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Chapter 3.11 : Respiratory Tract Cultures

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Abstract:

Specimens from the upper respiratory tract (throat specimens, nasopharyngeal swabs, nasal discharges) can be easily obtained but are contaminated with resident microbiota. In addition, many micro organisms present in the nares and throat are found in both the disease and the carrier states ( ). It is estimated that 60% of children sporadically carry in their nasal passages by the age of 2years ( ). Because of this contamination, these specimens often do not provide accurate, clinically useful information for diagnosis of bacterial respiratory infection caused by organisms such as , , and . On the other hand, these specimens are useful for the diagnosis of specific pathogens, whose presence in symptomatic patients most often indicates disease (i.e., , , , and respiratory viruses). Nasal cultures are also performed as a part of the infection control of hospitalized patients to detect carriage of oxacillin-resistant or as part of a staphylococcal outbreak. In the latter case, nasal carriage by hospital employees may also be important (procedure 13.17). However, culture of nasopharyngeal specimens to detect carriage of potential pathogens such as , , and should be discouraged. Since these pathogens are all part of the normal oropharyngeal flora, the clinical relevance of culturing them from this site cannot be determined. In addition, reporting of normal oropharyngeal flora from this site may result in the patient receiving an unnecessary course of antibiotic therapy, thus fostering the development of resistance. Antibiotic prophylaxis of individuals in close contact with a patient with meningococcemia should be directed by the CDC guidelines, and should not be withheld based on the nasopharyngeal culture result ( ). Likewise, nasopharyngeal specimen cultures for yeast or mold colonization in otherwise healthy asymptomatic individuals should be discouraged for similar reasons. Nasopharyngeal cultures for the detection of either spp., spp.,or other fungi may be warranted for immunocompromised patients who are suspected of having an invasive infection.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
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Image of Figure 3.11.2–A1
Figure 3.11.2–A1

Quantitative culture methods. Serial dilution method is in italics. Dashed line is optional. Adapted from reference .

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
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Image of Figure 3.11.3–1
Figure 3.11.3–1

Flowchart for the identification of complex. GNR, gram-negative rod.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
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Image of Figure 3.11.4–1
Figure 3.11.4–1

Colonies of on BCYE-α showing ground-glass appearance.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
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Image of Figure 3.11.6–1
Figure 3.11.6–1

Collection of nasal pharyngeal swab(s) (A), nasal wash specimen(s) by syringe method (B), nasal wash specimen(s) by bulb method (C), and nasal aspirate specimen(s), assisted by vacuum (D). Diagrams courtesy of BD Diagnostic Systems, Sparks, MD, with permission.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
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Image of Figure 3.11.7–1
Figure 3.11.7–1

Flow chart for evaluation of culture for

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
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Image of Figure 3.11.7–2
Figure 3.11.7–2

Microscopic morphology of three types of grown on Loeffler media and stained with Loeffler methylene blue: from right to left they are biotypes gravis, mitis, and intermedius. Photos reproduced from Clinical Microbiology, ASM Committee on Educational Materials, 1985.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
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Image of Figure 3.11.7–3
Figure 3.11.7–3

Colonial morphology of grown on BAP for 48 h; from right to left they are biotypes gravis, mitis, and intermedius. Photos reproduced from Clinical Microbiology, ASM Committee on Educational Materials, 1985.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
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Image of Figure 3.11.8–1
Figure 3.11.8–1

Method of streaking plate for throat culture with stabs in agar.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
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Image of Figure 3.11.8–2
Figure 3.11.8–2

