1. GeneXpert Installation and Xpert MTB/RIF Set-up
Module 5:
GeneXpert Installation and Xpert MTB/RIF Set-up
Slides adapted from Cepheid
Global Laboratory Initiative – Xpert MTB/RIF Training Package

2. World Health Organization
Contents of this module
19 April, 2017
How to unpack GeneXpert system components and place in laboratory
How to connect components
How to start up computer & software
How to create Admin and user accounts
How to import assay definition file
How to issue “Installation Qualification Report” and its importance

3. Learning Objectives At the end of this module, you will be able to:
Be familiar with the components of the GeneXpert system and how to install it in your laboratory
Learn how to use the software, create Admin and User accounts, and import an Assay Definition File
Understand the importance of the “Installation Qualification Report”

4. Instrument Package Contents
Unpack the system and make sure items are complete
Keep the packaging and all the provided documents for future re-packaging/ expeditions
Barcode reader
GeneXpert
Computer
Monitor, keypad, mouse

5. Installation of GeneXpert: Selection of Space
Place the GeneXpert on a hard, level surface
Provide at least 10 cm of clearance on each side of the GeneXpert
Do not block the fan exhaust on the lower back side or the air intake on the upper back side
Do not place GeneXpert in direct sun (i.e. in front of window)
Do not place GeneXpert directly under A/C unit
Ambient temperature in the room must be between 15-30°C
Make sure the power cord connection and the power switch (on the back side) are easily accessible
Picture: GeneXpert Users Manual, Cepheid

6. Installation of GeneXpert: Connection
Connect one end of the supplied Ethernet cable to the network port on the back side of the computer
Connect the other end of the Ethernet cable to the network port on the lower back panel of the GeneXpert machine
NOTE: Ethernet cable is uni- directional. If it does not detect the GeneXpert machine, turn the cable around

7. Installation of the barcode reader, mouse, UPS: connections
Desktop computer version is shown
Connect the supplied power cords to the instrument, the computer and the monitor and then connect the power cords to a UPS (uninterruptable power supply).
Connect the barcode reader and the mouse directly to the computer USB ports.
Switch on the instrument: a small blue light on the front of the instrument turns on.

8. Installation of the barcode reader, mouse, UPS: connections
Laptop computer version is shown
Connect the supplied power cords to the instrument, the computer and the monitor and then connect the power cords to a UPS (uninterruptable power supply).
Connect the barcode reader and the mouse directly to the computer USB ports.
Switch on the instrument: a small blue light on the front of the instrument turns on.

9. Starting and configuring the Computer Software
Switch on the GeneXpert: a small blue light will appear on the front panel
Switch on the computer
Log on to Windows (XP or 7) as Cepheid user to operate the system. To log on, use the following:
User name (Windows XP): Cepheid
User name (Windows 7): Cepheid-Amin
Password: cphd
Windows XP
Windows 7

10. Starting and configuring the Computer Software
Wait until the GeneXpert DX software starts automatically
In the Check Status screen, verify that all modules are “Available”
(If modules are not available, refer to chapter 11 of the Operator manual or call Cepheid technical support)
Windows XP
Windows 7

11. Starting and configuring the Computer Software
In case the software was closed (computer still on), the software may be restarted by clicking on the “GeneXpert Dx” icon on the desktop
Windows XP
Windows 7

12. Optimal installation: configuration of the software
Set up the local time in the Windows operation system
Rename your GeneXpert in the software, from SETUP → SYSTEM CONFIGURATION → replace “GeneXpert PC” by the laboratory name, country and serial number of the GeneXpert → see screenshot below and on next slide
Windows XP
Windows 7

13. Optimal installation: configuration of the software
Set up the options according to your needs (automatic printing, scanning a patient ID barcode, etc), from SETPUP → SYSTEM CONFIGURATION
Windows XP
Windows 7

14. Installation of accounts and definition file
ADMIN ACCOUNT: at first installation, before creating the User Account
USER ACCOUNT: enables staff to use the GeneXpert
ASSAY DEFINITION FILE (ADF): enables the device to run the XPERT MTB/RIF programme
INSTALLATION QUALIFICATION REPORT: report issued at the end of installation, to be signed and sent to Cepheid (necessary for machine calibration and warranty)

15. Create Accounts: ADMIN
Define the person in the lab that will have full access to the software. There can be more than one Administrator account per system.
1. Click on “Setup/User administration”
NOTE: The first account to be created must be an “Admin” account
2. Click on “Add”

16. Create Accounts: ADMIN (contd.)
3. Create user name & password:
(Ideally the same for all machines in the country)
4. Select User type: “Admin”
5. Click on “OK”

17. Create Accounts: USER 1. Click on “Setup/User administration”
2. Click on “Add”

18. Create Accounts: USER (contd.)
3. Create user name & password:
(select yourself)
4. Select User type: “Basic”
NOTE: If you select “Detail”, the user will see the individual curves for the molecular beacons.
5. Click on “OK”

19. How to login

20. Installation Qualification Report
Create a report at the end of installation:
Click on “Reports”, and then on “Installation Qualification”
A PDF file will come up: save this on computer and print a copy
Supervisor signs the report and sends a copy to Cepheid:
IMPORTANT NOTE:
The installation qualification report is required for machine calibration and warranty: it needs to be sent to Cepheid directly after installation.
If not sent, the warranty date starts from the day of shipment (see Module 10 for more on warranties and maintenance).

21. Virus protection
In order to protect the GeneXpert software it is recommended to:
Install the antivirus software that is provided with the instrument (NortonTM)
Do not connect the computer to the internet, except when undergoing Xpert calibration or if connected to a remote data monitoring system
Do not use a USB key to transfer files to/from the computer. Use a CD or hard-disk to collect data

22. Summary
Upon reception, carefully check the package components, prior to installing the device in your laboratory
Connect the GeneXpert machine to all its components (PC, monitor, UPS, barcode scanner) and to internet (via Ethernet cable)
Create your "Admin" (at first installation) and afterwards your "User" accounts
The Assay Definition File (ADF) enables the device to run the XPERT MTB/RIF programme: use the provided "blue CD" to import an ADF
The Installation Qualification Report is issued at the end of installation and has to be signed and sent to Cepheid (mandatory for GeneXpert warranty)

23. Assessment
List the major components of the instrument package and the major features for the selection of the physical space for installation
List all of the necessary steps to connect the device, install the computer software and create your accounts and reports
Why is it essential to import the Assay Definition File and to send the installation Qualification report to Cepehid?
What can you do to protect the XPERT MTB/RIF programme from misuse or viruses?

24. 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.