Fungal:

Candida spp.

Cryptococcus neoformans

Coccidioides immitis

Sporothrix schenckii

Viral:

Hepatitis B

Mumps

Rubella

Other viruses (rarely)

infectious arthritis is a prominent feature associated with Lyme disease. Chronic monoarticular arthritis is

frequently due to mycobacteria, Nocardia asteroides, and fungi. Some of the more frequently encountered

etiologic agents of infectious arthritis are listed in (Table 4)

These agents act to stimulate a host inflammatory response, which is initially responsible for the pathology of

the infection. Arthritis is also a symptom associated with infectious diseases caused by certain agents, such as

Neisseria meningitidis, group A streptococci (rheumatic fever), and Streptobacillus moniliformis, in which the

agent cannot be recovered from joint fluid.

 Presumably, antigen-antibody complexes formed during active infection accumulate in a joint, initiating an

inflammatory response that is responsible for the ensuing damage.

Infections in prosthetic joints are usually associated with somewhat different etiologic agents than those in

natural joints. After insertion of the prosthesis, organisms that gained access during the surgical procedure

slowly multiply until they reach a critical mass and produce a host response. This may occur long after the

initial surgery; approximately half of all prosthetic joint infections occur more than 1 year after surgery. Skin

flora is the most common etiologic agent, with Staphylococcus epidermidis, other coagulase-negative

staphylococci, Corynebacterium spp., and Propionibacterium spp. as the most common. However,

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Staphylococcus aureus is also a major pathogen in this infectious disease. Alternatively, organisms may reach

joints during hematogenous spread from distant, infected sites.

 Diagnosis of joint infections requires an aspiration of joint fluid for culture and microscopic examination.

Inoculating the fluid directly into blood culture bottles may prevent the fluid from clotting. Some of the fluid

may be Gram stained and inoculated onto blood as well as chocolate and anaerobic media. The use of AFB

(acid fast bacteria) and fungal media must also be considered.

BONE:

Bone Marrow Aspiration or Biopsy:

Diagnosis of diseases, including brucellosis, histoplasmosis, blastomycosis, tuberculosis, and leishmaniasis, can

sometimes be made by detection of the organisms in the bone marrow. Brucella spp. can be isolated on culture,

as can fungi, but parasitic agents must be visualized in smears or sections made from bone marrow material.

Many of the etiologic agents associated with disseminated infections in patients with human immunodeficiency

virus (HIV) may be visualized or isolated from the bone marrow. Some of these organisms include

cytomegalovirus, Cryptococcus neoformans, and Mycobacterium avium complex.

Bone Biopsy:

A small piece of infected bone is occasionally sent to the microbiology laboratory to identify the etiologic agent

of osteomyelitis (infection of bone). Patients develop osteomyelitis from hematogenous spread of an infectious

agent, invasion of bone tissue from an adjacent site (e.g., joint infection, dental infection), breakdown of tissue

caused by trauma or surgery, or lack of adequate circulation followed by colonization of a skin ulceration with

microorganisms. Once established, infections in bone may progress toward chronicity, particularly if blood

supply is insufficient in the affected area.

Staphylococcus aureus, seeded during bacteremia, is the most common etiologic agent of osteomyelitis among

patients of all age groups. The toxins and enzymes produced by this bacterium, as well as its ability to adhere to

smooth surfaces and produce a protective glycocalyx coating, seem to contribute to the organism’s

pathogenicity. Osteomyelitis in younger patients is often associated with a single agent. Such infections are

usually of hematogenous origin. Other organisms recovered from hematogenously acquired osteomyelitis

include Salmonella spp., Haemophilus spp., Enterobacteriaceae, Pseudomonasspp., Fusobacterium

necrophorum, and yeasts. S. aureus or P. aeruginosa is often recovered from cases in patients with drug

addictions. Parasites or viruses are rarely, if ever, etiologic agents of osteomyelitis. Bone biopsies from

infections that have spread to a bone from a contiguous source or that are associated with poor circulation,

especially in patients with diabetes, are likely to yield multiple isolates. Gram-negative bacilli are increasingly

common among hospitalized patients; a break in the skin (surgery or intravenous line) may precede

establishment of gram-negative osteomyelitis.

