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Microbiology

Specimen Sources

Urine specimen collection is a fundamental aspect of clinical microbiology. By understanding the various specimen sources, collection techniques, and key considerations, you can help ensure accurate and reliable results that aid in the diagnosis and treatment of UTIs. Remember, the goal is to collect a representative sample of the urine with minimal contamination to accurately reflect the presence or absence of bacterial pathogens

Overview

  • Purpose: Urine cultures are crucial for diagnosing urinary tract infections (UTIs), which are among the most common bacterial infections. Accurate specimen collection is paramount to avoid contamination and ensure the recovery of the causative agent
  • Key Considerations
    • Sterility: Maintaining a sterile collection environment is critical to prevent contamination from the patient’s skin, the collection container, or the collection technique itself
    • Timing: Collect the specimen at a time that minimizes the potential for contamination and maximizes the likelihood of detecting the pathogen
    • Transport and Storage: Prompt transport and appropriate storage of the specimen are essential to preserve the viability of bacteria and prevent overgrowth or degradation

Specimen Sources and Collection Methods

Here’s a breakdown of the common urine specimen sources, along with detailed collection instructions and considerations:

Midstream Clean-Catch Urine

  • Description: This is the most frequently used method for routine urine cultures. It aims to minimize contamination from the urethra and surrounding skin by collecting the “middle” portion of the urine stream
  • Patient Preparation and Procedure
    1. Hand Hygiene: Thoroughly wash hands with soap and water before starting
    2. Gather Supplies: Assemble the necessary materials:
      • Sterile container with a secure lid
      • Antiseptic wipes (e.g., povidone-iodine or chlorhexidine)
      • Sterile gloves (optional, but recommended)
      • Patient education materials
    3. Patient Education: Provide clear and concise instructions to the patient:
      • Wash Hands: Emphasize the importance of hand hygiene
      • Clean the Perineal Area
        • For Females: Separate the labia, and using the antiseptic wipes, clean the urethral opening from front to back (one wipe per area: front, left labia, right labia). Rinse with water and pat dry
        • For Males: Retract the foreskin (if uncircumcised), and clean the glans penis with the antiseptic wipes, moving in a circular motion from the tip outward. Rinse with water and pat dry
      • Initiate Voiding: Begin urinating into the toilet or a clean receptacle
      • Midstream Collection: After the first few milliliters have passed, position the sterile container into the urine stream to collect 20-30 mL of urine midstream. Avoid touching the container to the body
      • Finish Voiding: Finish urinating into the toilet
      • Seal and Label: Tightly seal the container and label it with the patient’s name, date, time of collection, and any relevant clinical information
    4. Special Considerations
      • First Morning Specimen: If possible, collect the first morning void, as this urine is more concentrated and may contain a higher bacterial load
      • Patient Mobility: Assist patients with limited mobility as needed

Catheterized Urine

  • Description: This method involves inserting a sterile catheter into the bladder through the urethra to collect the urine directly. It’s often used when patients are unable to void voluntarily or when a clean-catch specimen is difficult to obtain
  • Procedure
    1. Gather Supplies: Assemble the necessary materials:
      • Sterile catheter of appropriate size (e.g., Foley catheter)
      • Sterile gloves
      • Sterile lubricant
      • Antiseptic solution (e.g., povidone-iodine or chlorhexidine)
      • Sterile collection container
      • Syringe (for aspiration, if needed)
    2. Prepare the Patient
      • Explain the procedure to the patient and obtain consent
      • Position the patient appropriately (e.g., supine with legs slightly spread for females, supine for males)
      • Cleanse the perineal area with the antiseptic solution, following the same technique as for the clean-catch method
    3. Catheter Insertion
      • Don sterile gloves
      • Lubricate the catheter tip
      • Gently insert the catheter into the urethra
      • Advance the catheter until urine begins to flow
      • Collect the urine directly into the sterile container
    4. Specimen Collection
      • Aspiration (if needed): If the catheter is already in place, aspirate the urine from the catheter port using a sterile syringe
      • Removal: If the catheter is newly inserted, remove the catheter after collecting the urine
    5. Seal and Label: Tightly seal the container and label it with the patient’s name, date, time of collection, and any relevant clinical information
    6. Documentation: Document the procedure, including the catheter size and any difficulties encountered
  • Special Considerations
    • Risk of Infection: Catheterization carries a risk of introducing bacteria into the urinary tract. Strict aseptic technique is essential
    • Timing: Collect the specimen before initiating antibiotic therapy, if possible
    • Indwelling Catheters: If the patient has an indwelling catheter, collect the specimen from the catheter port (not the collection bag), after cleaning the port with an alcohol swab and allowing it to dry

