topics

patients should brush the buccal mucosa, tongue, and gums with a wet toothbrush. As an alternative, an aerosolinduced specimen may be collected for the isolation of mycobacterial or fungal agents. Induced sputum is also

recognized for its high diagnostic yield in cases of Pneumocystis jiroveci pneumonia. Aerosol-induced

specimens are collected 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

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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 children. Before the patient wakes up in the morning, a

nasogastric tube is inserted into the stomach and contents are withdrawn (on the assumption that acid-fast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

relative resistance of mycobacteria to acidity allows them to remain viable for a short period. Gastric aspirate

specimens must be delivered to the laboratory immediately so that the acidity can be neutralized. Specimens

can be 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. 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

pathogens. 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 bronchoalveolar

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 bronchoscopy has dramatically affected the evaluation and management

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

transbronchial biopsy for the evaluation of lung cancer and other lung diseases. Although transbronchial biopsy

is important, 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 specimens

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 contaminated with upper respiratory tract flora such as viridians

streptococci and Neisseria spp. Recovery of potentially pathogenic organisms from bronchial washings should

be attempted.

A deep sampling of desquamated host cells and secretions can be collected through bronchoscopy and BAL.

Lavages are especially suitable for detecting Pneumocystis 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 technique 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

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bacterial colonies per milliliter of BAL fluid. BAL has been shown to be a safe and practical method for

diagnosing opportunistic pulmonary infections in immunosuppressed 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

bronchoscopy examination. Specimens obtained by this moderately invasive collection procedure are suited for

microbiologic studies, particularly in aspiration pneumonia. Protected specimen brush bristles collect from

0.001 to 0.01 mL of material, Upon receipt, contents of the bronchial brush may be suspended in 1 mL of broth

solution with vigorous vortexing and inoculated onto culture media using a 0.01-mL calibrated inoculating

loop. Some researchers have indicated that specimens obtained via double-lumen–protected catheters are

suitable for both anaerobic and aerobic cultures.

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.

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

invasive 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 technique is rarely used, anaerobes, such as Actinomyces and those associated with aspiration

pneumonia, can be isolated 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

bacteriology of an associated pneumonia.

Blood 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,

thrombocytopenia, or pulmonary hypertension may be at increased risk of complication (primarily

pneumothorax [air in the pleural space] or bleeding) from this procedure.

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

diagnosing severe viral infections, such as herpes simplex pneumonia, for rapid diagnosis of Pneumocystis

pneumonia, and for other hard-to-diagnose or life-threatening pneumonias.

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Specimen processing:

Direct Visual Examination:

Lower respiratory tract specimens can be examined by direct wet preparation for parasites and special

procedures 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

expectorated sputum received for routine bacteriologic culture.

A portion of the specimen consisting of purulent material 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

unacceptable.

An acceptable specimen yields fewer than 10 squamous 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 presence of 25 or more polymorphonuclear leukocytes per 100× field, together with few squamous

epithelial cells, implies an excellent specimen.

Samples that contain predominantly upper respiratory tract material 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 acceptable specimen from patients with CF in selected clinical settings and should be processed in a

Figure 1Gram 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 squamousepithelial cells and rare

polymorphonuclear leukocytes, indicating an inadequate specimen for routine sputum culture.

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similar manner as CF sputum. Staining of respiratory samples is useful and should be compared to culture

results to reveal errors in procedures, specimen collection, and transport or specimen identification.

Respiratory secretions may need to be concentrated before staining. The cytocentrifuge instrument has been

used successfully for this purpose, concentrating the cellular 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

cultures.

For screening purposes, the presence of ciliated columnar bronchial epithelial cells, goblet cells, or pulmonary

macrophages in specimens obtained by bronchoscopy 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. Auramine or auramine-rhodamine is also used to detect

acidfast 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,

Actinomyces, 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 procedure.

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 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 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, Legionella culture, DFA or urinary antigen, and serology

should be performed for optimum sensitivity.

Commercially available DFA reagents are also used to detect antigens of numerous viruses, including herpes

simplex, cytomegalovirus, adenovirus, influenza viruses, and RSV .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 pneumonia.

A number of molecular amplification techniques 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 smearpositive

specimens.

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Rapid direct detection from respiratory samples is now available using nucleic acid-based methods. The xTAG

Respiratory Viral Panel (RVP) , can be used for the simultaneous detection of influenza (four types), RSV,

human metapneumovirus,

and adenovirus from nasopharyngeal swabs. In addition, the FilmArray Respiratory Panel 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 pneumonia 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. All of the previously mentioned methods are FDA-approved.