Breaks in skin from other causes, such as a bite wound or trauma, also may be the initial event leading to

underlying bone infection. For example, a human bite may lead to infection with Eikenella corrodens, whereas

an animal bite may result in Pasteurella multocida osteomyelitis.

Poor oral hygiene may lead to osteomyelitis of the jaw with Actinomyces spp., Capnocytophaga spp., and other

oral flora, particularly anaerobes. Pigmented Prevotella and Porphyromonas, Fusobacterium, and

Peptostreptococcus spp. are often involved. Pelvic infection in the female may result in a mixed aerobic and

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anaerobic osteomyelitis of the pubic bone. Patients with neuropathy (pathologic changes in the peripheral

nervous system) in the extremities, notably patients with diabetes, who may have poor circulation, may

experience an unrecognized or notable trauma.

They develop ulcers on the feet that do not heal, become infected, and may eventually progress to involve

underlying bone. These infections are usually polymicrobial, involving anaerobic and aerobic bacteria.

Prevotella or Porphyromonas, other gram-negative anaerobes, including the Bacteroides fragilis group,

Peptostreptococcus spp., Staphylococcus aureus, and group A and other streptococci are frequently

encountered.

 Molecular testing, such as polymerase chain reaction, may be useful in determining the infectious organism

associated with the patient’s condition when the laboratory is unable to recover the organism by traditional

culture.

Solid tissues:

Pieces of tissue are removed from patients during surgical or needle biopsy procedures or may be collected at

autopsy. Any agent of infection may cause disease in tissue, and laboratory practices should be adequate to

recover bacteria, fungi, and viruses and detect the presence of parasites. Fastidious organisms (e.g., Brucella

spp.) and agents of chronic disease (e.g., systemic fungi and mycobacteria) may require special media and long

incubation periods for isolation. Some agents requiring special supportive or selective media are listed in Table

(5).

Table( 5 )Infectious Agents in Tissue Requiring Special Media:

Actinomyces spp.

Brucella spp.

Legionella spp.

Bartonella (Rochalimaea) henselae (cat-scratch disease bacilli)

Systemic fungi

Mycoplasma spp.

Mycobacterium spp.

Viruses

Laboratory diagnostic procedures:

Specimen collection and transport:

Requirements for the collection and transport of specimens from sterile body sites vary because of the

numerous types of specimens that can be collected and submitted to the laboratory for testing.

Fluids and Aspirates

Most specimens (pleural, peritoneal, pericardial, and synovial fluids) are collected by aspiration with a needle

and syringe. Collecting pericardial fluid is not without risk to the patient because the sample is collected from

the cavity immediately adjacent to the heart.

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Collection is performed by needle aspiration with electrocardiographic monitoring or as a surgical procedure.

Laboratory personnel should be alerted in advance of the procedure, ensuring that the appropriate media, tissue

culture media, and stain procedures are available immediately. Body fluids from sterile sites should be

transported to the laboratory in a sterile tube or airtight vial. From 1 to 5 mL of specimen is adequate for

isolation of most bacteria, but the larger the specimen, the better, particularly for isolation of M. tuberculosis

and fungi; at least 5 mL should be submitted for recovery of these organisms. Ten milliliters of fluid is

recommended for the diagnosis of peritonitis. Anaerobic transport vials are available from several sources.

These vials are prepared in an oxygenfree atmosphere and are sealed with a rubber septum or short stopper

through which the fluid is injected. Transportation of fluid in a syringe capped with a sterile rubber stopper is

not recommended. Most clinically significant anaerobic bacteria survive adequately in aerobic transport

containers (e.g., sterile, screw-capped tubes) for short periods if the specimen is purulent and of adequate

volume. However, collection in anaerobic transport media is recommended, and procedures vary in different

laboratories. Specimens received in anaerobic transport vials should be inoculated to routine aerobic (an

enriched broth, blood, chocolate, and sometimes MacConkey agar plates) and anaerobic media as quickly as

possible.

Specimens for recovery of fungi or mycobacteria may be transported in sterile, screw-capped tubes. At least 5

to 10 mL of fluid are required for adequate recovery of small numbers of organisms. If gonococci or chlamydia

are suspected, additional aliquots should be sent to the laboratory for smears and appropriate cultures. With

respect to pericardial, pleural, synovial, and peritoneal fluids, the inoculation of blood culture broth bottles at

the bedside or in the laboratory may be beneficial.

