Collection, transportation and processing of clinical samples for microbiology investigations

Collection of Clinical Samples

• Selecting the Appropriate Sample:

  • The sample type depends on the clinical condition, site of infection, and suspected microorganism. For example:
    • Blood cultures for systemic infections like sepsis.
    • Sputum for respiratory infections, such as pneumonia or tuberculosis.
    • Urine for urinary tract infections.
    • CSF for suspected meningitis.
    • Stool for gastrointestinal infections.
  • Correct collection methods prevent contamination and ensure the presence of a sufficient number of viable organisms.

• Aseptic Technique:

  • Aseptic techniques are essential to prevent contamination by normal flora or external microbes.
  • For example:
    • Blood collection: The skin should be disinfected with an antiseptic solution (such as chlorhexidine or alcohol) before drawing blood.

      

    • Urine collection: Midstream clean-catch technique or use of a catheter, if required.
  • All instruments should be sterile, and personal protective equipment (PPE) should be used.

• Timing of Collection:

  • Samples should be collected before administering antibiotics, as antibiotics can reduce pathogen viability.
  • Some infections, especially septicemia, have diurnal patterns, and it’s best to collect samples when the microbial load is highest.
  • For blood cultures, multiple samples collected over time increase the likelihood of detecting intermittent bacteremia.

• Labeling and Documentation:

  • Samples must be accurately labeled with patient details (name, age, ID), collection date and time, and collection site.
  • Requisition forms should include relevant clinical history, recent antibiotic use, and the suspected pathogen.

 

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Transportation of Clinical Samples

• Temperature Control:

  • Temperature is crucial for preserving sample integrity.
    • Blood, CSF, and tissue: Usually transported at room temperature.
    • Urine: Often requires refrigeration if transport is delayed.
    • Stool: Refrigerated or kept at room temperature depending on suspected pathogens (e.g., parasitic samples should be kept at room temperature).
    • Viral samples: Typically require a viral transport medium and may need refrigeration.

• Transport Media:

  • Specialized transport media prevent drying and maintain the viability of organisms.
    • Viral Transport Media (VTM): For respiratory and other viral samples.
    • Stuart’s or Amies transport media: For swabs (throat, wound, etc.) to preserve bacterial samples.
    • Anaerobic transport media: For anaerobes, exposure to oxygen can kill these organisms.

• Secure Containers:

  • Containers should be sterile, leak-proof, and securely closed.
  • Samples should be double-bagged, with the outer bag carrying an absorbent material to contain spills.

• Timely Transport:

  • Transport delays can lead to bacterial overgrowth or death, especially for fastidious organisms. Samples should ideally reach the lab within 2 hours.
  • If a delay is unavoidable, refrigeration is preferred for most samples, except where refrigeration might compromise results (e.g., CSF).

• Documentation During Transport:

  • Documentation, including the chain of custody, is essential for traceability and to ensure samples aren’t lost or mishandled.

 

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Processing of Clinical Samples

• Receipt and Logging:

  • On arrival, each sample is inspected to ensure correct labeling and that it hasn’t been compromised (e.g., leakage, improper temperature).
  • The sample is logged into the laboratory information system, generating a unique ID for tracking.

• Biosafety Precautions:

  • Depending on the sample type, labs may use biosafety cabinets to prevent exposure to pathogens, especially for high-risk samples like TB or COVID-19.
  • Staff must follow biosafety guidelines, including wearing PPE (gloves, masks, lab coats, face shields).

• Preliminary Testing:

  • Direct microscopy (e.g., Gram stain, acid-fast stain, or wet mount) helps provide rapid information.
    • Gram stain: Used for bacteria, giving insights into the morphology and Gram reaction (positive or negative).
    • Acid-fast stain: Important for mycobacteria, such as tuberculosis.
    • Wet mount: Used for stool samples to detect parasites.
  • Rapid antigen tests or molecular methods (e.g., PCR) may be conducted for quick results on specific pathogens.

• Culture and Incubation:

  • Samples are plated on selective and differential media to support the growth of specific organisms and inhibit contaminants.
    • Blood agar: Supports a broad range of bacteria.
    • MacConkey agar: Selective for Gram-negative bacteria, differentiates lactose fermenters.
    • Sabouraud agar: For fungal cultures.
    • Anaerobic media: For obligate anaerobes incubated in an oxygen-free environment.
  • Incubation times and temperatures vary:
    • 37°C for most bacteria.
    • 25-30°C for fungi.
    • Cold enrichment (4°C) for specific pathogens like Listeria.

• Identification and Sensitivity Testing:

  • Identification can be achieved through:
    • Biochemical tests: For example, catalase and coagulase tests for Staphylococcus species.
    • Automated systems, Like MALDI-TOF, for precise species identification.
    • Molecular methods: PCR for identifying DNA/RNA sequences specific to certain pathogens.
  • Antimicrobial Susceptibility Testing (AST): Performed on isolated bacteria to determine effective antibiotics using methods like disk diffusion or automated systems.

• Reporting:

  • Results should be documented and interpreted by a microbiologist. Critical results, such as positive blood cultures, should be promptly communicated to clinicians.
  • AST results help guide clinicians in selecting appropriate antibiotics.