lowe or charcoal horse blood agar is recom-
mended for use in diagnostic laboratories. Because the
organisms are extremely delicate, specimens should be
plated directly onto media, if possible. The yield of posi-
tive isolations from clinical cases of pertussis seems to
vary from 20% to 98% depending on the stage of disease,
previous treatment of the patient, age of the patient, and
laboratory techniques. Due to the fastidious growth
requirements, additional methods, including 16SrRNA
sequencing and matrix-assisted laser desorption ioniza-
tion time-of-flight mass spectrometry (MALDI-TOF)
have proven effective. See Chapter 7 for a description of
MALDI-TOF methodology.
898 PART VII  Diagnosis by Organ System
Neisseria
Specimens received in the laboratory for isolation of Neis-
seria meningitidis (for detection of carriers) or N. gonorrhoeae
should be plated to a selective medium, either modified
Thayer-Martin or Martin-Lewis agar. After 24 to 48 hours of
incubation in 5% to 10% carbon dioxide, typical colonies
of Neisseria spp. may be visible (see Chapter 40).
Epiglottitis
Clinical specimens from cases of epiglottitis (swabs
obtained by a physician) should be plated to sheep blood
agar, chocolate agar (for recovery of Haemophilus spp.),
and a streptococcal selective medium. Staphylococcus
aureus, Streptococcus pneumoniae, and beta-hemolytic strep-
tococci are all potential etiologic agents of this disease.
Refer to Table 5-1 for an overview of the methods used
to collect, transport, and process different specimens
from the upper respiratory tract.
DIAGNOSIS OF INFECTIONS IN THE
ORAL CAVITY AND NECK
COLLECTION AND TRANSPORT
It is important to avoid or minimize contamination with
oral flora when collecting oral and dental material for
diagnosis of infection. For collection of material from
root canal infection, the tooth is isolated by means of a
rubber dam. A sterile field is established, the tooth is
swabbed with 70% alcohol, and after the root canal is
exposed, a sterile paper point is inserted, removed, and
placed into semisolid, nonnutritive, anaerobic transport
CASE STUDY  70-1 
A 2-year-old girl presented to her physician with a sore throat
and fever. On examination, her tonsils were enlarged and
inflamed. A rapid test was performed for group A streptococci;
the test result was negative. The physician decided to treat with
amoxicillin regardless of the test results and asked that a culture
be performed. The next day the laboratory reported that moder-
ate growth of beta-hemolytic group A streptococcus was present.
QUESTIONS
1. List the tests that rapidly identify group A Streptococcus
(Streptococcus pyogenes).
BIBLIOGRAPHY
Bourbeau PP: Role of the microbiology laboratory in diagnosis and
management of pharyngitis, J Clin Microbiol 41:3467, 2003.
Bourbeau PP, Heiter BJ: Use of swabs without transport media for the
Gen-Probe Group A Strep Direct Test, J Clin Microbiol 42:3207, 2004.
Cambier M, Janssens M, Wauters G: Isolation of Arcanobacterium haemo-
lyticum from patients with pharyngitis in Belgium, Acta Clin Belg
47:303, 1992.
Cassiday PK, Sanden GN, Kane CT, et al: Viability in Bordetella pertussis
in four suspending solutions at three temperatures, J Clin Microbiol
32:1550, 1994.
Cloud JL, Hymas W, Carroll KC: Impact of nasopharyngeal swab types
on detection of Bordetella pertussis by PCR and culture, J Clin Microbiol
40:3838, 2002.
Hallander HO, Reizenstein E, Renemar B, et al: Comparison of naso-
pharyngeal aspirates with swabs for culture of Bordetella pertussis, J
Clin Microbiol 31:50, 1993.
medium. Alternatively, needle aspiration can be used if
sufficient purulent material is present. Completely defin-
ing the flora of such infections is beyond the scope of
routine clinical microbiology laboratories.
Specimens from neck space infections can usually be
obtained with a syringe and needle or by biopsy during
a procedure by the surgeon. Transport must be under
anaerobic conditions.
DIRECT VISUAL EXAMINATION
All material submitted for culture should be smeared
and examined by Gram stain and other appropriate tech-
niques for fungi (i.e., calcofluor white, KOH, or PAS
stains), if requested.
CULTURE
Infections such as peritonsillar abscesses, oral and dental
infections, and neck space infections usually involve
anaerobic bacteria. The anaerobes involved typically
originate in the oral cavity and are often more delicate
than anaerobes isolated from other clinical material.
Very careful methods are required in order to provide
optimal specimens for anaerobic cultivation, as well as
collection and transport for the recovery and identifica-
tion of the etiologic agents. See Chapter 41 for more
information related to anaerobic organisms.
Visit the Evolve site to complete
the review questions.
2. Not all group A streptococci are S. pyogenes. How can the
nonpathogenic group A streptococci be differentiated from the
pathogenic strains?
3. Not all S. pyogenes are beta-hemolytic. What is the reason for this
phenomenon, and how can the laboratory ensure detection of the
nonhemolytic strains?
4. What is the sensitivity of rapid diagnostic tests to detect group A
streptococcal antigen?
