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Microbiology

Indeginous Flora

The upper respiratory tract (URT) harbors a complex and diverse microbial community. Understanding the normal flora of the URT is crucial for interpreting laboratory results and distinguishing between colonizing organisms and true pathogens. This knowledge informs proper diagnosis

General Principles

  • Diverse Microbial Ecosystem: The URT, including the throat, nasopharynx, and sinuses, is colonized by a variety of microorganisms
  • Normal Flora Role: Normal flora can:
    • Protect the Host: Compete with pathogens
    • Contaminate Specimens: Complicate interpretation of laboratory results
  • Distinguishing Pathogens from Colonizers: Requires integrating information from:
    • Colony morphology
    • Gram stain characteristics
    • Patient history and clinical presentation
  • Sample Sources: Appropriate collection is critical

Throat Flora

Streptococcus pyogenes (Group A Streptococcus (GAS))

  • Pathogen: Primary cause of strep throat
  • Colony Morphology
    • BAP: Small, translucent colonies with a large zone of beta-hemolysis (complete clearing)
  • Gram Stain: Gram-positive cocci in chains

Streptococcus pneumoniae

  • Pathogen
  • Colony Morphology
    • BAP: Small, alpha-hemolytic colonies (greening)
  • Gram Stain: Gram-positive, lancet-shaped diplococci

Staphylococcus aureus

  • Characteristics: Can be part of normal flora. Can cause infections
  • Colony Morphology
    • BAP: Medium to large, opaque, smooth, golden-yellow colonies
    • Hemolysis: Beta-hemolytic
  • Gram Stain: Gram-positive cocci in clusters

Haemophilus influenzae

  • Characteristics: Gram-negative coccobacilli
  • Colony Morphology
    • CHOC: Small, gray, translucent colonies. Will only grow with factors X and V
  • Gram Stain: Gram-negative coccobacilli

Moraxella catarrhalis

  • Characteristics: Gram-negative diplococci
  • Colony Morphology
    • BAP: Grayish, opaque, smooth colonies, often “hockey puck”
  • Gram Stain: Gram-negative diplococci

Diphtheroids

  • Characteristics: Gram-positive, pleomorphic rods (e.g., Corynebacterium spp.)
  • Colony Morphology
    • BAP: Small, grayish, non-hemolytic colonies. C. diphtheriae can be small, granular
  • Gram Stain: Gram-positive rods. Can have a “Chinese letter” or “palisades” arrangement

Candida spp.

  • Characteristics: Yeast. Commonly C. albicans
  • Colony Morphology
    • BAP: Creamy, white colonies
  • Gram Stain: Gram-positive budding yeast cells

Nasopharyngeal Flora

  • The nasopharynx has similar species as the throat, with a few differences

Streptococcus pneumoniae

  • Pathogen
  • Colony Morphology
    • BAP: Small, alpha-hemolytic colonies (greening)
  • Gram Stain: Gram-positive, lancet-shaped diplococci

Haemophilus influenzae

  • Characteristics: Gram-negative coccobacilli
  • Colony Morphology
    • CHOC: Small, gray, translucent colonies. Will only grow with factors X and V
  • Gram Stain: Gram-negative coccobacilli

Moraxella catarrhalis

  • Characteristics: Gram-negative diplococci
  • Colony Morphology
    • BAP: Grayish, opaque, smooth colonies, often “hockey puck”
  • Gram Stain: Gram-negative diplococci

Diphtheroids

  • Characteristics: Gram-positive, pleomorphic rods (e.g., Corynebacterium spp.)
  • Colony Morphology
    • BAP: Small, grayish, non-hemolytic colonies. C. diphtheriae can be small, granular
  • Gram Stain: Gram-positive rods. Can have a “Chinese letter” or “palisades” arrangement

Staphylococcus aureus

  • Characteristics: Gram-positive cocci in clusters
  • Colony Morphology
    • BAP: Medium to large, opaque, smooth, golden-yellow colonies
    • Hemolysis: Beta-hemolytic
  • Gram Stain: Gram-positive cocci in clusters

Other

  • Various other bacterial species
  • Viruses

Middle Ear and Sinus Flora

  • The middle ear and sinuses are normally sterile. The presence of bacteria indicates infection
  • Normal flora are the same as the throat and nasopharynx
    • Streptococcus pneumoniae
    • Haemophilus influenzae
    • Moraxella catarrhalis
    • Staphylococcus aureus

Interpreting Results

  • Throat Swabs: Rapid tests for S. pyogenes. If negative, culture is needed
  • Nasopharyngeal Swabs: For Bordetella pertussis (whooping cough), viral testing
  • Middle Ear Fluid: Must be carefully interpreted. The lab report is critical
  • Sinus Aspirates: This is from a normally sterile site

Key Terms

  • Upper Respiratory Tract (URT): The nose, sinuses, pharynx, and larynx
  • Normal Flora: The microorganisms that colonize the body’s surfaces
  • Throat Swab: A specimen from the back of the throat
  • Nasopharyngeal Swab (NP Swab): Specimen from the nasopharynx
  • Middle Ear Fluid: Sample from the middle ear
  • Sinus Aspirate: Specimen from the sinuses
  • Streptococcus pyogenes (Group A Streptococcus (GAS)): The main cause of strep throat
  • BAP: Blood agar plate
  • CHOC: Chocolate agar plate
  • Gram Stain: Staining technique to differentiate bacteria
  • Alpha-Hemolysis: Partial lysis of red blood cells
  • Beta-Hemolysis: Complete lysis of red blood cells
  • Diphtheroids: Corynebacterium spp.
  • Colony Morphology: The visual characteristics of bacterial colonies on culture media (e.g., size, shape, color, texture)
  • Pathogen: An organism that can cause disease
  • Opportunistic Pathogen: An organism that causes disease primarily in a host with a weakened immune system
  • Clinical Presentation: Refers to the patient’s symptoms, physical examination findings, and other relevant clinical information
  • PCR: Polymerase chain reaction (used to detect viruses)
  • Bordetella: A genus of bacteria that causes respiratory illnesses