Algorithm for laboratory diagnosis of streptococcal pharyngitis.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
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23. Friedman, R. L. 1988. Pertussis: the disease and new diagnostic methods. Clin. Microbiol. Rev. 1: 365 376.
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25. Müller, F. C.,, J. E. Hoppe,, and C. H. Wirsing von König. 1997. Laboratory diagnosis of pertussis: state of the art in 1997. J. Clin. Microbiol. 35: 2435 2443.
1. Ewanowich, C. A.,, L. W. L. Chui,, M. G. Paranchych,, M. S. Peppler,, R. G. Marusyk,, and W. L. Albritton. 1993. Major outbreak of pertussis in northern Alberta, Canada: analysis of discrepant direct fluorescent-antibody and culture results by using polymerase chain reaction methodology. J. Clin. Microbiol. 31: 1715 1725.
2. McNichol, P.,, S. M. Giercke,, M. Gray,, D. Martin,, B. Brodeur,, M. S. Peppler,, T. Williams,, and G. Hammond. 1995. Evaluation and validation of a monoclonal immunofluorescent reagent for direct detection of Bordetella pertussis. J. Clin. Microbiol. 33: 2868 2871.
3. Ng, V.,, L. Weir,, M. K. York,, and W. K. Hadley. 1992. Bordetella pertussis versus non-L. pneumophila Legionella spp.: a continuing diagnostic challenge. J. Clin. Microbiol. 30: 3300 3301.
118. Gilchrist, M. J. R. 1990. Laboratory diagnosis of pertussis. Clin. Microbiol. Newsl. 12: 49 53.
119. Halperin, S. A.,, R. Bortolussi,, and A. J. Wort. 1989. Evaluation of culture, immunofluorescence, and serology for the diagnosis of pertussis. J. Clin. Microbiol. 27: 752 757.
120. Müller, F. C.,, J. E. Hoppe,, and C. H. Wirsing von König. 1997. Laboratory diagnosis of pertussis: state of the art in 1997. J. Clin. Microbiol. 35: 2435 2443.
121. Streubel, P. M.,, S. L. Cochi,, K. M. Farizo,, B. J. Payne,, S. D. Hanauer,, and A. L. Baughman. 1993. Pertussis in Missouri: evaluation of nasopharyngeal culture, direct fluorescent antibody testing, and clinical case definitions in the diagnosis of pertussis. Clin. Infect. Dis. 16: 276 285.
122. Young, S. A.,, G. L. Anderson,, and P. D. Mitchell. 1987. Laboratory observations during an outbreak of pertussis. Clin. Microbiol. Newsl. 9: 176 179.
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1. Brook, I.,, P. Yocum,, and K. Shah. 2000. Aerobic and anaerobic bacteriology of con current chronic otitis media with effusion and chronic sinusitis in children. Arch. Otolaryn-gol. Head Neck Surg. 126: 174 176.
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Tables

Generic image for table
Table 3.11.1-1a

Appropriate specimens for diagnosis of bacterial and yeast upper and lower respiratory diseases

Lower respiratory includes sputa, endotracheal tube aspirates, auger suction samples, lung aspirates, bronchial washings, bronchoalveolar lavage specimens, protected brush specimens, and lung biopsy specimens. Procedures for detection of respiratory viruses (section 10), (section 7), aerobic (section 6), and fungi, such as and (section 8), should be included, depending on the patient's exposure history and clinical situation and condition.

Specimen is also used to diagnose infection caused by respiratory viruses (section 10).

Herpes simplex virus and cytomegalovirus are important causes, and biopsy samples should be sent for histopathology and virology testing.

MRSA, methicillin-resistant .

PCP, pneumonia.

HIV, human immunodeficiency virus.

VAP, ventilator-associated pneumonia.

AFB, acid-fast bacilli.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
Generic image for table
Table 3.11.1-1b

Appropriate specimens for diagnosis of bacterial and yeast upper and lower respiratory diseases

Lower respiratory includes sputa, endotracheal tube aspirates, auger suction samples, lung aspirates, bronchial washings, bronchoalveolar lavage specimens, protected brush specimens, and lung biopsy specimens. Procedures for detection of respiratory viruses (section 10), (section 7), aerobic (section 6), and fungi, such as and (section 8), should be included, depending on the patient's exposure history and clinical situation and condition.

Specimen is also used to diagnose infection caused by respiratory viruses (section 10).

Herpes simplex virus and cytomegalovirus are important causes, and biopsy samples should be sent for histopathology and virology testing.

MRSA, methicillin-resistant .

PCP, pneumonia.

HIV, human immunodeficiency virus.

VAP, ventilator-associated pneumonia.

AFB, acid-fast bacilli.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
Generic image for table
Untitled

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
Generic image for table
Untitled

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
Generic image for table
Table 3.11.2–1a

Guidelines for reporting of primary pathogens for lower respiratory cultures

The original specimen Gram stain should be correlated with the bacterial morphotypes grown on culture. Significant growth of a primary pathogen is defined as moderate to heavy growth into the second or greater quadrant of the plate that is more than the background normal microbiota. Smaller amounts of a primary pathogen may be clinically important if it is an almost pure growth (i.e., little or no growth of normal microbiota) and the bacteria are consistent with the morphotype seen in the Gram stain associated with PMNs.

