Chapter 34: Clinical Microbiology and Immunology

Overview

• Clinical microbiology is the application of microbiology methods to detect and identify pathogens causing infectious diseases.
• Identification is based on morphological, physiological, biochemical, and immunological procedures.
• Rapid identification systems and computers can speed up the process in life-threatening situations.
• The chapter concludes with in vitro antigen-antibody interactions used in diagnostic tests.

Key Terms

• Clinical Microbiologist: Isolates and identifies microorganisms from clinical specimens quickly.
• Clinical Specimen: Human material tested for the presence/absence of specific organisms.

Diagnostic Techniques

• Rapid Tests: For quick identification of bacteria and fungi.
• Biochemical Identification: Based on biochemical reactions.
• ELISA Assays: Used for bacteria, fungi, protozoa, and viruses.
• Microscopy: For observing organisms.
• Cultures: To grow and study organisms.
• Biochemical Tests: Identify and determine sensitivity.
• Molecular Testing: Analyzing nucleic acids and toxin detection.

Laboratory Safety

• Standard Practices: Wash hands, no food/drink in lab, handle sharps and contaminated materials carefully.
• Biohazard Symbol: Recognize it and dispose of materials properly.
• Biosafety Levels (BSL):
  • BSL 1: Standard lab practices.
  • BSL 2: Limited access, biohazard disposal, PPE required.
  • BSL 3: Controlled access, waste decontamination, more stringent PPE.
  • BSL 4: High containment, full body suits, separate facilities.

Risk Groups

• Risk Group 1: Non-disease causing.
• Risk Group 2: Potential hazard if ingested or through injury.
• Risk Group 3: Potential for aerosol transmission, high risk.
• Risk Group 4: Dangerous, exotic agents causing life-threatening diseases.

Identifying Microorganisms

• Sample Collection: Ensure specimen is clean, representative, and uncontaminated.
• Testing Methods:
  • Microscopy: Direct examination after staining.
  • Growth & Biochemical Tests: Assessing metabolic functions.
  • Rapid Methods: Include API 20E for Enterobacteriaceae.
  • Immunomagnetic Beads: For targeting specific microbes.
  • Dichotomous Keys: Used for identification using specific characteristics.

Molecular Methods

• Techniques:
  • Nucleic Acid Hybridization & Sequencing.
  • Ribotyping: Using rRNA genes.
  • Gas Liquid Chromatography: For identifying metabolites.
  • Plasmid Fingerprinting: Analyzing plasmids.
  • PCR: Amplifying DNA for identification.

Serology

• Serotyping: Differentiating strains using antigen-antibody specificity.
• Agglutination Tests: For detecting visible clumps of cells.
• Complement Fixation: Detects serum antibodies.
• ELISA Assays:
  • Direct & Indirect: Detects antigens and antibodies.
• Lateral Flow Assays: For quick antigen-antibody detection.
• Western Blotting: Separates proteins for analysis.
• Immunoprecipitation: Detects immune complexes.
• Flow Cytometry: Detects microorganisms using light and fluorescence.

Conclusion

• Chapter 34 provides a comprehensive overview of clinical microbiology techniques, safety practices, and diagnostic methods.
• Understanding these processes is crucial for accurate diagnosis and treatment of infectious diseases.