In addition to these, there are a variety of research-useonly 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

chocolate agar for Haemophilus and Neisseria spp. Because of contaminating oral flora, sputum specimens,

specimens obtained by bronchial washing and lavage, tracheal aspirates, 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 protected bronchial brush are suitable for

anaerobic culture; the latter must be done quantitatively for proper interpretation. 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

semiquantitatio 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 specimens contaminated by

normal oropharyngeal flora (e.g., expectorated and induced sputum, bronchial washings), growth of the

predominant aerobic and facultative anaerobic 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 respiratory tract infections are not detected by routine bacteriologic

culture. Mycobacteria, Chlamydia, Nocardia, Bordetella pertussis, Legionella, and Mycoplasma pneumonia

require special procedures for detection; this also applies

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to viruses and fungi. Optimal recovery for Mycobacterium tuberculosis requires multiple specimens for acidfast staining 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 information 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.

Upper Respiratory Tract Infections and other Infections of the Oral Cavity and Neck:

The upper respiratory tract includes all the structures down to the larynx: the sinuses, throat, nasal cavity,

epiglottis, and larynx; the throat is also called the pharynx.

The pharynx is a tubelike structure that extends from the base of the skull to the esophagus. 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 stratified squamous epithelial cells that are teeming with

microbial flora. The tonsils are contained within the oropharynx; the larynx is located between the root of the

tongue and the upper end of the trachea.

Pathogenesis

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

Diseases of the upper respiratory tract are named according to the anatomic sites involved. Most of these

infections are self-limiting, and the majority of infections are of viral origin.

Laryngitis:Acute laryngitis is usually associated with the common 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

laryngitis, adenoviruses, coronavirus, and human metapneumovirus are the most common etiologic agents.

If examination of the larynx reveals an exudate or membrane on the pharyngeal or laryngeal mucosa,

streptococcal infection, mononucleosis, or diphtheria should be suspected. Chronic laryngitis, although less

frequently associated with infectious 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.

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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 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 frequently, 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 inflammation. 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 inspiratory stridor. Epiglottitis is a

potentially life-threatening disease because the patient’s airway can become completely obstructed (blocked) if

not treated.

In contrast to laryngitis, epiglottitis is usually associated with bacterial infections. In the past, 2- to 4-year-old

children were typically infected with Haemophilus influenza 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

respiratory obstruction. Of importance, H. influenzae bacteremia usually occurs in children with epiglottitis

caused by this organism.

Pharyngitis and Tonsillitis:Pharyngitis (sore throat) and tonsillitis 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

nasopharyngeal 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

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elaborate toxins and other virulence factors at the site (e.g., Corynebacterium diphtheriae), and still others

invade the pharyngeal mucosa and elaborate toxins and other virulence factors (e.g., group A streptococci

[Streptococcus pyogenes]).

Epidemiology/Etiologic Agents. Most cases of pharyngitis occur during the colder months and often

accompany other infections, primarily those caused by viruses. Patients with respiratory tract infections caused

by influenza types A and B, parainfluenza, coxsackie A, rhinoviruses, or coronaviruses frequently complain of

a sore throat. Pharyngitis, often with ulceration, is also commonly 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 streptococci).

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

antimicrobials, 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 complications are referred to as poststreptococcal sequelae (diseases that follow a streptococcal

infection) and are primarily immunologically mediated.

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. Accordingly, 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 rheumatic fever.

Recent studies have demonstrated that these streptococci can exchange genetic information with S. pyogenes

and thus potentially obtain virulence factors usually associated with S. pyogenes such as M proteins,

streptolysin O, and superantigen genes. Arcanobacterium haemolyticum is also a cause of pharyngitis among

adolescents. Examples of agents that can cause pharyngitis or tonsillitis are listed in (Table 1).

Table 1: Examples of bacteria that can cause acute pharyngitis and/or tonsillitis:

Organism Disease RelativeFrequency

Pharyngitis/tonsillitis/ rheumatic 15% to 35%

fever/ scarlet fever

Streptococcus

Pyogenes

Group C and G beta-hemolytic Pharyngitis/tonsillitis <3% to 11%

streptococci

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Pharyngitis/tonsillitis/ <1% to 10%

Pharyngitis/ disseminated Rare*

Disease

Neisseria

gonorrhoeae

Corynebacterium Pharyngitis Rare

ulcerans

Pneumonia/bronchitis/ Rare

Pharyngitis

Mycoplasma

pneumoniae

Yersinia Pharyngitis/enterocolitis Rare

enterocolitica

Human immunodeficiency Pharyngitis/acute retroviral disease Rare

virus-1

Although H. influenzae, S. aureus, and S. pneumoniae are frequently isolated from nasopharyngeal and throat

cultures, they have not been shown to cause pharyngitis. Carriage of any of these organisms, as well as

Neisseria meningitidis, may have clinical importance for some patients. Cultures of specimens obtained from

the anterior often yield S. aureus. The carriage rate for this organism is especially high among health care

workers, and 10%-30% of the general population can be colonized with this microbe, depending on the

population characteristics.

