Module 10: Maintenance Slides adapted from Cepheid Global Laboratory Initiative – Xpert MTB/RIF Training Package

World Health Organization Contents of this module 14 April, 2017 Discussion of the GeneXpert warranty Overview of maintenance Discussion of maintenance tasks: daily, weekly, monthly and annual Updating an assay definition file (ADF)

World Health Organization Learning objectives 14 April, 2017 At the end of this module, you will be able to: Describe current Cepheid warranty and service agreements Explain requirements for GeneXpert maintenance including periodic tasks, calibration of modules and updating the software with a new Assay Definition File

GeneXpert warranty (1 of 3) Each instrument procured after 24 April 2012 has an initial 2-year warranty: The warranty starts on the date of initial installation – that is, the date on the installation qualification report sent to Cepheid If the installation qualification report is not sent, the warranty starts from the date of shipment. If the machine is not calibrated after 1 year, the second year of the warranty is not valid.

GeneXpert warranty (2 of 3) The warranty covers repairs to the GeneXpert instrument and the replacement of any parts. The initial warranty is provided free of charge except for annual calibration costs: A calibration kit must be procured separately. As of 2014, an extended warranty may be purchased for US$ 2,900 per year (or for a discounted price as part of a 3-year package) to cover the machine after the initial 2-year warranty had ended: A calibration kit is included in the price of the extended warranty.

GeneXpert warranty (3 of 3) (send the report immediately to Cepheid) Qualification (send immediately to Cepheid)

Authorized service providers If Cepheid has appointed a local authorized service provider (ASP), the provider will offer certain services free of charge; these include: Exchanging or swapping modules after calibration if required; however, the price of the new modules is not included unless they are under warranty Repairing parts of the GeneXpert instrument; however, the price of parts is not included unless they are under warranty Placing orders for GeneXpert cartridges On-site installation and 1-day training at the time of installation. However, travel costs for the ASP (such as flights and accommodation) are NOT included. Additional training can be provided for a fee.

World Health Organization Maintenance overview 14 April, 2017 Frequency Task Daily Remove and properly dispose of cartridges Clean and disinfect work area Ensure 10 cm clearance around instrument Put on dust cover when instrument not in use Weekly Disinfect the interior of the cartridge bay Restart the GeneXpert instrument and computer Monthly Disinfect plungers Disinfect the instrument’s surfaces Clean the instrument’s filter (this applies only to newer model GeneXpert instruments, which have a white cover) Archive and back-up test results Annually or after 2,000 tests per module Calibrate the module

Materials required for maintenance Sodium hypochlorite solution (bleach with 0.72% active chlorine; use within 1 day after preparation) 70% ethanol or isopropyl alcohol solution (or equivalent) Wipes, tissues, or cotton or PET (polyethylene terephthalate) swabs Disposable gloves Clean water and soap (for washing the filters) Replacement filters for the fan (available from Cepheid)

Disinfection procedures for the work area, cartridge bay, plunger and instrument surfaces Dampen the wipe, tissue or swab with the sodium hypochlorite solution. Wipe the surface or element to be cleaned with the wipe, tissue or swab. Discard the used wipe, tissue or swab. Wait 10 minutes. Dampen a new wipe, tissue or swab with the ethanol or isopropyl alcohol solution. Repeat steps 5 through 7.

Daily tasks After testing, remove the cartridges from the instrument . Dispose of cartridges in the appropriate biohazardous waste container. Remove clutter from the work area. Disinfect the work area. Ensure that there is 10 cm clearance around all sides of the instrument. Put on the dust cover when the instrument is not in use, in order to reduce the amount of dust that may enter the system

Disinfect the interior of the cartridge bay Weekly task: Disinfect the interior of the cartridge bay Open the module door of the GeneXpert instrument. Clean the surfaces inside the module’s cartridge bay following the instructions on slide 10. CAUTION: Do not touch the slit in the back of the cartridge bay into which the cartridge-reaction tube is inserted. Close the module’s door. Repeat steps 1 through 3 for each module .

Restart the instrument and computer Weekly task: Restart the instrument and computer Note: This task is necessary only if the instrument and computer are not routinely turned off at the end of each day. On the computer, close the GeneXpert DX software. Turn off the GeneXpert instrument. Turn off the computer. Turn on the GeneXpert instrument. Turn on the computer. Launch the GeneXpert DX software.

Monthly task: Disinfect plungers (1 of 2) On the Maintenance menu, select “Plunger Maintenance”. In the “Plunger Maintenance” window, select a module to clean or select “Clean All”. Follow the instructions in the dialog box. Click “OK”.

Monthly task: Disinfect plungers (2 of 2) The plunger rod in the chosen module will be automatically lowered. Plunger Cartridge bay interior Module door open After cleaning the plungers, click on “Move Up All” and the plungers will return to their original position. Click “Close” .

Monthly task: Clean the instrument’s filter (1 of 2) Unscrew the 4 screws on the rear grey panel of the GeneXpert instrument.

Monthly Task: Clean the instrument’s filter (2 of 2) Remove the grey cover from the back of the instrument. Remove the filter (sponge). Wash the filter with soap and water . Allow the filter to dry completely, then replace it in the instrument. NOTE: Replacement filters are available from Cepheid if necessary. It is important to use only filters provided by Cepheid or the warranty may be compromised.

Monthly task: Archive and save results Archiving tests creates copies of test data in .gxx files (see also Module 7). Archiving allows you to: Back-up your data to ensure it will not be lost if the computer breaks down Create a copy of the data to send to Cepheid for assistance in troubleshooting problems. Files should be archived and saved to a CD or other appropriate external media (preferably an external drive) at least once a month to ensure that no test data are lost.