Counts of ≥10 CFU/ml are considered significant for quantitative PBS cultures, and counts of ≥10 CFU/ml are considered significant for BAL specimens.

Normal respiratory tract microbiota is defined as viridans group streptococci, commensal spp., , diphtheroids, coagulase-negative staphylococci, , group F streptococci, anaerobes, spp. (not ), enterococci, spp., , and .

MRSA, methicillin-resistant .

NA, not applicable.

ESBL, extended-spectrum beta-lactamase.

CF, cystic fibrosi.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
Generic image for table
Table 3.11.2–1b

Guidelines for reporting of primary pathogens for lower respiratory cultures

The original specimen Gram stain should be correlated with the bacterial morphotypes grown on culture. Significant growth of a primary pathogen is defined as moderate to heavy growth into the second or greater quadrant of the plate that is more than the background normal microbiota. Smaller amounts of a primary pathogen may be clinically important if it is an almost pure growth (i.e., little or no growth of normal microbiota) and the bacteria are consistent with the morphotype seen in the Gram stain associated with PMNs.

Counts of ≥10 CFU/ml are considered significant for quantitative PBS cultures, and counts of ≥10 CFU/ml are considered significant for BAL specimens.

Normal respiratory tract microbiota is defined as viridans group streptococci, commensal spp., , diphtheroids, coagulase-negative staphylococci, , group F streptococci, anaerobes, spp. (not ), enterococci, spp., , and .

MRSA, methicillin-resistant .

NA, not applicable.

ESBL, extended-spectrum beta-lactamase.

CF, cystic fibrosi.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
Generic image for table
Table 3.11.2–1c

Guidelines for reporting of primary pathogens for lower respiratory cultures

The original specimen Gram stain should be correlated with the bacterial morphotypes grown on culture. Significant growth of a primary pathogen is defined as moderate to heavy growth into the second or greater quadrant of the plate that is more than the background normal microbiota. Smaller amounts of a primary pathogen may be clinically important if it is an almost pure growth (i.e., little or no growth of normal microbiota) and the bacteria are consistent with the morphotype seen in the Gram stain associated with PMNs.

Counts of ≥10 CFU/ml are considered significant for quantitative PBS cultures, and counts of ≥10 CFU/ml are considered significant for BAL specimens.

Normal respiratory tract microbiota is defined as viridans group streptococci, commensal spp., , diphtheroids, coagulase-negative staphylococci, , group F streptococci, anaerobes, spp. (not ), enterococci, spp., , and .

MRSA, methicillin-resistant .

NA, not applicable.

ESBL, extended-spectrum beta-lactamase.

CF, cystic fibrosi.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
Generic image for table
Table 3.11.3–1

Characteristics of complex and related organisms

Data are from reference ; all isolates are colistin or polymyxin B resistant.

+, >75% of isolates gave a positive result.

(+), 20 to 75% of isolates gave a positive result.

(+), <20% of isolates gave a positive result.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
Generic image for table
Table 3.11.3–2

Processing of organisms

NA, not applicable.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
Generic image for table

To determine length of catheter tubing, measure distance from tip of nose to external opening of ear.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
Generic image for table
Untitled

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
Generic image for table
Table 3.11.6–1

Biochemical differentiation of species of importance in respiratory cultures

Table extrapolated from references , and . NA, not applicable; W, weak; V, variable; D, delayed.

grows on salmonella-shigella agar and is tartrate negative, unlike other closely related organisms ( and [IVc-2]). Also see Table 3.18.2–12 for other tests to separate these genera. spp. are similar to but the former are not motile and generally do not grow on MAC.

is malonate negative, and is malonate positive; is not a human pathogen ( ).

The nitrate reaction is first; if the gas reaction is known, it is listed second, preceded by a slash.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
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Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
Generic image for table
Untitled

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
Generic image for table
Table 3.11.7–1

Key biochemical reactions to identify toxic species

Table extrapolated from text and tables in reference . +,positive; −,negative; V, variable. is trehalose and glycogen positive; is not. Many commercial kits do an excellent job of identification of these species. , and are pyrazinamidase negative; and many common corynebacteria are positive. For laboratories that must screen numerous isolates for , tablets to rapidly test for pyrazinamidase activity are available from Key Scientific.

biotype belfani is nitrate reductase negative.

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11
Generic image for table
Untitled

Citation: Garcia L. 2010. Respiratory Tract Cultures, p 321-409. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch3.11

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