Gastrointestinal

This section discusses the essential analytic procedures for bacteriology in the context of gastrointestinal (GI) infections, covering key diagnostic methods

General Principles

• Fecal Specimens: Most diagnostic tests use stool samples
• Key Pathogens: Salmonella spp., Shigella spp., toxigenic Escherichia coli, Campylobacter spp., Vibrio spp., Yersinia enterocolitica, Aeromonas spp., Plesiomonas shigelloides, Clostridioides difficile, and Helicobacter pylori
• Diagnosis and Management: The goals are:
  • Accurate identification
  • Guiding treatment
  • Public health surveillance
• Methods: Culture, antigen detection, and molecular methods are used
• Proper Handling: Proper collection and transport are essential

Colony Morphology and Identification of Major Pathogens

• Culture and Colony Characteristics
  • Salmonella spp.:
    • MacConkey Agar: Colorless
    • Hektoen Enteric Agar (HEA): Blue-green colonies, with or without black centers
    • XLD Agar: Red colonies, with or without black centers
    • Gram Stain: Gram-negative rods
  • Shigella spp.:
    • MacConkey Agar: Colorless
    • HEA: Green colonies
    • XLD Agar: Red colonies
    • Gram Stain: Gram-negative rods
  • Escherichia coli: (Toxigenic):
    • MacConkey Agar: Pink, lactose-fermenting
    • Selective Media: SMAC
    • Gram Stain: Gram-negative rods
  • Campylobacter spp.:
    • Campy-blood agar: Small, gray, non-hemolytic, often smear across the agar
    • Gram Stain: Gram-negative curved or S-shaped rods
  • Vibrio spp.:
    • TCBS Agar: Used for isolation
    • V. cholerae: Yellow colonies
    • V. parahaemolyticus: Green colonies
    • Gram Stain: Gram-negative rods (curved)
  • Yersinia enterocolitica:
    • CIN Agar: Red “bull’s eye”
    • Gram Stain: Gram-negative rods
  • Aeromonas spp.:
    • Blood Agar: Gray, beta-hemolytic
  • Plesiomonas shigelloides:
    • Blood Agar: Gray, non-hemolytic
• Identification
  • Biochemical Tests: TSI, urease, oxidase, etc
  • Commercial Identification Systems: Automated methods

Antigen Detection and Molecular Methods

• Rapid and Sensitive Tests: These tests supplement culture
• Methods
  • Antigen Detection
    • Clostridioides difficile: (formerly Clostridium difficile): EIAs, lateral flow assays
  • Molecular Methods
    • PCR: Amplifies specific DNA or RNA sequences
    • Real-time PCR (qPCR): Quantifies the amount of DNA
    • Targets: C. difficile toxins, Shiga toxin genes
• Advantages: Fast results, high sensitivity
• Disadvantages: Cost, technical expertise
• Clinical Application: Rapid and accurate diagnosis

Serotyping of Escherichia coli, Salmonella spp., and Shigella spp.

• Purpose: Identifying specific strains for epidemiology
• Procedure
  • Isolate from culture
  • Use specific antisera to identify the O, H, and K antigens
  • Agglutination is key
  • Interpret based on the results
• Clinical Significance: Important to track outbreaks
• Example: E. coli O157:H7

Organism Pathogenicity

• Understanding Disease: The process of how organisms cause illness
• Key Aspects: Adherence, Invasion, Toxins
• Examples
  • Salmonella spp.: Invasion, Type III secretion system
  • Shigella spp.: Invasion, Shiga toxin
  • E. coli (Toxigenic): Toxin production
  • Campylobacter spp.: Adherence, invasion, toxin
  • Vibrio spp.: Toxin production
• Implications: Guides diagnosis, treatment, and prevention

Detection Methods for Helicobacter pylori

• Diagnosis: Testing for H. pylori
• Invasive Tests (Endoscopy Required)
  • Gastric Biopsy: Histology
    • H&E stain
    • Special stains
  • Rapid Urease Test (CLO Test): Biopsy specimen
  • Culture: Biopsy specimen
• Non-Invasive Tests (No Endoscopy Required)
  • Urea Breath Test (UBT): Patient drinks a solution containing urea labeled with a carbon isotope (e.g., 13C or 14C)
  • Fecal Antigen Test (FAT): Detects H. pylori antigens
  • Serology (Antibody Detection): Detects antibodies
• Test Selection and Interpretation: Correct choice is needed
• Eradication Monitoring: UBT, FAT, or biopsy with culture