Difference between Archive/Backup: how to archive, retrieve, backup and restore data from a backup

How to archive results 1. Click “Data Management” 2. Click on “Archive test” 3. Choose the tests that need to be archived (or “Select All”) CAUTION !!! Leave “Delete Archived Tests” UNCHECKED

How to archive results (contd.) 5. In the nest dialog box click “Proceed” 6. The files will be saved in the folder “Export”. In the file name you will see the date of archiving It is highly advised to save (write) your archived data on a RW-CD or external drive 7. Click on “SAVE” 8. Click “OK”

How to retrieve results 1. Click “Data Management” and Click “Retrieve Test” 2. Select the file you want to retrieve 3. Click on ”Open”

How to retrieve results (contd.) 4. Select the test you may want to retrieve (or Select All) 5. Click “OK” 6. Click on “Proceed” 7. Click “OK”

How to back up data At the end of the working day when closing the GeneXpert software, you will have the following screen: 1. Click “YES” 2. Click on “Database Backup” 3. Click on “Proceed”

The zip file cannot be unzipped How to back up data The software will create a zip file with all the results. The file is saved on the desktop, in the GeneXpert folder -> Backup section 4. Click on “SAVE” 5. Click “OK” The zip file cannot be unzipped

How to restore data from a back up In case of computer failure you might have to restore your data after reinstallation of the system. By closing the GeneXpert software, you will have the following screen: 1. Click “YES” 2. Click on “Database Restore” 3. Click on “Proceed”

How to restore data from a back up (contd.) A warning message tells you that current database will be lost Click « Proceed » to continue Select the database to be restored and Click « Open » to continue

How to restore data from a back up (contd. 2) A dialog box asks you if you want to create a backup of the current database. Click « Proceed » to create the backup Click « Cancel » to continue Backup Restore

Annual task: Module calibration (1 of 3) Calibration should take place each year or after every 2,000 runs on each instrument module (whichever comes first) The date is calculated from the initial installation date (or based on the previous calibration date) , which is the date on the installation qualification report sent to Cepheid. NOTE: Order 1 calibration kit for each 4-module GeneXpert instrument. In 2014, the cost was US$ 450 plus shipping . If an extended warranty is purchased, a calibration kit is included. A calibration kit is not included in the initial warranty. Shipping costs are free if calibration kits are ordered with cartridges. The shelf-life of a calibration kit is 6-12 months (confirm the expiry date when you place order).

Annual task: Module calibration (2 of 3)

Annual calibration: Module calibration (3 of 3) Usually, this remote calibration process will be sufficient to readjust the modules for another year of operation. However, it is possible that the calibration of one or more of the modules may fail. If calibration fails, then the modules must be exchanged or swapped for new or refurbished modules from Cepheid, and the old modules must be sent to Cepheid.

Updating an assay definition file (ADF) (1 of 4) Occasionally Cepheid updates its software, and this requires an updated ADF to be imported. Insert the blue CD, which will be supplied with the cartridges, into the CD drive. In the GeneXpert DX software, click “Define Assays”. NOTE: The ADF is supplied on the CD that comes with the cartridge kit. Click on “Import”.

Updating an assay definition file (2 of 4) The “Import Assay” window will open. Find the CD on the appropriate drive.

Updating an assay definition file (3 of 4) Open the “GeneXpert Systems” folder. Click on the file “Xpert MTB-RIF.gxa”. NOTE: The name of this file will vary depending on the version of the software. In any case, choose the “.gxa” file, of which there will be only one on the CD. Click on “Import”.

Updating an assay definition file (4 of 4) The assay is now available for use. It will be listed as shown.

Cepheid assistance and support Before asking for support, have the following items ready: GeneXpert serial number, error code (or codes), description of the incident and archived run (if available). Cepheid HBDC Europe Training and Assistance (Monday to Friday, 8 am - 18 pm Central European time) Phone: +33.5.63.82.53.60 (53.78) (53.86) Cepheid Technical Support (for issues with the instrument and error codes) Europe (Monday to Friday, 8 am - 18 pm Central European time) Phone: +33.5.63.82.53.19 E-mail : support@cepheideurope.com United States (Monday to Friday, 6 am - 21 pm Pacific time) Phone: +1.888.838.3222; select option 2 E-mail: techsupport@cepheid.com

Log for documenting maintenance tasks To be customized by each country Example of a maintenance log:

Summary The warranty starts from the initial date of installation or from the date of shipment if the installation qualification report is not sent to Cepheid within 1 year of the shipment date. If the machine is not calibrated after 1 year, the second year of the warranty is not valid. An extended warranty can be purchased annually (or as a 3-year package) after the end of the initial 2-year warranty; a calibration kit is included with the extended warranty. Local authorized service providers (or ASPs) can provide specific services free of charge, including additional training; however, travel costs are NOT included. A number of maintenance procedures must be performed regularly (daily, weekly, monthly and annually, or after 2,000 tests per module) in order to ensure that the GeneXpert system functions properly. Cepheid occasionally updates its software; when this happens, the GeneXpert’s assay definition file (ADF) must be updated.

Assessment Why is it important to promptly send the installation qualification report as well as the calibration report to Cepheid? When should these two reports be sent? What is included in the warranty and what is excluded? List the daily, weekly, monthly and annual maintenance tasks, and specify those that are performed using the software. Describe the disinfection process and list the parts of the instrument that need to be disinfected as well as the disinfecting solutions that should be used for maintenance.

Acknowledgements The Xpert MTB/RIF Training Package has been developed by a consortium of GLI partners, including FIND, KNCV, US CDC, USAID, TB CARE I and WHO, with funding from USAID. The modules are based on materials originally developed by FIND, KNCV and Cepheid.