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Microbiology

Specimen Sources

This section covers MRSA/MSSA, VRE, ESBL/CRE screening and pinpoints those crucial specimen sources. This is a critical area in clinical microbiology, and understanding the “where” is just as important as the “how.”

MRSA/MSSA Screening

  • Primary Goal: To identify the presence of Staphylococcus aureus (SA) and determine if it carries the mecA gene, which confers methicillin-resistance (MRSA)

  • Specimen Sources

    • Nasal Swabs: This is the most common and often the initial site for screening. The anterior nares (nostrils) are frequently colonized with S. aureus
    • Wound Swabs: Any open wound, surgical site, or skin lesion is a potential source, especially in healthcare settings
    • Perineal Swabs: Can be collected to detect colonization
    • Other sites: (e.g. indwelling catheters)

VRE Screening

  • Primary Goal: To identify the presence of Vancomycin-Resistant Enterococci (VRE), typically Enterococcus faecalis or Enterococcus faecium, and determine if they are resistant to vancomycin

  • Specimen Sources

    • Rectal Swabs: This is the most common site. The gastrointestinal tract is a primary reservoir for enterococci
    • Stool Samples: May be requested for patients with diarrhea or suspected GI infections
    • Wound Swabs: If the wound is infected, especially in patients with risk factors for VRE colonization or infection
    • Urine: In patients with suspected urinary tract infections

ESBL/CRE Screening

  • Primary Goal: To identify the presence of Extended-Spectrum Beta-Lactamase (ESBL)-producing or Carbapenem-Resistant Enterobacteriaceae (CRE)

  • Specimen Sources

    • Rectal Swabs: Similar to VRE screening, the GI tract is a key reservoir
    • Stool Samples: Similar to VRE screening, may be requested for patients with diarrhea or suspected GI infections
    • Wound Swabs: If the wound is infected, especially in patients with risk factors for ESBL/CRE colonization or infection
    • Urine: In patients with suspected urinary tract infections
    • Respiratory Specimens: (e.g., sputum, endotracheal aspirate) if the patient has pneumonia or respiratory symptoms
    • Blood Cultures: If the patient is suspected of having a bloodstream infection (bacteremia or sepsis)

Important Considerations for all three

  • Patient Population/Risk Factors
    • Healthcare-associated infections: Patients in hospitals, nursing homes, or long-term care facilities are at higher risk
    • Prior antibiotic use: Especially broad-spectrum antibiotics
    • Previous MRSA/VRE/ESBL/CRE colonization or infection
    • Recent hospitalization or surgery
    • Presence of indwelling medical devices: (e.g., catheters)
  • Specimen Collection Technique: Proper collection is crucial to ensure accurate results
    • Use appropriate swabs and transport media
    • Follow institutional protocols for collection and handling
    • Ensure the specimen is labeled correctly with patient information
  • Timing of Screening
    • Upon admission to a healthcare facility, especially for high-risk patients
    • During outbreaks or when there’s a high index of suspicion
    • Follow-up screenings may be performed to monitor colonization status

Key Terms

  • MRSA (Methicillin-Resistant Staphylococcus aureus): A strain of Staphylococcus aureus that is resistant to methicillin and other beta-lactam antibiotics (penicillins, cephalosporins) due to the presence of the mecA gene
  • MSSA (Methicillin-Susceptible Staphylococcus aureus): A strain of Staphylococcus aureus that is susceptible to methicillin and other beta-lactam antibiotics
  • VRE (Vancomycin-Resistant Enterococci): Enterococci (typically Enterococcus faecalis or Enterococcus faecium) that are resistant to the antibiotic vancomycin. This resistance is often due to the vanA or vanB genes
  • ESBL (Extended-Spectrum Beta-Lactamase): Enzymes produced by certain Gram-negative bacteria (e.g., Escherichia coli, Klebsiella pneumoniae) that confer resistance to a broad range of beta-lactam antibiotics, including penicillins, cephalosporins, and aztreonam
  • CRE (Carbapenem-Resistant Enterobacteriaceae): Enterobacteriaceae (e.g., Escherichia coli, Klebsiella pneumoniae) that are resistant to carbapenem antibiotics, which are often used as a last resort for treating serious infections. Resistance is often due to carbapenemase enzymes (e.g., KPC, OXA-48)
  • mecA gene: A gene found in MRSA that encodes for a modified penicillin-binding protein (PBP2a) that has a low affinity for beta-lactam antibiotics, leading to resistance
  • vanA or vanB genes: Genes found in VRE that encode for proteins that alter the cell wall structure, reducing the binding of vancomycin to its target
  • Colonization: The presence of bacteria on a body surface (e.g., skin, nares, gut) without causing active infection or symptoms
  • Infection: The invasion and multiplication of pathogenic microorganisms in a body tissue or organ, causing illness or disease
  • Screening: The process of testing individuals or populations for the presence of a specific organism or resistance marker, often without regard to symptoms, to identify carriers or those at risk for infection