An additional specimen should be submitted to the laboratory for a Gram stain. The specimen in the blood

culture bottle is processed as a blood culture, facilitating the recovery of small numbers of organisms and

diluting out the effects of antibiotics. Citrate or sodium polyanetholsulfonate (SPS) may be used as an

anticoagulant.

Specimens collected by percutaneous needle aspiration (paracentesis) or at the time of surgery should be

inoculated into aerobic and anaerobic blood culture bottles immediately at the bedside. Fluid from CAPD

patients can be submitted to the laboratory in a sterile tube, urine cup, or the original bag. The bag is entered

with a sterile needle and syringe to withdraw fluid for culture. Fluid should be directly inoculated into blood

culture bottles (at least 20 mL [10 mL in each of two culture bottles]). Numerous studies indicate that in

addition to blood culture bottles, an adult Isolator tube is a sensitive and specific method for culture.

Bone:

Bone marrow is typically aspirated from the interstitium of the iliac crest. Usually, this material is not

processed for routine bacteria, because blood cultures are equally useful, and false-positive cultures for skin

bacteria (Staphylococcus epidermidis) are frequent. Some laboratories report good recovery from bone marrow

material injected into a pediatric Isolator tube (ISOLATOR 1.5 mL, Alere,

altham, MA) as a collection and transport device. The lytic agents within the Isolator tube are thought to lyse

cellular components, presumably freeing intracellular bacteria for enhanced recovery. Bone removed at surgery

or by percutaneous biopsy is sent to the laboratory in a sterile container.

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Tissue:

Tissue specimens are obtained following careful preparation of the skin. It is critical that biopsy specimens be

collected aseptically and submitted to the microbiology laboratory in a sterile container. A wide-mouthed,

screwcapped bottle or plastic container is recommended.

Anaerobic organisms survive within infected tissue long enough to be recovered from culture. A small amount

of sterile, nonbacteriostatic saline may be added to keep the specimen moist. Because homogenizing with a

tissue grinder can destroy some organisms by the shearing forces generated during grinding, it is often best to

use a sterile scissors and forceps to mince larger tissue specimens into small pieces suitable for culturing.

Note that Legionella spp. may be inhibited by saline; a section of lung should be submitted without saline for

Legionella isolation.

If anaerobic organisms are of concern, a small amount of tissue can be placed into a loosely capped, wide

mouthed plastic tube and sealed into an anaerobic pouch system, which also seals in moisture enough for

survival of organisms in tissue until the specimen is plated. The surgeon should take responsibility for seeing

that a second specimen is submitted to anatomic pathology for histologic studies. Formaldehyde-fixed tissue is

not useful for recovery of viable microorganisms, although some organisms can be recovered after very short

periods. Material from draining sinus tracts should include a portion of the tract’s wall obtained by deep

curettage. Tissue from infective endocarditis should contain a

portion of the valve and vegetation if the patient is undergoing valve replacement. In some instances,

contaminated material may be submitted for microbiologic examination. Specimens, such as tonsils or autopsy

tissue, may be surface cauterized with a heated spatula or blanched by immersing in boiling water for 5 to 10

seconds to reduce surface contamination.

The specimen may then be dissected with sterile instruments to permit culturing of the specimen’s center,

which will not be affected by the heating. Alternatively, larger tissues may be cut in half with sterile scissors or

a blade and the interior portion cultured for microbes.

Because surgical specimens are obtained at great risk and expense to the patient, and because supplementary

specimens cannot be obtained easily, it is important that the laboratory save a portion of the original tissue (if

enough material is available) in a small amount of sterile broth in the refrigerator and at –70° C (or, if

necessary, at –20° C) for at least 4 weeks in case additional studies are indicated. If the entire tissue must be

ground up for culture, a small amount of the suspension should be placed into a sterile tube and refrigerated.

