Module 10:
Maintenance
Slides adapted from Cepheid
Global Laboratory Initiative – Xpert MTB/RIF Training Package
Contents of this module

Discussion of the GeneXpert warranty

Overview of maintenance

Discussion of maintenance tasks: daily, weekly, monthly and annual

Updating an assay definition file (ADF)
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Learning objectives
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
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GeneXpert warranty (1 of 3)

Each instrument procured after 24 April 2012 has an initial 2year warranty:
◦ The warranty starts on the date of instrument delivery

If the machine is not calibrated after 1 year, the second year of
the warranty is not valid.
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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.
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GeneXpert warranty (3 of 3)
(send the report
immediately to
Cepheid)
Delivery
Qualification
(send immediately to Cepheid)
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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.
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However, travel costs for the ASP (such as flights and accommodation)
are NOT included.
Additional training can be provided for a fee.
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Maintenance overview
Frequency
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
•
Calibrate the module
Annually or after 2,000 tests
per module
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Task
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Materials required for maintenance
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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)
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Disinfection procedures
for the work area, cartridge bay, plunger and instrument surfaces
1.
Dampen the wipe, tissue or swab with the sodium hypochlorite solution.
2.
Wipe the surface or element to be cleaned with the wipe, tissue or swab.
3.
Discard the used wipe, tissue or swab.
4.
Wait 10 minutes.
5.
Dampen a new wipe, tissue or swab with the ethanol or isopropyl alcohol
solution.
6.
Wipe the surface or element to be cleaned with the wipe, tissue or swab.
7.
Discard the used wipe, tissue or swab.
8.
Repeat steps 5 through 7.
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Daily tasks
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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
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Weekly task:
Disinfect the interior of the cartridge bay
1. Open the module door of the GeneXpert instrument.
2. 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.
3. Close the module’s door.
4. Repeat steps 1 through 3 for each module .
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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.
1.
2.
3.
4.
5.
6.
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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.
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1.
On the Maintenance menu, select “Plunger
Maintenance”.
2.
In the “Plunger Maintenance” window,
select a module to clean or select “Clean
All”.
3.
Follow the instructions in the dialog box.
4.
Click “OK”.
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5.
The plunger rod in the chosen
module will be automatically
lowered.
Plunger
Cartridge bay interior
Module door open
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6.
After cleaning the plungers, click on “Move
Up All” and the plungers will return to their
original position.
7.
Click “Close” .
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1. Unscrew the 4 screws on the
rear grey panel of the
GeneXpert instrument.
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2.
Remove the grey cover
from the back of the
instrument.
3.
Remove the filter
(sponge).
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.
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4.
Wash the filter with soap
and water .
5.
Allow the filter to dry
completely, then replace it
in the instrument.
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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.
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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
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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 RWCD or external
drive
7. Click on “SAVE”
8. Click “OK”
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1. Click “Data Management”
and
Click “Retrieve Test”
2. Select the file you want to
retrieve
3. Click on ”Open”
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4. Select the test you may want to
retrieve (or Select All)
5. Click “OK”
6. Click on “Proceed”
7. Click “OK”
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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”
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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
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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”
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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
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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
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
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 delivery date (or based on the previous
calibration date)
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).
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
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.
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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”.
1.
2.
NOTE: The ADF is supplied
on the CD that comes with
the cartridge kit.
3. Click on “Import”.
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4.
5.
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The “Import Assay”
window will open.
Find the CD on the
appropriate drive.
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Open the “GeneXpert
Systems” folder.
Click on the file “Xpert
MTB-RIF.gxa”.
6.
7.
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.
8. Click on “Import”.
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The assay is now available for use. It will be listed as shown.
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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
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Log for documenting maintenance tasks
To be customized by
each country
Example of a maintenance log:
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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.
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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.
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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.