Sample Sources

Accurate diagnosis of lower respiratory tract infections is essential for proper patient care, and this requires the proper collection, handling, and processing of respiratory specimens. A thorough understanding of the various specimen sources and their associated procedures is critical for clinical microbiology

General Principles

Infection Sites: The lower respiratory tract (lungs, bronchi, bronchioles) is normally sterile
Specimen Collection: Obtaining appropriate samples is crucial, and will often require special procedures
Challenges: The specimens are often contaminated by upper respiratory flora. Also, the methods of specimen collection can be difficult
Purpose of Laboratory Testing: To isolate and identify the pathogens responsible for the infection
Quality of the Specimen: The quality of the specimen is important. The laboratory may need to assess the quality of the sample

Specific Specimen Sources

Sputum

Source: Secretions from the lower respiratory tract that are expectorated (coughed up)
Indications
- Suspicion of pneumonia (lung infection)
- Suspected lower respiratory tract infection
- Follow-up of patients with respiratory infections
Collection Procedure
- Patient Education: Educate the patient on how to collect a good specimen
- Timing: Collect the specimen in the morning, before the patient eats or drinks
- Method: Have the patient cough deeply and forcefully to bring up secretions from the lungs
- Volume: The patient needs to provide an adequate volume (e.g., 1-5 mL)
- Collection Container: Collect into a sterile, wide-mouthed container
Specimen Quality
- Adequate Sample: The specimen must be representative of the lower respiratory tract
- Mucoid, not Saliva: Saliva is not a good specimen
- Assessment: The lab can assess the quality of the sample
- Rejection criteria: If a sample has an excessive amount of squamous epithelial cells, it may be rejected
- Gram Stain: Perform Gram stain, and count squamous epithelial cells and neutrophils
Processing and Testing
- Gram Stain: Perform Gram stain
- Culture: Inoculate on appropriate media
  - BAP
  - CHOC
  - Selective media, if needed
- Testing for specific organisms, as indicated

Endotracheal Aspirate (ETA)

Source: Secretions collected through an endotracheal tube
Indications
- Patients who are intubated
- Suspected lower respiratory tract infection
Collection Procedure
- Sterile Technique: Maintain sterile technique
- Aspiration: Aspirate secretions using a sterile suction catheter
- Volume: Collect an adequate volume (e.g., 1-3 mL)
Specimen Quality
- Usually of good quality because the specimen is directly from the lower respiratory tract
Processing and Testing
- Gram Stain: Perform Gram stain
- Culture: Inoculate on appropriate media
  - BAP
  - CHOC
  - Selective media, if needed
  - Test for specific organisms

Bronchoalveolar Lavage (BAL)

Source: Fluid obtained from the lungs using a bronchoscope
Indications
- Diagnosis of pneumonia, especially in immunocompromised patients
- Diagnosis of other lung infections
- Evaluation of interstitial lung disease
Collection Procedure
- Performed by a physician, using a bronchoscope
- The bronchoscope is inserted into the lungs
- Sterile saline is infused into a lung segment
- The fluid is then aspirated
Specimen Quality
- Directly from the lungs
- Good quality
Processing and Testing
- Gram Stain: Perform Gram stain
- Culture: Inoculate on appropriate media
  - BAP
  - CHOC
  - Selective media, if needed
  - Test for specific organisms
- Cytology
- Special Stains
- Molecular testing

Bronchial Wash (BW)

Source: Fluid collected from the bronchi using a bronchoscope
Indications
- Diagnosis of pneumonia and other lung infections
Collection Procedure
- Performed by a physician, using a bronchoscope
- The bronchoscope is inserted into the bronchi
- Sterile saline is instilled into the bronchi
- The fluid is then aspirated
Specimen Quality
- Directly from the bronchi
- Good quality
Processing and Testing
- Gram Stain: Perform Gram stain
- Culture: Inoculate on appropriate media
  - BAP
  - CHOC
  - Selective media, if needed
  - Test for specific organisms

Bronchial Brush (BB)

Source: Cells collected from the bronchi using a brush
Indications
- Diagnosis of pneumonia and other lung infections
Collection Procedure
- Performed by a physician, using a bronchoscope
- A brush is passed through the bronchoscope to collect cells from the bronchial walls
Specimen Quality
- Directly from the bronchi
- Small volume
Processing and Testing
- Gram Stain: Perform Gram stain
- Culture: Inoculate on appropriate media
  - BAP
  - CHOC
  - Selective media, if needed
  - Test for specific organisms

Specimen Handling and Processing

Prompt Transport: Transport specimens to the laboratory as soon as possible after collection
Proper Storage
- If immediate processing is not possible, store specimens at 4°C
- Store for as short a time as possible
Volume Considerations: Collect an adequate volume, as required
Initial Processing
- Visual Inspection: Note the appearance (e.g., mucoid, purulent, bloody)
- Quality Assessment: Assess the quality of the specimen

Factors Affecting Specimen Quality

Contamination
- Sputum: Can be contaminated with oral flora
- ETA: Less contamination than sputum, but still possible
- BAL, BW, BB: Less prone to contamination
Collection Technique: Proper technique is essential
Specimen Transport: Prompt transport is important to maintain the viability of organisms
Processing Delays: Minimize delays

Key Terms

Lower Respiratory Tract: Lungs, bronchi, and bronchioles
Sputum: Secretions from the lower respiratory tract
Endotracheal Aspirate (ETA): Secretions collected through an endotracheal tube
Bronchoalveolar Lavage (BAL): Fluid obtained from the lungs via bronchoscope
Bronchial Wash (BW): Fluid collected from the bronchi via bronchoscope
Bronchial Brush (BB): Cells collected from the bronchi using a brush via bronchoscope
Pneumonia: Lung infection
Aseptic Technique: Procedures to prevent contamination
Gram Stain: A staining technique to differentiate bacteria
Culture: Growth of microorganisms in the laboratory
Mucoid: Resembling mucus
Purulent: Containing pus
Squamous Epithelial Cells: Cells from the mouth and throat (saliva)
Neutrophils: A type of white blood cell
Viability: The ability of microorganisms to live and grow
Bronchoscope: An instrument for examining the airways

Lower Respiratory

Quantitative Reporting