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Microbiology

Lower Respiratory

This section covers the essential aspects of the analysis of lower respiratory tract specimens in bacteriology, emphasizing the key steps in the diagnostic process

Specimen Sources

  • Purpose: To obtain samples from the lower respiratory tract for culture and analysis
  • Key Sources
    • Sputum: Expectorated secretions from the lungs. Requires a good collection
    • Endotracheal Aspirate (ETA): Secretions collected through an endotracheal tube (for intubated patients)
    • Bronchoalveolar Lavage (BAL): Fluid obtained from the lungs using a bronchoscope
    • Bronchial Wash (BW)
    • Bronchial Brush (BB)
  • Critical Considerations
    • Specimen Quality: Crucial for obtaining accurate results. Sputum samples are assessed based on the number of squamous epithelial cells
    • Collection Technique: Aseptic technique is needed. The method of obtaining the sample depends on the situation

Significance of Quantitative and Semiquantitative Reporting of Results

  • Purpose: To determine the significance of bacterial growth and guide clinical decisions
  • Quantitative Reporting
    • Specimens: BAL, protected brush samples, or other invasive procedures
    • Method: Serial dilutions, plating, and colony counting to determine CFU/mL
    • Interpretation: Using specific cut-offs (e.g., >10,000 CFU/mL for BAL)
    • Advantages: Provides a more objective measure, helps differentiate between colonization and infection, and is useful for monitoring treatment
  • Semiquantitative Reporting
    • Specimens: Sputum, ETA
    • Method: Visual estimation of colony growth (e.g., few, moderate, many)
    • Reporting: Descriptors of growth based on the amount of colonies
    • Advantages: Faster, often more practical for some specimen types
    • Disadvantages: Less precise and subjective
  • Key Factors for Interpretation
    • Clinical Context: Symptoms, radiographic findings, risk factors
    • Specimen Quality: Adequate for samples
    • Organism Characteristics: Potential pathogens
    • Multiple Organisms: This can complicate interpretation

Colony Morphology and Identification of Major Pathogens

  • Core Skills: Essential for successful lab identification
  • Key Steps
    • Gram Stain: Performed on all appropriate samples
    • Culture
      • Media: BAP (blood agar plate), CHOC (chocolate agar), and potentially other selective media
      • Incubation: 35-37°C, appropriate atmosphere
      • Inspection: Colony morphology, hemolysis
    • Identification: Utilizes:
      • Morphological findings
      • Biochemical testing
      • Commercial identification systems (e.g., automated systems, MALDI-TOF)
  • Major Pathogens and Their Characteristics: (Examples)
    • Streptococcus pneumoniae: Alpha-hemolytic, lancet-shaped diplococci
    • Haemophilus influenzae: Small, pleomorphic rods, requiring X and V factors
    • Moraxella catarrhalis: Gram-negative diplococci, “hockey puck” colonies
    • Legionella pneumophila: Culture on BCYE agar. Requires special testing
    • Staphylococcus aureus: Beta-hemolytic, golden colonies, clusters
    • Pseudomonas aeruginosa: Blue-green pigment, grape-like odor, Gram-negative rods
    • Acinetobacter baumannii: Gram-negative coccobacilli, oxidase-negative
    • Stenotrophomonas maltophilia: Gram-negative rods, lavender-green colonies

Molecular Methods

  • Advantages: High sensitivity, rapid turnaround, detect non-culturable organisms
  • Common Methods
    • PCR and RT-PCR
    • Multiplex PCR: Many targets in a single test
    • Next-generation sequencing
  • Applications: Identification of pathogens

Organism Pathogenicity

  • Understanding Disease: Determining how organisms cause disease
  • Etiology: Identification of the cause of the disease
  • Transmission: How an organism spreads
  • Virulence Mechanisms: The tools the organism uses to cause disease
  • Pathogenicity
    • Colonization: Ability to establish themselves
    • Invasion: How it invades
    • Immune Evasion: How they avoid the immune system
    • Toxins: Production of harmful substances
  • Examples
    • Streptococcus pneumoniae: Capsule prevents phagocytosis
    • Haemophilus influenzae: Capsule and endotoxin
    • Pseudomonas aeruginosa: Adhesins, capsule, exotoxin A
    • Staphylococcus aureus: Adherence, enzymes, immune evasion, toxins (e.g., superantigens)
  • Implications of Pathogenicity
    • Clinical Presentation: The signs and symptoms of the disease
    • Diagnosis: Guide the selection of appropriate testing
    • Treatment: Inform the choice of antibiotics
    • Prevention: Determines all infection control measures