Indigenous Organisms

This section delves into the normal bacterial inhabitants of the female and male genital tracts and their corresponding Gram stain and colony morphology characteristics. Understanding these organisms is crucial for differentiating between normal flora and clinically significant pathogens

Female Genital Tract

Vagina

• Normal Flora: The vaginal microbiome is a dynamic ecosystem primarily influenced by estrogen levels. The most abundant organisms are typically Lactobacillus species
• Gram Stain Morphology
  • Lactobacillus spp.: Gram-positive, large, rod-shaped bacteria (bacilli). May appear as long, chain-like structures or as individual rods
  • Other Gram-Positive Bacilli: Corynebacterium spp. and other non-hemolytic Gram-positive rods can also be present, often shorter than Lactobacillus
  • Gram-Variable or Gram-Negative Bacteria: Often present in small amounts; may include Gardnerella vaginalis (gram-variable) or other Gram-negative rods
  • Yeast: Candida spp. (if present) will appear as large, oval-shaped cells with budding yeast forms
• Colony Morphology
  • Lactobacillus spp.: Generally, Lactobacillus species are difficult or impossible to culture on routine laboratory media. If grown, they may produce small, non-hemolytic, greyish colonies
  • Other Gram-Positive Bacilli: Colonies are variable depending on the species, but often small, non-hemolytic, and greyish
  • Gram-Variable or Gram-Negative Bacteria: Gardnerella vaginalis typically produces small, grey, pinpoint colonies on blood agar
  • Yeast: Candida spp. will produce creamy, often white or buff-colored colonies on Sabouraud’s dextrose agar or blood agar

Cervix

• Normal Flora: The cervix generally has fewer organisms than the vagina. Common organisms include:
• Gram Stain Morphology
  • Gram-Positive Cocci: Staphylococcus spp. (coagulase-negative staphylococci, or “CoNS”) and Streptococcus spp. (non-hemolytic or alpha-hemolytic)
  • Gram-Negative Cocci: Neisseria spp. (non-pathogenic species)
  • Gram-Positive Bacilli: Corynebacterium spp. and Lactobacillus spp. (may be present, but less abundant than in the vagina)
• Colony Morphology
  • Staphylococcus spp. (CoNS): Typically produce small to medium-sized, white, cream-colored, or slightly yellow colonies on blood agar
  • Streptococcus spp.: May produce small, translucent, alpha-hemolytic or non-hemolytic colonies on blood agar
  • Neisseria spp.: Non-pathogenic Neisseria spp. usually produce small, translucent, greyish colonies on chocolate agar
  • Corynebacterium spp.: Colonies are variable depending on the species, but often small, non-hemolytic, and greyish

Male Genital Tract

Urethra

• Normal Flora: The urethra contains a variety of organisms, including:
• Gram Stain Morphology
  • Gram-Positive Cocci: Staphylococcus spp. (CoNS) and Streptococcus spp
  • Gram-Negative Cocci: Neisseria spp. (non-pathogenic species)
  • Gram-Negative Bacilli: Corynebacterium spp. and Lactobacillus spp. (may be present)
• Colony Morphology
  • Staphylococcus spp. (CoNS): Typically produce small to medium-sized, white, cream-colored, or slightly yellow colonies on blood agar
  • Streptococcus spp.: May produce small, translucent, alpha-hemolytic or non-hemolytic colonies on blood agar
  • Neisseria spp.: Non-pathogenic Neisseria spp. usually produce small, translucent, greyish colonies on chocolate agar
  • Corynebacterium spp.: Colonies are variable depending on the species, but often small, non-hemolytic, and greyish

Prostate

• Normal Flora: The prostate is generally considered a sterile site in healthy individuals. However, some organisms can be present
• Gram Stain Morphology
  • The same organisms that are found in the urethra may be present
• Colony Morphology
  • The same organisms that are found in the urethra may be present

Key Considerations

• Clinical Significance: The presence of normal flora in genital specimens is expected. The significance of these organisms depends on the clinical context
• Overgrowth: Overgrowth of certain organisms (e.g., Gardnerella vaginalis in BV, Candida spp. in yeast infections) can indicate an imbalance in the normal flora and lead to clinical symptoms
• Pathogen vs. Normal Flora: Differentiating between normal flora and potential pathogens (e.g., Neisseria gonorrhoeae, Chlamydia trachomatis) is crucial for accurate diagnosis and treatment
• Mixed Flora: Mixed flora with the presence of multiple organisms is common
• Reporting: The lab report should reflect the Gram stain findings and colony morphology, along with any presumptive identification of organisms, and the presence of any pathogens
• Culture Media: Different types of culture media are used to isolate and identify organisms from genital specimens. Blood agar is a common medium for general bacterial growth. Chocolate agar is often used for fastidious organisms like Neisseria gonorrhoeae. Selective media may be used to isolate specific pathogens
• Correlation with Clinical Findings: The laboratory results must always be interpreted in conjunction with the patient’s clinical presentation, symptoms, and other relevant information
• Microscopic Examination: Microscopic examination of Gram-stained smears is a vital part of the analysis. This allows for initial assessment of the bacterial composition and the presence of any abnormal cells or organisms. It is an important step in determining the need for further testing

Key Terms

• Normal Flora: The microorganisms that typically live in a specific environment (e.g., vagina, urethra) without causing disease
• Gram Stain: A staining method used to differentiate bacteria based on their cell wall structure
• Colony Morphology: The visual characteristics of bacterial colonies on a culture plate, including size, shape, color, and texture
• Bacilli: Rod-shaped bacteria
• Cocci: Spherical-shaped bacteria
• Hemolysis: The breakdown of red blood cells in blood agar, indicated by a change in color around the bacterial colonies
• Alpha-hemolysis: Partial breakdown of red blood cells, resulting in a greenish discoloration around the colonies
• Beta-hemolysis: Complete breakdown of red blood cells, resulting in a clear zone around the colonies
• Non-hemolytic: No breakdown of red blood cells, no change in the appearance of the blood agar around the colonies
• Fastidious: Bacteria that have complex nutritional requirements and are difficult to grow in the laboratory
• Presumptive Identification: Initial identification of an organism based on Gram stain, colony morphology, and rapid tests
• Ecosystem: A community of interacting organisms and their environment
• Microbiome: The collective genomes of the microorganisms (bacteria, fungi, viruses, and other microbes) that live in a particular environment, such as the human body
• Selective Media: Culture media that are designed to inhibit the growth of certain organisms while promoting the growth of others
• Chocolate Agar: A type of culture media that contains heated blood, which releases growth factors that are needed by some bacteria
• Blood Agar: A type of culture media that contains blood
• Mixed Flora: The presence of multiple types of bacteria in a sample
• Gram-variable: Bacteria that may appear Gram-positive or Gram-negative depending on the age of the culture and the staining technique