Specimen processing, direct examination, and culture:

Fluids and Aspirates: Techniques for laboratory processing of sterile body fluids are similar except for those

previously discussed that are directly inoculated into blood culture bottles. Clear fluids may be concentrated by

centrifugation or filtration, whereas purulent material can be inoculated directly to media. Anybody fluid

received in the laboratory that is already clotted must be homogenized to release trapped bacteria and minced or

cut to release fungal cells. Either processing such specimens in a motorized tissue homogenizer or grinding

them manually in a mortar and pestle or glass tissue grinder allows better recovery of bacteria. Hand grinding is

often preferred, because motorized grinding can generate considerable heat and thereby kill microorganisms in

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the specimen. Grinding may lyse fungal elements; therefore, it is not recommended with specimens processed

for fungi. Small amounts of whole material from a clot should be aseptically cut with a scalpel and placed

directly onto media for isolation of fungi.

All fluids should be processed for direct microscopic examination. In general, if one organism is seen per oil

immersion field, at least 105 organisms per milliliter of specimen are present. In such cases, often only a few

organisms are present in normally sterile body fluids. Therefore, organisms must be concentrated in body

fluids. For microscopic examination, cytocentrifugation should be used to prepare Gram-stained

smears because organisms can be further concentrated up to 1000-fold. Body fluids should be concentrated by

either filtration or high-speed centrifugation. Once the sample is concentrated, the supernatant is aseptically

decanted or aspirated with a sterile pipette, leaving approximately 1 mL liquid in which to thoroughly mix the

sediment. Vigorous vortexing or drawing the sediment up and down into a pipette several times is required to

adequately suspend the sediment. This procedure should be done in a biologic safety cabinet. The suspension

is used to inoculate media. Direct potassium hydroxide (KOH) or calcofluor white preparations for fungi and

acid-fast stain for mycobacteria can also be performed.

 Specimens for fungi should be examined by direct wet preparation or by preparing a separate smear for

periodic acid-Schiff (PAS) staining in addition to Gram stain. Either 10% KOH or calcofluor white is

recommended for visualization of fungal elements from a wet preparation.

In addition to hyphal forms, material from the thoracic cavity may contain spherules of Coccidioides or

budding yeast cells.

Lysis of leukocytes before concentration of CAPD effluents can significantly enhance recovery of organisms.

Filtration of CAPD fluid through a 0.45-mm pore membrane filter allows a greater volume of fluid to be

processed and usually yields better results. Because the numbers of infecting organisms may be low (fewer than

1 organism per 10 mL of fluid), a large quantity of fluid must be processed. Sediment obtained from at least 50

mL of fluid has been recommended. If the specimen is filtered, the filter should be cut aseptically into three

pieces, one of which is placed on chocolate agar for incubation in 5% carbon dioxide, one on MacConkey agar,

and the other on a blood agar plate for anaerobic incubation. If fluids have been concentrated by centrifugation,

the resulting sediment should be inoculated to an enrichment broth, blood, and chocolate agars. Because

these specimens are from normally sterile sites, selective media are inadvisable because they may inhibit the

isolation of anaerobes, mycobacteria, fungi, Chlamydia spp., and viruses should be used when such cultures are

clinically indicated.

Bone: Clotted bone marrow aspirates or biopsies must be homogenized or ground to release trapped

microorganisms. Specimens are inoculated to the same media as for other sterile body fluids. A special medium

for enhancement of growth of Brucella spp. and incubation in 10% carbon dioxide may be needed. A portion of

the specimen may be inoculated directly to fungal media. Sections are also made from biopsy material (bone)

for fixation, staining, and examination (usually by anatomic pathologists) for the presence of mycobacterial,

fungal, or parasitic agents. With respect to obtaining specimens from patients suspected of having

osteomyelitis, cultures taken from open wound sites above infected bone or material taken from a draining

sinus leading to an area of osteomyelitis may not reflect the actual etiologic agent of the underlying

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osteomyelitis. Cultures of samples of bone obtained during wound debridement surgery appear to be more

useful for directing antibiotic therapy for better clinical outcome.

Diagnosis of prosthetic (artificial) joint infections is often difficult. Unfortunately, there is no universally

accepted definition for the diagnosis of infection in the absence of microbiologic evidence because clinical

symptoms such as pain do not differentiate infection from mechanical joint failure. There is no standardized

approach to the laboratory diagnosis of these infections, and published data are conflicting. Further

complicating the diagnosis is that the most common bacteria causing prosthesis infections are common skin

contaminants such as coagulase-negative staphylococci. Some studies have reported that culture is relatively

insensitive, possibly because of the organisms residing in biofilms, whereas polymerase chain reaction (PCR)

assays were able to detect a majority of prosthetic joint infections. Atkins

and colleagues recommended that five or six operative bone specimens be submitted for culture and that the

cutoff for a definite diagnosis of infection be three or more of these specimens yielding the same organism.

