Specimen Sources

Mycobacteria and Nocardia hinges on obtaining the right specimen from the right location. The specimen source (like sputum from the lower respiratory tract, blood, or soft tissue) is the first critical step in accurate diagnosis. The location of the suspected infection dictates the specimen type needed, as this directly impacts the ability to detect these organisms

General Principles

• Sterility is Key: Always use sterile containers and follow strict aseptic techniques to avoid contamination
• Adequate Volume: Collect sufficient volume to allow for direct smears, culture, and potentially molecular testing. Remember, Mycobacteria often have slow growth rates, so maximizing the sample increases the chances of detection
• Prompt Processing: Transport specimens to the lab as quickly as possible. If delays are unavoidable, follow the lab’s specific protocols for storage (usually refrigeration)
• Safety First: Work under a certified biological safety cabinet, wear appropriate PPE

Specific Specimen Sources

Here’s a breakdown by source, with considerations for Mycobacterium and Nocardia:

Lower Respiratory Tract

• Specimens: Sputum (induced or expectorated), Bronchial Washings/Lavage (BAL), Tracheal Aspirates
• Target Pathogens
  • Mycobacterium tuberculosis: The primary suspect in pulmonary infections
  • Mycobacterium avium complex (MAC): Increasingly common, especially in immunocompromised patients or those with underlying lung disease
  • Mycobacterium kansasii: Another potential cause of pulmonary disease
  • Nocardia spp.: While less common than Mycobacteria in respiratory specimens, Nocardia can cause pulmonary infections, particularly in individuals with COPD, structural lung disease, or immunocompromise
• Collection Considerations
  • Sputum: First morning specimens are preferred due to higher bacterial load. Ensure the patient produces a deep cough specimen from the lungs, not just saliva. 3 specimens is considered adequate
  • BAL/Washings: Collected during bronchoscopy. These are more invasive but can provide better samples, especially when sputum is difficult to obtain
  • Tracheal Aspirates: Used for patients who are intubated

Blood

• Specimens: Whole blood collected in special mycobacteria blood culture tubes (e.g., lysis centrifugation tubes)
• Target Pathogens
  • Mycobacterium avium complex (MAC): Common cause of disseminated infection in individuals with advanced HIV/AIDS
  • Mycobacterium tuberculosis: Can occur in disseminated TB
  • Nocardia spp.: Can cause disseminated infection, especially in immunocompromised patients
• Collection Considerations
  • Follow the specific instructions for the blood culture system used in your lab. This usually involves a specific blood-to-broth ratio
  • Lysis centrifugation can improve recovery by lysing blood cells and concentrating the bacteria

Soft Tissue/Skin

• Specimens: Aspirates, biopsies, swabs
• Target Pathogens
  • Mycobacterium marinum: Associated with aquarium or swimming pool exposure. Causes skin infections
  • Mycobacterium abscessus: Rapidly growing mycobacterium that can cause skin and soft tissue infections, particularly after cosmetic procedures or trauma
  • Nocardia spp.: Can cause cutaneous or subcutaneous infections, often after trauma or introduction of the bacteria into the skin
  • Mycobacterium ulcerans: Causes Buruli ulcer, a chronic necrotizing skin infection (less common in many areas, but important to consider in endemic regions)
  • Mycobacterium tuberculosis: Can cause scrofula (lymph node infection) or lupus vulgaris (skin infection)
• Collection Considerations
  • Aspirates are preferred over swabs when possible, as they provide a larger sample volume
  • Biopsies are often necessary for diagnosis, especially when other methods are inconclusive

Sterile Body Fluids (CSF, Pleural Fluid, Peritoneal Fluid, Synovial Fluid, Pericardial Fluid)

• Target Pathogens
  • Mycobacterium tuberculosis: Can cause meningitis (CSF), pleuritis (pleural fluid), peritonitis (peritoneal fluid), arthritis (synovial fluid), or pericarditis (pericardial fluid)
  • Nocardia spp.: Rarely, can cause infections in these sites, especially in immunocompromised individuals
• Collection Considerations
  • Collect as much fluid as possible
  • Concentrate the specimen by centrifugation before processing

Other Sources

• Bone Marrow: For disseminated infections
• Urine: For genitourinary TB (less common). Collect first morning specimens
• Tissue Biopsies (e.g., Liver, Lymph Node): For disseminated infections or when TB is suspected in a specific organ

Important Considerations

• Clinical Information: Always provide the lab with relevant clinical information, such as patient history, travel history, and potential exposures. This helps the lab prioritize testing and consider less common pathogens
• Communication is Key: If you’re unsure about the appropriate specimen type or collection method, contact the microbiology lab for guidance
• Laboratory Protocols: Always follow your laboratory’s specific protocols for specimen collection, transport, and processing

Key Terms

• Sputum: Mucus and other matter brought up from the lungs, bronchi, and trachea through coughing
• Bronchoscopy: A procedure in which a flexible tube (bronchoscope) is inserted into the airways to visualize the respiratory tract, collect samples (washings, brushings, biopsies), and diagnose lung conditions
• Blood Culture: A laboratory test to detect the presence of microorganisms in the blood
• Tissue Biopsy: The removal of a small piece of tissue for examination under a microscope
• Aspirate: Fluid withdrawn from a body cavity, cyst, abscess, or other lesion using a needle and syringe
• Sterile Body Fluid: A fluid normally found in a specific body cavity that is free from microorganisms (e.g., CSF, pleural fluid, synovial fluid)
• Cerebrospinal Fluid (CSF): The clear fluid that surrounds the brain and spinal cord
• Clean-Catch Midstream Urine: A method of collecting a urine sample that minimizes contamination from the external genitalia
• Decontamination: The process of removing or reducing the number of microorganisms on a surface or in a substance
• Aseptic Technique: A set of practices and procedures performed under carefully controlled conditions with the goal of minimizing contamination by pathogens