Standard Operating Procedure: GeneXpert Diagnostic Testing

This Standard Operating Procedure (SOP) outlines the mandatory protocols for the operation of the GeneXpert System for molecular diagnostic testing. Adherence to these procedures is critical to ensure operator safety, maintain sample integrity, and guarantee the accuracy of results. This document is intended for trained laboratory personnel responsible for the processing of clinical specimens using GeneXpert technology.

1. Pre-Analytical Phase: Preparation and Safety

• Personal Protective Equipment (PPE): Don appropriate PPE, including lab coat, gloves, and eye protection, prior to entering the testing area.
• Workstation Sanitation: Decontaminate the work surface with 10% bleach solution, followed by 70% ethanol to prevent cross-contamination.
• Module Inspection: Verify that the GeneXpert instrument is powered on, connected to the workstation, and that the LED status lights on the modules are blinking green (ready state).
• Reagent Inventory: Ensure the GeneXpert cartridges are at room temperature (if stored refrigerated) and verify the expiration date on the packaging.

2. Sample Preparation and Cartridge Loading

• Specimen Verification: Cross-reference the patient identifier on the clinical specimen container with the laboratory request form.
• Sample Processing: Follow the specific assay-specific instructions (e.g., Mycobacterium tuberculosis/RIF) to add the required volume of sample reagent to the specimen.
• Vortexing/Mixing: Agitate the specimen-reagent mixture according to the specific protocol to ensure complete liquefaction and homogenization.
• Transfer: Using a sterile, single-use pipette, transfer the exact required volume into the sample chamber of the cartridge. Ensure no bubbles are present.
• Sealing: Firmly close the cartridge lid until a click is heard.

3. Instrument Operation and Data Management

• Initiating the Run: Open the GeneXpert software on the workstation. Click "Create Test" and scan the cartridge barcode.
• Data Entry: Enter the patient information, specimen ID, and sample type into the required fields.
• Loading: Open the instrument module door, insert the cartridge until it clicks into place, and close the door.
• Monitoring: Verify the status window shows "Running" and monitor the progress bar. Do not attempt to open the module door while the status is "Running."
• Result Interpretation: Once the run is complete, review the result (Detected/Not Detected/Invalid). Ensure the internal controls have passed.

4. Post-Analytical Phase: Waste and Documentation

• Cartridge Disposal: Remove the cartridge and dispose of it immediately in a biohazard sharps container. Do not reuse cartridges.
• Reporting: Export or print the final result report and attach it to the patient file according to institutional policy.
• Shutdown/Maintenance: Perform daily cleaning of the instrument modules if required by the manufacturer’s maintenance schedule.

Pro Tips & Pitfalls

• Pro Tip: Always keep the pipette tips at eye level when drawing sample fluid to ensure precision; even a 50µl discrepancy can cause an "Invalid" result.
• Pro Tip: If you encounter a "System Error," do not force the module door; restart the software and the instrument before re-attempting.
• Pitfall: Never use a cartridge that has been dropped on the floor, as internal microfluidics may have been compromised.
• Pitfall: Avoid "pipette fatigue." If processing large batches, ensure consistent technique to prevent uneven sample volume distribution.

Frequently Asked Questions (FAQ)

Q: What should I do if a result comes back as "Invalid"? A: An "Invalid" result typically indicates a failure in the internal control. Ensure the sample was processed correctly, check the expiration of the cartridge, and re-run the test using a new cartridge and a fresh aliquot of the original specimen.

Q: Can I open the GeneXpert module door during a test to check the cartridge? A: No. Opening the door during a run will immediately abort the test and invalidate the result. The instrument is designed as a closed system to prevent aerosolization of pathogens.

Q: How often should the GeneXpert system be calibrated? A: Calibration is typically required annually or as specified by the manufacturer's service contract. Always verify the calibration sticker on the back of your specific unit.