However, a recent study using PCR and culture using multiple media types and prolonged incubation found that

appropriate culture was adequate to exclude bacterial infection in hip prostheses and PCR did not enhance

diagnostic sensitivity for infection.

Normal bone is difficult to break up; however, most infected bone is soft and necrotic. Therefore, grinding the

specimen in a mortar and pestle may break off some pieces. Small shavings from the most necrotic-looking

areas of the bone specimen may sometimes be scraped off aseptically and inoculated to media. Pieces should be

placed directly into media for recovery of fungi. Small bits of bone can be ground with sterile broth to form a

suspension for bacteriologic and mycobacterial cultures.

If anaerobes are to be recovered, all manipulations are best performed in an anaerobic chamber. If such an

environment is unavailable, microbiologists should work quickly within a biosafety cabinet to inoculate

prereduced anaerobic plates and broth with material from the bone.

Solid Tissue:Tissue should be manipulated in a laminar flow biologicsafety cabinet. Processing tissue within

an anaerobic chamber is even better. The microbiologist should cut through the infected area (which is often

discolored) with a sterile scalpel blade. Half of the specimen can be used for fungal cultures and the other half

for bacterial cultures. Both types of microbial agents should be considered in all tissue specimens. Some

samples should also be sent to surgical pathology for histologic examination.

 Specimens should be cultured for viruses or acid-fast bacilli when requested. Material that is to be cultured

for parasites should be finely minced or teased before inoculation into broth. Direct examination of stained

tissue for parasites is often performed in the anatomic pathology lab. Imprint cultures of tissues may yield

bacteriologic results identical to homogenates and may help differentiate microbial infection within the tissue’s

center from surface colonization (growth only at the edge).

Additional media can be inoculated for incubation at lower temperatures, which may facilitate recovery of

certain systemic fungi and mycobacteria.

Tissue may also be inoculated to tissue culture cells for isolation of viruses. Brain, lung, spinal fluid, and blood

are generally good specimens for viral isolation. Tissue may be examined by immunofluorescence for the

presence of herpes simplex virus, varicella-zoster virus, cytomegalovirus, or rabies viral particles. Lung tissue

should be examined by direct fluorescent antibody test for Legionella spp.

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The tissues of all fetuses, premature infants, and babies who have died of an infectious process should be

cultured for Listeria. Specimens of the brain, spinal fluid, blood, liver, and spleen are most likely to contain the

organism.

Infections of the Lower Respiratory System:

The respiratory tract can be divided into two major areas: the upper respiratory tract consists of all structures

above 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.

 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 thoracic 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.

 The lungs occupy the right and left pleural cavities, whereas the mediastinum (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. Because these

mechanisms relate to respiratory tract infections. 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 nonspecifically 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 secretions; 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. Aspiration of minor amounts of oropharyngeal material, as

occurs often during sleep, plays an important role in the pathogenesis of many types of pneumonia. Once

particles escape the mucociliary sweeping activity and enter the alveoli, alveolar macrophages ingest them and

carry them to the lymphatics. In addition to these nonspecific host defenses, normal flora of the nasopharynx

and oropharynx help prevent colonization by pathogenic organisms of the upper respiratory tract.

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Normal bacterial flora prevent the colonization by pathogens by competing for the same space and nutrients as

well as production of bacteriocins and metabolic products that are toxic to invading organisms.

Some of the bacteria that can be isolated as part of the indigenous flora of healthy hosts, as well as many

species that may cause disease under certain circumstances and are often isolated from the respiratory tracts of

healthy persons, are listed in Table(1).

 Under certain circumstances and for unknown reasons, these colonizing organisms can cause disease—

perhaps because of previous damage by a viral infection, loss of some host immunity, or physical damage to the

respiratory epithelium (e.g., from smoking).

 Differentiation of normal flora of the respiratory tract is important for determining the importance of an

isolate in the clinical laboratory. Colonization does not always represent an infection. It is important to

differentiate colonization from infection based on the specimen source, number of organisms present, and

presence or quantity of white blood cells.