Kellogg JA: Suitability of throat culture procedures for detection of
group A streptococci and as reference standards for evaluation of
streptococcal antigen kits, J Clin Microb 28:165, 1990.
Kobayashi RH, Rosenblatt HM, Carney JM, et al: Candida esophagitis
and laryngitis in chronic mucocutaneous candidiasis, Pediatrics
66(3):380-384, 1980.
Liakos T, Kaye K, Rubin AD: Methicillin-resistant Staphylococcus
aureus laryngitis, Ann Otol Rhinol Laryngol 119(9):590-593, 2010.
Mandell GL, Bennett JE, Dolin R, editors: Principles and practice of infectious
diseases, ed 7, Philadelphia, 2010, Elsevier Churchill Livingstone.
McGowan KL: Diagnostic tests for pertussis: culture vs. DFA vs. PCR,
Clin Microbiol Newsl 24:143, 2002.
Moulis G, Martin-Blondel G: Scrofula, the king’s evil, CMAJ 184(9):2012.
Sachse S, Seidel P, Gerlach D, et al: Superantigen-like gene(s) in human
pathogenic Streptococcus dysgalactiae, subsp. equisimilis: genomic local-
ization of the gene encoding streptococcal pyrogenic exotoxin G
(spe Gdys), FEMS Immunol Med Microbiol 34:159, 2002.
Versalovic J: Manual of clinical microbiology, ed 10, Washington, DC,
2011, ASM Press.
 Upper Respiratory Tract Infections and Other Infections of the Oral Cavity and Neck   CHAPTER 70 898.e1

10. True or False

CHAPTER REVIEW _____ Gram stains of material collected from upper respiratory
secretions or lesions can serve as a valuable tool when
1. What is the hallmark physical manifestation for infections with
used to determine the cause of pharyngitis.
Corynebacterium diphtheriae?
_____ Cotton swabs should always be used for the culture of
a. malaise
Bordetella pertussis because the fibers contain fatty acids
b. presence of an exudates or membrane on the tonsils or
on the surface, which enhance the growth of Bordetella in
pharyngeal wall
culture.
c. presence of white vesicles on the tonsils or pharyngeal wall
_____ Swabs collected from the upper respiratory tract, as long as
d. edema and inflammation of the tonsils and pharyngeal wall
they remain moist, do not need to be put in transport
2. What is the primary cause of stomatitis, inflammation of the medium when cultured within 4 hours of collection.
mucous membranes of the oral cavity? _____ Pharyngitis caused by adenovirus or herpes simplex virus is
a. herpes simplex virus usually less severe than pharyngitis caused by other viruses.
b. Klebsiella spp. _____ If a child presents with a red swollen epiglottis, the epiglottis
c. Candida spp. should be swabbed to determine the etiologic agent.
d. Enterobacteriaceae _____ Studies have demonstrated that group C and group G
3. What is the primary etiologic agent in children with epiglottis? streptococci can exchange genetic information with
a. Haemophilus influenzae type b S. pyogenes and potentially obtain virulence factors
b. Corynebacterium diphtheriae normally associated with S. pyogenes.
c. Streptococcus pyogenes 11. Matching: Match the term with the appropriate definition.
d. Staphylococcus aureus _____ Vincent’s angina a. inflammation of bone
4. Peritonsillar abscesses are caused by all of the following bacteria, _____ parotitis b. granulomatous infection of
except: _____ inflammatory exudates the nasal passages
a. Fusobacterium _____ poststreptococcal sequelae c. difficulty in moving air
b. Bacteroides _____ malaise through the larynx
c. Anaerobic cocci _____ paroxysmal d. sudden/intense
d. S. pneumoniae _____ inspiratory stridor e. acute necrotizing ulcerative
5. Oral thrush is a disease often found in what population of patients? _____ Rhinoscleroma gingivitis
a. adults older than 65 years of age _____ ozena f. swollen salivary glands
b. young adults 18 to 24 years of age _____ osteomyelitis g. diseases that follow a
c. immunocompromised patients streptococcal infection
d. children younger than 12 years of age h. foul-smelling macropurulent
nasal discharge
6. What virus traditionally causes viral parotitis?
i. fluid filled with protein
a. influenza virus
j. body discomfort
b. parainfluenza virus
c. rhinovirus 12. Short Answer
d. mumps virus 1. What complications can arise from an untreated case of
7. Which of the following organisms is highly resistant to desiccation pharyngitis caused by Streptococcus pyogenes? What is the
and remains viable on a dry swab for as long as 48 to 72 hours? general term used to describe these complications?
a. Corynebacterium diphtheriae 2. Explain what causes the production of the gray, white membrane
b. Bordetella pertussis on the pharyngeal wall in patients infected with C. diphtheriae.
c. Streptococcus pyogenes 3. What produces the “whoop” in the cough of individuals infected
d. Haemophilus influenzae type b with Bordetella pertussis?
8. Which of the following swabs cannot be used for respiratory
specimens intended for viral testing?
a. cotton swabs
b. Dacron swabs
c. calcium alginate swabs
d. rayon swabs
9. Loeffler’s agar slant is a special culture medium used to recover
which organism?
a. Streptococcus pyogenes
b. Corynebacterium diphtheriae
c. Bordetella pertussis
d. Neisseria meningitidis