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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, and nasal discharges) can be easily obtained but are contaminated with resident microbiota. In addition, many microorganisms 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 2 years ( ). 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 (e.g., , 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 13.6.1). 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: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.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. Dotted line is optional. Adapted from reference .

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.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: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11
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Image of Figure 3.11.4–2
Figure 3.11.4–2

Workflow for working up Gram-negative bacilli.

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11
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Image of Figure 3.11.6–1
Figure 3.11.6–1

Collection of nasal pharyngeal swabs. Image from Faulkner A, Skoff T, Martin S, Cassiday P, Tondella ML, Liang J. 2008. Pertussis. Roush SW, Baldy LM (ed), . CDC (http://www.cdc.gov/vaccines/pubs/surv-manual/chpt10-pertussis.html, accessed 27 June 2015).

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11
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Image of Figure 3.11.7–1
Figure 3.11.7–1

Flowchart for evaluation of culture for .

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.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: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.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: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.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: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.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: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11
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Tables

Generic image for table
Table 3.11.1–1

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

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11
Generic image for table
Untitled

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11
Generic image for table
Table 3.11.2–1

Guidelines for reporting of primary pathogens for lower respiratory cultures

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11
Generic image for table
Untitled

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11
Generic image for table
Table 3.11.3–1

Processing of organisms

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11
Generic image for table
Table 3.11.4–1

Plating guidelines for culture

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11
Generic image for table
Untitled

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11
Generic image for table
Untitled

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11
Generic image for table
Table 3.11.6–1

Biochemical differentiation of species of importance in respiratory cultures

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11
Generic image for table
Untitled

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11
Generic image for table
Table 3.11.7–1

Key biochemical reactions to identify toxic species

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11
Generic image for table
Untitled

Citation: Leber A. 2016. Respiratory Tract Cultures, p 3.11.1.1-3.11.9.4. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.11

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