(Organisms isolated from normally sterile sites in the respiratory tract by sterile methods that avoid

contamination with normal flora should be definitively identified and reported to the clinician.)

Microorganism Factors:

Organisms possess traits or produce products that promote colonization and subsequent infection in the host.

The virulence, or disease-producing capability of an organism, depends on several factors including adherence,

production of toxins, amount of growth or proliferation, tissue damage, avoiding the host immune response, and

ability to disseminate.

( Table 1) Organisms Present in the Nasopharynx and Oropharynx of Healthy Humans:

Possible Pathogens

Acinetobacter spp.

Viridans streptococci, including Streptococcus anginosus

group

Beta-hemolytic streptococci

Streptococcus pneumoniae

Staphylococcus aureus

Neisseria meningitidis

Mycoplasma spp.

Haemophilus influenzae

Haemophilus parainfluenzae

Moraxella catarrhalis

Candida albicans

Herpes simplex virus

Enterobacteriaceae

Mycobacterium spp.

Pseudomonas spp.

Burkholderia cepacia

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Filamentous fungi

Klebsiella ozaenae

Eikenella corrodens

Bacteroides spp.

Peptostreptococcus spp.

Actinomyces spp.

Capnocytophaga spp.

Actinobacillus spp., A. actinomycetemcomitans

Haemophilus aphrophilus

Entamoeba gingivalis

Trichomonas tenax

Rarely Pathogens

Nonhemolytic streptococci

Staphylococci

Micrococci

Corynebacterium spp.

Coagulase-negative staphylococci

Neisseria spp., other than N. gonorrhoeae and

N. meningitidis

Lactobacillus spp.

Veillonella spp.

Spirochetes

Rothia dentocariosa

Leptotrichia buccalis

Selenomonas

Wolinella

Stomatococcus mucilaginosus

Campylobacter spp.

Adherence. For any organism to cause disease, it must first gain a foothold within the respiratory tract to grow

to sufficient numbers to produce symptoms. Therefore, most etiologic agents of respiratory tract disease must

first adhere to the mucosa of the respiratory tract. The presence of normal flora and the overall state of the host

affect the ability of microorganisms to adhere. Surviving or growing on host tissue without causing overt

harmful effects is termed colonization. Except for those microorganisms 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

lipoteichoic acids and M proteins. These molecules appear as a thin layer of fuzz surrounding the bacteria.

Staphylococcus 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

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Enterobacteriaceae, Legionella spp., Pseudomonas spp., Bordetella pertussis, and Haemophilus spp., also

adhere by means of proteinaceous finger-like surface fimbriae. Viruses possess either a hemagglutinin

(influenza and parainfluenza viruses) or other proteins that mediate their epithelial attachment.

(Table2): 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

Toxins. Certain microorganisms are almost always considered 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 Table 2.

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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 produces disease through the action of an

extracellular toxin.

Once the organism colonizes the upper respiratory 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 neuritis, 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 interfere 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 streptococci

produce extracellular enzymes capable of damaging 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 pharyngitis.

Enzymes of streptococci, including hyaluronidase, allow rapid dissemination of the bacteria.

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 nonspecific and immunologic factors being attracted to the

area, increasing the amount of host tissue damage. Respiratory 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 tuberculosis, and most gram-negative bacilli.

Avoiding the Host Response. Another virulence mechanism 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 immunoglobulins. 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 tha

Vaccine consisting of capsular antigens provides host protection to infection, indicating that the capsular

polysaccharide is a major virulence mechanism of H. influenzae, S. pneumoniae, and N. meningitidis.

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 Arranged by Sarah Mohssen

Section I– Microbiology By Nada Sajet

Some respiratory pathogens evade the host immune system by multiplying within host cells. Chlamydia

trachomatis, 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 respiratory tract disease comprises organisms capable of survival 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 organisms slowly multiply within macrophages.

Ultimately,M. tuberculosis destroys the macrophage and is subsequently 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 macrophages,

through the lymphatics, and into the bloodstream, 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

multiplicationvand disease (secondary tuberculosis). In certain patients with primary immune defects, the initial

bacteremia 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, including lymphocytes, neutrophils, and histiocytes, eventually resulting in granuloma formation, then

tissue destruction and cavity formation. The lesion consists of a semisolid, amorphous tissue mass resembling

semisoft cheese, from which it received the name caseating