Vincent’s angina, also called acute necrotizing ulcerative gingivitis, or trench mouth, is a mixed

bacterialspirochetal infection of the gingival edge. The infection is relatively rare today, but it is considered a

serious disease because it is often complicated by septic jugular thrombophlebitis, bacteremia, and widespread

metastatic infection.

Adults are more often affected than children; poor oral hygiene is a predisposing factor. Multiple anaerobes,

especially Fusobacterium necrophorum, are implicated in this syndrome. Although Gram stain of a throat

specimen is usually not predictive, in those patients with symptoms suggestive of Vincent’s angina, Gram stain

reveals numerous fusiform, gram-negative bacilli, and spirochetes.

Peritonsillar Abscesses:Peritonsillar abscesses are generally considered a complication of tonsillitis. This

infection is most common in children older than 5 years of age and in young adults. It is important to treat these

infections because they can spread to adjacent tissues, as well as erode into the carotid artery to cause an acute

hemorrhage. The predominant organisms isolated in peritonsillar abscesses include non–spore-forming

anaerobes, such as Fusobacterium (especially F. necrophorum), Bacteroides (including the B. fragilis group),

and anaerobic cocci. Streptococcus pyogenes and viridans streptococci may also be involved.

Rhinitis:Rhinitis (common cold) is an inflammation of the nasal mucous membrane or lining. Depending on

the host response and the etiologic agent, rhinitis is characterized by variable fever, increased mucous

secretions, inflammatory edema of the nasal mucosa, sneezing, and watery eyes. With rare exceptions, rhinitis

is typically associated with viral infections (20%-25%); some of these agents are listed in (Table 1). Rhinitis is

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common because of the large number of different causative viruses, and reinfections may occur. Bacterial

agents associated with rhinitis (10%-15%) include Chlamydia pneumoniae, Mycoplasma

pneumoniae, and Group A streptococci.

(Table 1): Viral Agents That Can Cause Rhinitis:

Rhinoviruses

Coronaviruses

Adenoviruses

Parainfluenza and influenza viruses

Respiratory syncytial virus

Enterovirus

Miscellaneous Infections Caused by Other Agents:

Corynebacterium diphtheriae. Pharyngitis caused by Corynebacterium diphtheriae is less common than

streptococcal pharyngitis. After an incubation period of 2 to 4 days, diphtheria usually presents as pharyngitis

or tonsillitis.

Patients are often febrile and complain of sore throat and malaise (body discomfort). The hallmark for

diphtheria is the presence of an exudate or membrane that is usually on the tonsils or pharyngeal wall. The

graywhite

membrane is a result of the action of diphtheria toxin on the epithelium at the site of infection. Complications

occur frequently with diphtheria and are usually seen during the last stage of the disease (paroxysmal stage).

The most feared complications are those involving the central nervous system such as seizures, coma, or

blindness.

Bordetella pertussis. Although mass immunization programs have greatly reduced the incidence of pertussis,

enough cases (because of outbreaks and regional epidemics) still occur. In 2010, the CDC reported 27,500

cases of pertussis. This increased number of identifiable cases may be due to improved awareness and

improved diagnostic methods, such as nucleic acid-based testing.

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, characterized by a chronic, mucopurulent nasal discharge that is

often foul smelling. It is caused by secondary, low-grade anaerobic infection.

ORAL CAVITY: 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.

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Thrush: Candida spp. can also invade the oral mucosa. Immunosuppressed 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 syndrome 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 pharyngitis in the

granulocytopenic patient may be caused by Enterobacteriaceae, S. aureus, or Candida spp. and is

manifested by erythema, sore throat, and possibly exudates or ulceration.

Diagnosis of upper respiratory tract infections:

Collection and transport of specimens:

Sterile swabs are suitable for collecting most upper respiratory tract microorganisms. Swabs for detection of

group A streptococci (Streptococcus pyogenes) are the only exception. 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, parainfluenza virus, and the other viruses causing rhinitis.

nasopharyngeal secretions collected by either aspiration or washing

Direct visual examination or detection

A Gram stain of material obtained from upper respiratory secretions or lesions may not improve diagnosis.

Yeast-like cells can be identified, which are helpful in identifying thrush, and the characteristic pattern of

fusiform and spirochetes of Vincent’s angina may be visualized. 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 pseudohyphae, 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 has been shown to yield some early positive results for detection of B. pertussis.

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10/11/22

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