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Microbiology

Sites with Flora

When collecting specimens from sites with normal flora, the goal is to obtain a sample that accurately represents the infection while minimizing contamination from the surrounding commensal organisms. This requires careful technique and a clear understanding of the specific requirements for each site

General Principles

  • Target the Infection: Focus on collecting the specimen from the area most likely to be infected. This might involve sampling the base of a wound, the purulent portion of sputum, or the inflamed area of the throat
  • Minimize Contamination: Take steps to reduce contamination from surrounding normal flora. This could include cleaning the area before collection, using selective collection devices, or carefully avoiding contact with surrounding surfaces
  • Collect Adequate Volume: Ensure that you collect a sufficient amount of specimen for the required tests. Insufficient volume can lead to false-negative results
  • Use Appropriate Collection Devices: Select collection devices that are appropriate for the site and type of specimen being collected. This might include swabs, sterile containers, or aspiration needles
  • Transport Promptly: Transport the specimen to the laboratory as soon as possible to maintain the viability of the microorganisms. Use appropriate transport media to preserve the specimen during transport

Specimen-Specific Guidelines

Stool

  • Indications: Suspected bacterial, parasitic, or viral gastrointestinal infection
  • Collection Method
    • Preferred: Collect stool directly into a clean, dry container
    • Alternative: If the patient cannot collect a stool sample, a rectal swab can be used, but this is less sensitive
  • Procedure
    1. Provide the patient with clear instructions on how to collect the stool sample without contaminating it with urine or water
    2. Instruct the patient to pass the stool into a clean, dry container
    3. Using a sterile collection device, transfer a representative portion of the stool (approximately 2-5 grams) into the appropriate transport container (e.g., Cary-Blair medium for bacterial culture, formalin for ova and parasite examination)
    4. If testing for Clostridioides difficile, collect a liquid or soft stool sample. Formed stools are not suitable
    5. For rectal swabs, insert the swab approximately 1 inch into the anal canal, rotate gently, and withdraw. Place the swab into the appropriate transport medium
  • Considerations
    • Collect stool specimens early in the course of illness, if possible
    • Collect multiple stool specimens (typically three) to increase the sensitivity of detection
    • Avoid collecting stool specimens after barium enemas or administration of oil-based laxatives
    • Refrigerate the specimen if transport to the laboratory is delayed
  • Common Flora: Large numbers of anaerobes, Enterobacteriaceae, Enterococcus, and other Gram-negative bacteria

Wound

  • Indications: Suspected wound infection
  • Collection Method
    • Preferred: Aspirate material from deep within the wound using a needle and syringe
    • Alternative: If aspiration is not possible, collect a swab sample from the base of the wound after cleaning the surface
  • Procedure
    1. Clean the skin surface around the wound with sterile saline to remove any superficial debris or contaminants
    2. Aspiration: Using a sterile needle and syringe, aspirate material from the base of the wound
    3. Swab: If aspiration is not possible, use a sterile swab to collect a sample from the base of the wound, avoiding contact with the surrounding skin
  • Considerations
    • Collect the specimen before starting antibiotic therapy, if possible
    • Avoid swabbing the surface of the wound, as this may only collect superficial contaminants
    • If the wound is dry, moisten the swab with sterile saline before collection
    • Transport the specimen to the laboratory promptly in an appropriate transport medium
  • Common Flora: Staphylococcus species, Corynebacterium species, and other skin commensals

Sputum

  • Indications: Suspected lower respiratory tract infection (e.g., pneumonia, bronchitis)
  • Collection Method
    • Preferred: A spontaneously expectorated sputum specimen collected first thing in the morning
    • Alternative: Induced sputum or bronchoalveolar lavage (BAL) in patients unable to produce sputum spontaneously
  • Procedure
    1. Instruct the patient to rinse their mouth with water to remove any superficial contaminants
    2. Instruct the patient to take several deep breaths and then cough deeply from the chest
    3. Collect the expectorated sputum into a sterile container
    4. Ensure the specimen is sputum, not saliva. Sputum is thick and purulent, whereas saliva is thin and watery
  • Considerations
    • Collect sputum specimens before starting antibiotic therapy, if possible
    • Collect multiple sputum specimens (typically three) on consecutive days to increase the sensitivity of detection for tuberculosis
    • If the patient is unable to produce sputum spontaneously, consider induced sputum or BAL
    • Evaluate the quality of the sputum specimen using a Gram stain. A good sputum specimen will have many neutrophils and few squamous epithelial cells
  • Common Flora: Upper respiratory tract flora, including Streptococcus species, Haemophilus species, and Moraxella catarrhalis

Throat

  • Indications: Suspected pharyngitis or tonsillitis, especially for the detection of Group A Streptococcus
  • Collection Method
    • Swab the posterior pharynx and tonsils, avoiding contact with the tongue, cheeks, or uvula
  • Procedure
    1. Instruct the patient to open their mouth wide and say “ah.”
    2. Depress the tongue with a tongue depressor
    3. Using a sterile swab, vigorously swab the posterior pharynx and tonsils, focusing on any areas of inflammation or exudate
    4. Place the swab into the appropriate transport medium
  • Considerations
    • Avoid touching the tongue, cheeks, or uvula with the swab, as this can introduce contaminants
    • If the patient has exudate on the tonsils, focus on swabbing those areas
    • Transport the specimen to the laboratory promptly in an appropriate transport medium
  • Common Flora: Streptococcus species, Haemophilus species, Neisseria species, and Moraxella catarrhalis

Collection Devices and Transport Media

  • Swabs: Use sterile swabs made of Dacron or rayon. Avoid cotton swabs, as they can inhibit the growth of some bacteria
  • Sterile Containers: Use sterile, leak-proof containers for collecting stool, sputum, and other specimens
  • Transport Media: Use appropriate transport media to maintain the viability of microorganisms during transport. Examples include:
    • Amies medium: A general-purpose transport medium for bacteria
    • Cary-Blair medium: For stool specimens for bacterial culture
    • Formalin: For stool specimens for ova and parasite examination

Quality Control

  • Training: Ensure that all personnel collecting specimens are properly trained in the correct techniques
  • Procedure Manuals: Develop and maintain up-to-date procedure manuals that outline the correct procedures for collecting and transporting specimens from different sites
  • Monitoring: Regularly monitor specimen collection practices to ensure that they are being performed correctly
  • Feedback: Provide feedback to personnel on their specimen collection techniques

Key Terms

  • Normal Flora: The microorganisms that normally live on or in the human body
  • Commensal Organisms: Microorganisms that live in or on the human body without causing harm
  • Contamination: The introduction of unwanted microorganisms into a specimen
  • Exudate: Fluid, such as pus or serum, that leaks out of blood vessels and into nearby tissues
  • Aspiration: The act of withdrawing fluid or other substances from the body using a needle and syringe
  • Transport Medium: A liquid or gel that is used to maintain the viability of microorganisms during transport