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Microbiology

Sample Sources

Accurate diagnosis of upper respiratory tract (URT) infections is essential for appropriate treatment and for preventing the spread of contagious diseases. The laboratory plays a vital role, and effective specimen collection is essential for the lab

General Principles

  • Infection Sites: The URT includes the throat, nasopharynx, middle ear (otitis media), and sinuses (sinusitis)
  • Common Pathogens: Viruses and bacteria
  • Specimen Collection: Methods must be appropriate for the site of infection
  • Contamination Risk: URT samples are often contaminated by normal flora. This makes accurate diagnosis a challenge
  • Purpose of Laboratory Testing: To identify the causative agents and guide therapy

Specific Sources

Throat Swab

  • Source: The posterior pharynx and tonsils
  • Indications
    • Pharyngitis (sore throat)
    • Suspicion of Streptococcus pyogenes (Group A Streptococcus (GAS)) infection, for example
    • Suspicion of other pharyngitis
  • Procedure
    • Materials: Sterile swab, tongue depressor, gloves, lighting
    • Method
      • Depress the tongue to visualize the tonsils and posterior pharynx
      • Swab the tonsils and posterior pharynx, avoiding the tongue and oral mucosa
      • Rotate the swab firmly over the areas
  • Considerations
    • Swab the tonsils and posterior pharynx
    • Avoid touching the tongue
    • Ensure the swab is placed in the transport medium
    • To enhance the diagnosis of GAS pharyngitis, laboratories may perform a rapid antigen test on the swab. The swab can also be used to culture the bacteria

Nasopharyngeal Swab (NP Swab)

  • Source: The nasopharynx (the upper part of the pharynx, behind the nasal cavity)
  • Indications
    • Detection of respiratory viruses
    • Bordetella pertussis (whooping cough)
    • Other nasopharyngeal infections
  • Procedure
    • Materials: Flexible swab (e.g., calcium alginate or Dacron), gloves, lighting
    • Method
      • Gently insert the swab through the nostril, parallel to the palate
      • Advance the swab until it reaches the nasopharynx
      • Rotate the swab gently, and leave in place for a few seconds to absorb secretions
      • Remove the swab
  • Considerations
    • Gentle insertion to avoid patient discomfort
    • Swab should be inserted far enough back
    • Swab should be placed in transport medium

Middle Ear Fluid (Tympanocentesis)

  • Source: Fluid from the middle ear
  • Indications
    • Otitis media (middle ear infection)
  • Procedure
    • Performed by a physician (otolaryngologist)
    • Materials: Otoscope, sterile needle, local anesthetic (sometimes)
    • Method
      • Clean the external ear canal
      • Insert the needle through the tympanic membrane (eardrum)
      • Aspirate fluid from the middle ear
  • Considerations
    • Performed under sterile conditions
    • A small amount of fluid is collected
    • Specimen is immediately transported to the lab

Sinus Aspirate

  • Source: Fluid from the sinuses
  • Indications
    • Sinusitis (sinus infection)
  • Procedure
    • Performed by a physician (otolaryngologist)
    • Materials: Local anesthetic, sterile needle
    • Method
      • The sinus is punctured through the cheek or through the nose
      • Fluid is aspirated
  • Considerations
    • Performed under sterile conditions
    • Must be transported to the lab immediately

Handling and Processing

  • Prompt Transport: Transport specimens to the laboratory as soon as possible after collection
  • Proper Storage
    • Room temperature for most swabs
    • Refrigeration may be needed
  • Appropriate Media
    • Throat Swabs: Blood agar
    • NP Swabs: Viral transport media, Bordetella transport media
    • Middle Ear Fluid, Sinus Aspirates: Blood agar, CHOC
  • Testing and Procedures
    • Rapid Antigen Tests: Often done for throat swabs
    • Gram Stain: Examine middle ear fluid and sinus aspirates
    • Culture: Inoculate appropriate media
    • PCR: Molecular methods, used to detect viruses and Bordetella
  • Proper Labeling: Labeling must be done properly

Key Terms

  • Upper Respiratory Tract (URT): Structures from the nose to the larynx
  • Pharyngitis: Inflammation of the pharynx (sore throat)
  • Streptococcus pyogenes (Group A Streptococcus (GAS)): The main cause of strep throat
  • Nasopharynx: The upper part of the pharynx, behind the nasal cavity
  • Otitis Media: Middle ear infection
  • Sinusitis: Sinus infection
  • Throat Swab: Specimen from the back of the throat
  • Nasopharyngeal Swab (NP Swab): Specimen from the nasopharynx
  • Middle Ear Fluid (Tympanocentesis): Sample from the middle ear
  • Sinus Aspirate: Specimen from the sinuses
  • Blood Agar (BAP): General-purpose culture medium
  • CHOC: Chocolate agar
  • Viral transport media: Media to keep a virus alive during transport
  • Rapid Antigen Test: Test to detect the presence of an antigen
  • Gram Stain: Staining technique to differentiate bacteria
  • Culture: Growth of microorganisms in the laboratory
  • PCR: Polymerase chain reaction (used to detect viruses)
  • Bordetella: A genus of bacteria that causes respiratory illnesses
  • Transport Media: Media to keep organisms alive