Commercial Kits

This section explores the theory, interpretation, and application of commercial kits used for bacterial identification. These kits offer convenience, speed, and standardized procedures, making them a valuable tool in the clinical microbiology laboratory

Theory: The Science Behind the Packaged Solutions

What are Commercial Kits?
- Commercial kits are prepackaged, standardized systems for identifying bacteria
- They contain pre-formulated reagents, substrates, and often, miniaturized test systems
- They are designed to simplify and streamline the identification process
- They are based on various biochemical reactions, including substrate utilization, enzyme detection, and other metabolic activities
Why Use Commercial Kits?
- Convenience and Speed: Easy to use and provide rapid results compared to traditional methods
- Standardization: Standardized procedures and reagents reduce variability and increase reproducibility
- Ease of Use: Simplified protocols often require less technical expertise
- Comprehensive: Many kits offer a broad range of tests for identifying a wide variety of organisms
- Data Management: Some kits integrate with computer systems for data entry and reporting
- Cost-Effective: Can be cost-effective in the long run by reducing labor and reagent waste
Types of Commercial Kits
- Automated Systems: (e.g., Vitek, MicroScan): Fully automated systems that perform multiple tests simultaneously
- Semi-Automated Systems: (e.g., API, Crystal): Kits with pre-filled wells or strips that require manual inoculation and observation
- Rapid Identification Kits: (e.g., Gram-positive identification kits, Neisseria identification kits): Designed for rapid identification of specific groups of organisms
Principles of Operation
- Substrate Utilization: Bacteria are inoculated into wells containing different substrates. Growth and/or a change in the media (e.g., pH indicator) indicate substrate utilization
- Enzyme Detection: Reactions are designed to detect the presence of a specific enzyme. Colorimetric or other visual changes indicate a positive result
- Metabolic Product Detection: Tests detect the production of specific metabolic products (e.g., acid, gas)
Key Components
- Test Strips/Cards/Wells: Contain dried substrates, reagents, and/or pre-filled media
- Inoculation Devices: Used to introduce the bacterial inoculum into the test system
- Incubation Chamber: Provides the appropriate temperature and atmosphere for bacterial growth
- Reading System: Can be visual (manual) or automated (instrument-based) for result interpretation
- Database: Software that interprets the test results and provides an identification

Interpretation: Deciphering the Results

Reading the Results
- Visual Reading: Observe for color changes, turbidity, gas production, or other visual indicators
- Automated Reading: Automated systems use optical or other sensors to detect changes and provide an interpretation
Interpreting the Results
- Pattern Recognition: Match the observed test results (positive/negative reactions) to a database of known organisms
- Code Numbers: Some kits use code numbers to represent the results, which are then looked up in a database
- Computer-Generated Identification: Automated systems automatically generate an identification based on the test results
Accuracy and Reliability
- Database Accuracy: The accuracy of the identification depends on the accuracy and completeness of the kit’s database
- User Technique: Proper technique is essential for accurate results
- Limitations: Some kits may not be able to differentiate between closely related species
- Quality Control: Strict adherence to QC protocols is critical
Typical Result Formats
- Code Profiles: Series of numbers or letters representing the pattern of positive and negative reactions
- Percentage Probabilities: Identification is reported with a probability percentage
- Confidence Levels: Some systems provide a confidence level for the identification

Application: Putting Knowledge into Practice

Quality Control (QC)
- Control Strains: Use known positive and negative control organisms for each kit
- Frequency: Perform QC according to the manufacturer’s recommendations (e.g., daily, weekly, with each new lot of reagents)
- Documentation: Record QC results in a logbook or LIS
- QC Failure: If QC fails, investigate the cause and repeat the test with new reagents and/or a new control strain
Procedure
1. Gram Stain and Colony Morphology: Perform a Gram stain and observe colony morphology before using a kit
2. Inoculum Preparation: Prepare a pure culture of the organism according to the kit’s instructions
3. Inoculation: Inoculate the test system (strips, wells, etc.) with the prepared inoculum
4. Incubation: Incubate the test system under the recommended conditions (temperature, atmosphere)
5. Reading the Results: Read the results visually or with the automated system, following the manufacturer’s instructions
6. Interpretation: Interpret the results using the kit’s database or software
7. Documentation: Record the results in a lab notebook or LIS
8. Correlation: Correlate the results with other test results (Gram stain, colony morphology) and clinical information to arrive at a definitive identification
9. Reporting: Report the identification to the clinician
Examples: Using Commercial Kits
- API 20E (bioMérieux): Used for identifying Enterobacteriaceae and other Gram-negative rods
- API Staph (bioMérieux): Used for identifying Staphylococcus species
- Vitek 2 (bioMérieux): Automated system with a wide range of identification capabilities
- MicroScan (Beckman Coulter): Automated system with a wide range of identification capabilities
- Rapid ID Kits (e.g., Neisseria Identification Kits): Designed for rapid identification of specific organisms
Troubleshooting
- Incorrect Results
  - Incorrect Inoculum: Ensure proper inoculum preparation and concentration
  - Contamination: Use pure cultures and maintain aseptic technique
  - Expired Reagents: Use fresh reagents and store them properly
  - Incorrect Incubation: Follow the recommended incubation conditions
  - Database Errors: Check the kit’s database and software
- Weak or Indeterminate Results
  - Old Cultures: Use fresh cultures
  - Incorrect Procedure: Review the test procedure
  - Incubation Conditions: Ensure proper incubation temperature and atmosphere
  - Follow-up Testing: Perform additional tests to confirm the identification

Key Terms

Commercial Kits: Prepackaged, standardized systems for bacterial identification
Automated Systems: Systems that perform multiple tests simultaneously and provide automated result interpretation
Semi-Automated Systems: Kits that require manual inoculation and observation, but may have automated reading systems
Substrate: A substance that is acted upon by an enzyme
Enzyme: A protein that catalyzes a specific biochemical reaction
Inoculum: The material used to inoculate a culture medium or test system
Incubation: The process of maintaining a culture at a specific temperature and atmosphere to promote growth
Code Profile: A series of numbers or letters representing the pattern of positive and negative reactions in a test system
Percentage Probability: The likelihood that an organism is identified correctly, expressed as a percentage
Quality Control (QC): Procedures used to monitor and ensure the reliability of laboratory testing
Control Strains: Known organisms used as positive and negative controls in laboratory tests
Database: A collection of data used for identification, typically including the biochemical profiles of known organisms
Gram Stain: A differential staining technique used to classify bacteria based on their cell wall structure
Colony Morphology: The visual characteristics of bacterial colonies on solid media
Aseptic Technique: Procedures used to prevent contamination
Biochemical Reaction: A chemical reaction that occurs within a living organism or in a test system
Turbidity: The cloudiness or haziness of a liquid, often indicating bacterial growth

Conventional Biochemical ID

Automated Methods