Indigenous Flora

This section focuses on the normal (indigenous) flora found on the skin, in soft tissues, and in bone, as well as their Gram stain and colony morphology characteristics. Understanding normal flora is crucial for differentiating between commensal organisms and true pathogens when analyzing clinical specimens

Normal Flora

• Skin: The skin harbors a diverse community of microorganisms, with the composition varying depending on factors like moisture, pH, and the presence of sebaceous glands
  • Predominant Genera
    • Staphylococcus spp.: These are the most common inhabitants, particularly Staphylococcus epidermidis
    • Corynebacterium spp. (Diphtheroids): Gram-positive, pleomorphic rods
    • Propionibacterium spp.: Anaerobic or aerotolerant, often found in hair follicles and sebaceous glands. Propionibacterium acnes is a common example
    • Micrococcus spp.: Gram-positive cocci
    • Malassezia spp.: Yeasts, often found in areas with high sebum production
    • Acinetobacter spp.: Gram-negative coccobacilli
    • Less Common, but Present: Bacillus spp., Candida spp., Enterococcus spp
• Soft Tissues: The normal flora in deeper soft tissues is usually sparse, as these areas are not typically exposed to the external environment. However, bacteria can be introduced through minor breaches in the skin
  • Common Genera
    • Staphylococcus spp.: Similar to the skin
    • Corynebacterium spp. (Diphtheroids): Also present
    • Anaerobes spp.: These are present in deeper tissues, including Peptoniphilus, Finegoldia, and Cutibacterium
• Bone: Bone is normally sterile. Therefore, the presence of any bacteria in bone tissue is considered significant
  • Sterile Site: Bone is usually sterile, and any organisms isolated from bone biopsies are considered clinically significant

Gram Stain Morphology

The Gram stain is a crucial initial step in the identification process, providing valuable information about the bacteria’s cell wall structure and morphology

• Skin Flora
  • Staphylococcus spp.: Gram-positive cocci, typically arranged in clusters, often appearing as “grape-like” clusters
  • Corynebacterium spp.: Gram-positive rods, often pleomorphic (varying in shape), can appear as “Chinese letters” or “palisades”
  • Propionibacterium spp.: Gram-positive rods, often short and plump, can appear singly or in small groups. Can be slightly curved
  • Micrococcus spp.: Gram-positive cocci, typically in tetrads or clusters
  • Malassezia spp.: Gram stain will show yeast cells (often oval or round) and hyphae or pseudohyphae
  • Acinetobacter spp.: Gram-negative coccobacilli, can appear as pairs or short chains
  • Bacillus spp.: Gram-positive rods, often larger than other Gram-positive rods
  • Candida spp.: Gram positive yeast, budding yeast
  • Enterococcus spp.: Gram-positive cocci, often in pairs or short chains
• Soft Tissue Flora
  • The Gram stain morphology is similar to that of skin flora, but the presence of anaerobic bacteria may be more likely
  • Anaerobes: Gram stain characteristics vary, ranging from Gram-positive cocci and rods to Gram-negative rods
• Bone Flora
  • The Gram stain morphology will depend on the specific organism isolated

Colony Morphology

Colony morphology refers to the visual characteristics of bacterial colonies growing on agar plates. These characteristics provide important clues for identification

• Skin Flora
  • Staphylococcus spp.
    • Appearance: Typically, colonies are round, smooth, and opaque
    • Color: Can range from white to cream to sometimes yellowish
    • Size: Colonies are usually moderate in size
    • Hemolysis: S. aureus is often beta-hemolytic (complete clearing of the blood agar). S. epidermidis is usually non-hemolytic
  • Corynebacterium spp.
    • Appearance: Colonies can be small and pinpoint or larger and more variable
    • Color: Can be white, cream, or yellowish
    • Texture: Can be smooth, rough, or dry
  • Propionibacterium spp.
    • Appearance: Colonies are usually small, pinpoint, and translucent or opaque
    • Color: Can be white to cream
    • Other: Often requires anaerobic conditions for optimal growth
  • Micrococcus spp.
    • Appearance: Colonies are small, round, and smooth
    • Color: Typically yellow, sometimes white or cream
    • Texture: Smooth, often with a glistening appearance
  • Malassezia spp.
    • Appearance: Colonies are typically small, cream-colored, and may appear “yeasty.”
    • Growth: Requires special media (e.g., Sabouraud dextrose agar with olive oil) and prolonged incubation
  • Acinetobacter spp.
    • Appearance: Colonies can be smooth, round, and opaque, or they may have a slightly irregular edge
    • Color: Can be white, cream, or slightly gray
    • Texture: Can be mucoid or sticky
  • Bacillus spp.:
    • Appearance: Colonies are large, often irregular, and may be spreading
    • Color: Can be white, cream, or gray
    • Texture: Often have a “ground glass” appearance
    • Other: Often produce spores
  • Candida spp.:
    • Appearance: Colonies are typically creamy, pasty, and have a “yeasty” odor
    • Color: White to cream
  • Enterococcus spp.:
    • Appearance: Colonies are typically small, round, and smooth
    • Color: Can be white, cream, or gray
    • Other: Often grow well on blood agar and may show alpha-hemolysis (greenish discoloration) or no hemolysis
• Soft Tissue Flora
  • The colony morphology is similar to that of skin flora
  • Anaerobes: Colonies often have a characteristic odor and may exhibit varying colony morphology
• Bone Flora
  • The colony morphology will depend on the specific organism isolated

Clinical Significance

• Differentiating between Colonization and Infection
  • The presence of normal skin flora in a wound or soft tissue culture does not necessarily indicate infection. It is crucial to consider the patient’s clinical presentation, the quantity of the organism, and the presence of other organisms
  • True Pathogens: The isolation of organisms not typically found in the normal flora (e.g., Pseudomonas aeruginosa, Enterobacteriaceae in a skin wound) is more likely to indicate infection
  • Increased Numbers: A high number of organisms that are part of the normal flora may indicate infection, especially if the patient has risk factors such as a weakened immune system or a foreign body present
• Contamination: Normal skin flora can contaminate specimens during collection. Careful attention to sterile technique is essential to minimize contamination
• Polymicrobial Infections: Skin and soft tissue infections can be polymicrobial, involving multiple organisms, including both normal flora and potential pathogens
• Osteomyelitis: In bone infections, any organism isolated is considered clinically significant

Key Terms

• Normal Flora: The microorganisms that typically colonize a specific body site without causing disease under normal circumstances
• Commensal Organisms: Microorganisms that live in or on a host without causing harm
• Opportunistic Pathogens: Organisms that are normally harmless but can cause disease in individuals with weakened immune systems or other predisposing factors
• Gram-Positive: Bacteria that retain the crystal violet dye in the Gram stain, appearing purple
• Gram-Negative: Bacteria that do not retain the crystal violet dye in the Gram stain, appearing pink or red
• Cocci: Spherical-shaped bacteria
• Rods (Bacilli): Rod-shaped bacteria
• Pleomorphic: Having variable shapes
• Hemolysis: The breakdown of red blood cells in blood agar, often indicated by a clear (beta-hemolysis) or green (alpha-hemolysis) zone around the colonies
• Mucoid: Having a slimy or sticky consistency
• Anaerobic: Growing in the absence of oxygen
• Sterile Site: A body site that is normally free of microorganisms
• Polymicrobial: Involving multiple microorganisms