Standard Operating Procedure: GeneXpert Diagnostic Testing

This Standard Operating Procedure (SOP) outlines the mandatory protocols for the operation of the GeneXpert system to ensure accurate, reproducible, and safe molecular diagnostic testing. All laboratory personnel must adhere strictly to these guidelines to maintain clinical integrity, prevent cross-contamination, and ensure the longevity of the instrumentation. This procedure covers the workflow from initial system power-up to data reporting and cartridge disposal.

1. Pre-Analytical Preparation

• Personal Protective Equipment (PPE): Don full lab attire, including a laboratory coat, nitrile gloves, and safety goggles.
• Workspace Sanitization: Decontaminate the work surface using a 10% bleach solution (or manufacturer-approved disinfectant) followed by 70% ethanol to remove residual bleach.
• System Check: Ensure the GeneXpert instrument and the connected computer are powered on. Verify that the GeneXpert software is running and that the system status indicator is green.
• Reagent Verification: Inspect the cartridge packaging for damage or expiration. Ensure cartridges have equilibrated to room temperature (15–30°C) if stored in a refrigerator.

2. Sample Processing and Cartridge Loading

• Sample Labeling: Verify that the specimen container label matches the patient requisition form.
• Specimen Preparation: Transfer the required volume of clinical specimen (e.g., sputum, plasma, or swab media) into the designated reagent container using the provided transfer pipette.
• Homogenization: Close the cap tightly and agitate the reagent-specimen mixture as specified by the specific assay protocol (typically 10–20 times).
• Cartridge Loading: Open the cartridge lid, pipette the entire volume of the prepared mixture into the sample chamber, and snap the lid shut firmly until an audible click is heard.
• Initiating the Run: Scan the cartridge barcode or manually enter the Lot ID and expiration date into the software interface. Enter the Patient ID and Sample ID carefully.

3. Execution and Monitoring

• Instrument Loading: Open the module door and insert the cartridge into the module until it clicks into place.
• Start Test: Confirm the module status changes to "Processing" on the software screen.
• Monitoring: Periodically observe the software dashboard for error codes or warnings throughout the run cycle.
• Data Integrity: Do not attempt to open the module door or cancel a run while the "In Progress" light is blinking, as this will invalidate the test.

4. Post-Analytical Handling

• Result Verification: Once the run is complete, review the "Results" tab. Verify that the internal controls (IC) passed.
• Data Export: Save the results to the laboratory information system (LIS) or print the report for the patient file.
• Waste Disposal: Remove the cartridge, ensuring the lid remains closed. Place the used cartridge directly into the biohazardous waste container.
• Post-Run Cleaning: Decontaminate the exterior of the module and the surrounding work area to prevent aerosol contamination.

Pro Tips & Pitfalls

• Pitfall - Aerosol Contamination: Never open a used cartridge. Opening the cartridge after the run releases concentrated amplicons into the environment, which will cause false-positive results in future tests.
• Pro Tip - Cartridge Equilibration: If you are in a high-throughput environment, keep a "ready-to-use" supply of cartridges at room temperature, but ensure they are used within the manufacturer's specified shelf-life to prevent reagent degradation.
• Pitfall - Incorrect Pipetting: Avoid introducing air bubbles during the transfer of the sample into the cartridge, as bubbles can interfere with the optical reading of the PCR cycles.
• Pro Tip - Software Backups: Perform a weekly database backup of the GeneXpert software to an external, encrypted drive to prevent data loss in the event of a computer hardware failure.

FAQ

Q: What should I do if the module displays an "Error" status? A: Do not attempt to force the door open. Note the specific error code provided in the software, consult the GeneXpert user manual for troubleshooting steps, and if the issue persists, contact technical support.

Q: Can I use cartridges that have expired? A: No. Expired reagents may result in failed internal controls or inaccurate results. Always verify the expiration date on the cartridge pouch before use.

Q: How often should the system undergo preventative maintenance? A: The GeneXpert system typically requires an annual calibration and preventative maintenance service by an authorized field engineer to ensure optical and mechanical precision.