Suprapubic Aspirate

  • Description: This method involves percutaneous aspiration of urine directly from the bladder using a needle and syringe. It’s considered the most sterile method but is invasive and typically reserved for specific situations
  • Procedure
    1. Gather Supplies: Assemble the necessary materials:
      • Sterile gloves
      • Antiseptic solution (e.g., povidone-iodine or chlorhexidine)
      • Sterile needles and syringes (typically 22-gauge needle and 10-20 mL syringe)
      • Sterile collection container
      • Ultrasound guidance (recommended)
    2. Patient Preparation
      • Explain the procedure to the patient and obtain consent
      • Ensure the patient has a full bladder (encourage fluid intake beforehand)
      • Position the patient supine
      • Cleanse the suprapubic area with the antiseptic solution
    3. Aspiration
      • Don sterile gloves
      • Under ultrasound guidance (preferred) or by palpation, insert the needle through the abdominal wall into the bladder
      • Aspirate urine into the syringe
    4. Specimen Collection
      • Withdraw the needle and syringe
      • Transfer the urine to the sterile collection container
    5. Seal and Label: Tightly seal the container and label it with the patient’s name, date, time of collection, and any relevant clinical information
    6. Post-Procedure Care: Apply a sterile dressing to the puncture site. Monitor the patient for any complications (e.g., bleeding, hematuria)
  • Special Considerations
    • Invasive Procedure: Requires physician expertise and carries a risk of complications, such as bleeding, bladder perforation, or peritonitis
    • Indications: Typically used for infants, patients with suspected bladder obstruction, or when other collection methods are not feasible
    • Ultrasound Guidance: Highly recommended to ensure accurate needle placement and minimize the risk of complications

Nephrostomy Tube

  • Description: A nephrostomy tube is a catheter inserted directly into the renal pelvis of the kidney to drain urine. Urine can be collected from the tube for culture
  • Procedure
    1. Gather Supplies: Assemble the necessary materials:
      • Sterile gloves
      • Alcohol swabs
      • Sterile syringe (usually a 5-10 mL syringe)
      • Sterile collection container
    2. Procedure
      • Don sterile gloves
      • Clean the nephrostomy tube port with an alcohol swab and allow it to dry
      • Attach a sterile syringe to the port and aspirate urine
      • Transfer the urine to the sterile collection container
    3. Seal and Label: Tightly seal the container and label it with the patient’s name, date, time of collection, and any relevant clinical information
  • Special Considerations
    • Established Catheter: This method is used when a nephrostomy tube is already in place
    • Aseptic Technique: Strict aseptic technique is essential to prevent contamination
    • Volume: Collect an adequate volume of urine for culture

Transport and Storage

  • Prompt Transport: Transport urine specimens to the laboratory as quickly as possible (ideally within 30 minutes to 2 hours) to prevent bacterial overgrowth or degradation
  • Refrigeration: If immediate transport is not possible, refrigerate the specimen at 2-8°C (35.6-46.4°F). Refrigeration can preserve the viability of bacteria for up to 24 hours
  • Preservatives: For longer storage or transport delays, certain preservatives (e.g., boric acid) may be added to the collection container. Follow the laboratory’s specific guidelines

Key Considerations

  • Patient Education: Thorough patient education is critical for proper specimen collection, especially for the clean-catch method
  • Aseptic Technique: Strict adherence to aseptic technique is essential to minimize contamination
  • Proper Labeling: Ensure the specimen container is labeled correctly with the patient’s name, date, time of collection, and any relevant clinical information
  • Volume: Collect an adequate volume of urine (typically 20-30 mL) for accurate testing
  • Timing: Collect the specimen at the appropriate time, considering the patient’s clinical condition and any medications they are taking
  • Communication: Communicate any difficulties or unusual circumstances encountered during the collection process to the laboratory

Key Terms

  • Midstream Clean-Catch: A urine collection method where the patient cleanses the urethral area and then, after initiating urination, collects a mid-portion of the urine stream into a sterile container. This technique aims to minimize contamination
  • Catheterization: The insertion of a sterile catheter (tube) into the bladder via the urethra to collect urine directly. This is often used when patients cannot void voluntarily
  • Suprapubic Aspirate: A urine collection method involving the percutaneous (through the skin) aspiration of urine directly from the bladder using a needle and syringe. It is the most sterile method but is invasive
  • Urine Culture: A laboratory test to identify and quantify bacteria present in a urine sample. It helps diagnose urinary tract infections (UTIs)
  • Colony-Forming Units (CFU): A unit of measurement used in urine cultures to quantify the number of bacteria present in a sample. The result is expressed as CFU/mL (colony-forming units per milliliter)
  • Contamination: The presence of unwanted microorganisms in a urine sample, often from the skin, surrounding environment, or improper collection technique. This can lead to inaccurate results
  • Pyuria: The presence of white blood cells (pus) in the urine, often indicating an infection in the urinary tract
  • Bacteriuria: The presence of bacteria in the urine. This can range from asymptomatic (no symptoms) to symptomatic (causing UTI symptoms)
  • Antimicrobial Susceptibility Testing (AST): Laboratory tests performed to determine the susceptibility (sensitivity) or resistance of bacterial isolates to various antimicrobial agents (antibiotics). This helps guide antibiotic therapy
  • Uropathogen: A microorganism capable of causing a urinary tract infection (UTI). Common examples include Escherichia coli, Staphylococcus saprophyticus, and Proteus mirabilis