Lecture 20

Exam Overview

• Exam 4 format similar to Exam 3
• Strategy: Answer short answer questions first
• Open office hours on Zoom (Apr 8, 7-8 pm)
• Email notifications for homework and team activities
• Extra credit for 75% completion on TRACE

Topics Covered Today

• Pathogen Identification
  • Biochemical Profiles
  • Nucleic Acid Amplification Tests (NAATs, e.g., PCR)
  • Point-of-Care Rapid Diagnostics Tests
• Review for Exam 4

Case Study: Thomas's Illness

• Background: Thomas (5 years old) and family visit a fair
• Symptoms: Stomach cramps, vomiting, diarrhea, blood in diarrhea
• Treatment Journey: Initial doctor's appointment leads to diagnosis of acute renal failure
• Sample Collection: Urine, blood, and stool samples collected for testing

Pathogen Identification Techniques

1. Biochemical Profiles

• Definition: Used primarily for bacteria to identify microbial pathogens
• Methods: Employ selective and differential media, dichotomous keys
• Key Bacterial Examples:
  • Streptococcus pneumoniae: Identified via optochin sensitivity
  • Staphylococcus aureus: Has positive coagulase test | Catalase positive

2. PCR (Polymerase Chain Reaction)

• Function: Amplifies DNA from pathogens (no need for viable cells)
  • Allows detection of specific sequences from pathogens (viral & hard-to-culture bacteria)
  • Provides visual results through gel electrophoresis
• Procedure Overview:
  • Primers bind to specific pathogen genes
  • RNA extracted from samples, converted to DNA
  • Amplification with specific primers followed by result interpretation

3. Advantages and Disadvantages of Identification Techniques

• Biochemical Tests:
  • Advantages: Provide pure cultures, useful for antibiotic susceptibility testing
  • Disadvantages: Time-consuming, not effective on hard-to-culture organisms, infection risk to staff
• PCR - NAATs:
  • Advantages: High sensitivity, rapid results, effective for hard-to-culture pathogens
  • Disadvantages: High cost, complex technology, limited information on pathogen susceptibility

Point-of-Care Rapid Diagnostics

• Focus: Fast diagnosis of infectious diseases
• Sensitivity vs. Specificity:
  • Sensitivity: Correctly identifies those with the disease (true positives)
  • Specificity: Correctly identifies those without the disease (true negatives)
• Immunochromatography (example: pregnancy tests)
• Advantages: Fast results, no culturing, helps prevent unnecessary antibiotic use
• Disadvantages: Risk of missing multiple infections, no data on antibiotic sensitivity

Important Metrics:

• Sensitivity & Specificity in Diagnostic Tests
• Understanding percentage values and how they affect test credibility

Summary of Case Study Tests

• Testing Focus on E. coli 0157:H7:
  • Toxin Production: Produces Shiga toxin impacting kidneys
  • PCR analysis confirms presence of toxin gene, indicating pathogenic strain

Review Points for Exam 4

• Review all identification techniques, case studies, and diagnostic tests
• Understand key microbial characteristics and their implications for diagnosis and treatment
• Prepare for questions about symptoms, pathogen tests, and immunological responses.