Skip to main content

Microbiology

MRSA/MSSA, VRE, ESBL/CRE

This section covers the essential components of the laboratory workflow for detecting and characterizing these clinically significant organisms and resistance markers

Specimen Sources

The choice of specimen source is critical for accurate and timely detection. The selection depends on the suspected site of colonization or infection and the patient’s risk factors

MRSA/MSSA

  • Primary: Nasal swabs (most common screening site)
  • Secondary: Wound swabs, perineal swabs, other sites based on clinical suspicion (e.g., indwelling catheters)

VRE

  • Primary: Rectal swabs (GI tract as a primary reservoir)
  • Secondary: Stool samples, wound swabs, urine (if UTI is suspected)

ESBL/CRE

  • Primary: Rectal swabs (GI tract as a primary reservoir)
  • Secondary: Stool samples, wound swabs, urine (if UTI suspected), respiratory specimens (if pneumonia), blood cultures (if bacteremia/sepsis)

Common Considerations

  • Patient risk factors (healthcare exposure, antibiotic use, prior colonization/infection, indwelling devices)
  • Proper collection technique to minimize contamination
  • Appropriate labeling and transport to maintain specimen integrity

Culture Methods

Culture methods are still essential for isolating and identifying the organisms, as well as performing susceptibility testing

MRSA/MSSA

  • Selective Media
    • Chromogenic media (color-coded colonies)
    • Mannitol Salt Agar (MSA)
  • Non-Selective Media: Blood Agar Plate (BAP)
  • Identification
    • Colony morphology on BAP (creamy, golden)
    • Gram stain (Gram-positive cocci in clusters)
    • Coagulase test (to differentiate S. aureus)
    • Oxacillin/Cefoxitin disk diffusion (to detect methicillin resistance)
    • Latex agglutination (to detect PBP2a or confirm S. aureus)

VRE

  • Selective Media
    • Bile Esculin Agar (BEA) with Vancomycin
    • Chromogenic media
  • Identification
    • Colony morphology on BAP or BEA (small, white/gray)
    • Gram stain (Gram-positive cocci in pairs/short chains)
    • Catalase test (negative)
    • Vancomycin susceptibility testing (to confirm resistance)

ESBL/CRE

  • Selective Media
    • Chromogenic media (color-coded colonies)
    • MacConkey Agar
  • Identification
    • Colony morphology (variable, depends on organism)
    • Gram stain (Gram-negative bacilli)
    • Automated identification and susceptibility testing (e.g., Vitek, Phoenix)
    • Modified Kirby-Bauer disk diffusion (ESBL detection)
    • Phenotypic tests (e.g., double-disk synergy for ESBL; Modified Hodge test, Carba NP for carbapenemases)

Molecular Methods

Molecular methods offer rapid and sensitive detection of resistance genes, often directly from clinical specimens

MRSA/MSSA

  • Target: mecA gene
  • Methods
    • Real-Time PCR (qPCR) (most common)
    • Conventional PCR
    • Isothermal amplification (LAMP)
    • Molecular hybridization

VRE

  • Target: vanA, vanB, or other van genes
  • Methods
    • Real-Time PCR (qPCR)
    • Conventional PCR
    • Isothermal amplification (LAMP)
    • Molecular hybridization

ESBL/CRE

  • Targets: Genes encoding ESBLs (e.g., blaCTX-M, blaTEM, blaSHV) and carbapenemases (e.g., blaKPC, blaOXA-48, blaNDM)
  • Methods
    • Real-Time PCR (qPCR) (often multiplex)
    • Conventional PCR
    • Multiplex PCR
    • Microarrays
    • Next-Generation Sequencing (NGS)

General Considerations {-}

  • Advantages: Rapid, sensitive, specific, direct detection
  • Disadvantages: Cost, equipment/expertise, potential for false positives, and limited to the targets of the assay
  • Quality Control: Positive/negative controls, internal controls, validation
  • Interpretation: Detects the presence of resistance genes, phenotypic confirmation is often needed