1

It is imperative that all users read the GeneXpert® Operator’s Manual and the Xpert®

MTB/RIF protocols (CD-ROM) for comprehensive operating instructions, including

important warnings relating to operator safety.

2

INDEX

• Log book p.3

• What you need to run an Xpert® MTB/RIF assay p.4

• Optimal installation: define the best location p.5

• Installation of the system with a desktop/laptop p.6-7

• Prepare your instrument for a routine use p.8

• Optimal installation: configuration of the software p.9

• Installation Qualification report p.10

• Sample Collection for Xpert® MTB/RIF assay p.11

• Xpert® MTB/RIF procedure from fresh sputum p.12

• Xpert® MTB/RIF procedure from deposit p.13

• Routine operation, create test p.14

• View your results p.15

• Generate a report p.16

• Software key messages p.18-25

• In case of test update p.26

• Save your data p.27

• Save your data on a RW- CD ROM or CD-ROM p.28

• Instrument troubleshooting p.30-31

• Barcode reader troubleshooting p.32

• Maintenance p.33

• GeneXpert® System log-sheet p.34

• Do’s/ Don’ts p.35

• Assistance from Cepheid p.36

2

3

LOG BOOK

Intervention date/ time

Reason of intervention Solution Technician name

Company

3

4

WHAY YOU NEED TO RUN AN XPERT

® MTB/RIF ASSAY

Provided: • GeneXpert® System (GeneXpert + Computer + Barcode scanner)

• Xpert® MTB/RIF kit: (1 cartridge + buffer(s) related 1 sample)

Not provided: • Translucent, screw-capped specimen collection containers

• Lab coat/ Disposable gloves/Respiratory protection

• Timer

• Indelible labeling marker

Optional: • Safety Cabinet, up to the institution to decide if safety cabinet is required

• Printer

• Surge protector - UPS

• Additional 2 ml plastic transfer pipettes

4

5

OPTIMAL INSTALLATION DEFINE THE BEST LOCATION

1- Well ventilated room

2- Not directly under an air conditioning vent or window (no direct sunlight)

3- Controlled lab temperature (15-30°C)

4- GeneXpert® placed on stable work bench, no centrifuge close to it

5- Stable electricity supply (connected to UPS/surge protector)

6- Provide 5-10cm of clearance on each side of the instrument

5

6

INSTALLATION OF A SYSTEM WITH A DESKTOP

6

7

INSTALLATION OF A SYSTEM WITH A LAPTOP

7

8

PREPARE YOUR INSTRUMENT FOR A ROUTINE USE

1- Switch on the GeneXpert®: a small blue light will appear at the front of the system

2- Switch on the Computer

3- Login in the Windows session called Cepheid:

Username: Cepheid Password: cphd

4- Wait: the GeneXpert® software will automatically open

5- When the GeneXpert® Dx software is open, check if all the modules are AVAILABLE in CHECK STATUS screen

8

9

OPTIMAL INSTALLATION – CONFIGURATION OF THE SOFTWARE

Set up the local time in Windows Operating System (do not change the Unicode country)

Rename your GeneXpert® in the software from SETUP SYSTEM CONFIGURATION replace ‘’GeneXpert® PC’’ by the laboratory name,

country and serial number of the system see below screen

Set up the options according to the need: automatic printing, scanning the patient-sample ID barcode from SETUP SYSTEM CONFIGURATION see below screen

1

2

3

2

3

9

10

INSTALLATION QUALIFICATION REPORT

In order to update your warranty status, please generate a report to complete your installation:

Go to: Reports Installation Qualification

Save this report

Send the file with contact name, phone number, email address and

physical address of the GeneXpert ® to :

training@cepheidhbdc.com or CEPHEID - HBDC Training - Vira Solelh

F-81470 Maurens-Scopont - FRANCE

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11

SAMPLE COLLECTION FOR XPERT

® MTB/RIF ASSAY

To obtain adequate specimen, follow the instructions in this section closely.

Note: Procedures in the current package insert supersede these procedures. Please

refer to it (from the blue CD in each kit)

Note: Collect a minimum of 1 ml of sputum per specimen. Subject must be seated or standing. - Rinse the patient’s mouth twice with water.

- Unscrew the lid on the sputum collection container.

- Have the patient inhale deeply, cough vigorously, and expectorate the material into the sterile screw-capped specimen collection container. Avoid spills or soiling the outside of the container

- Secure the lid on the collection device. Specimens can be stored at a maximum of 35 °C for less than 3 days and at 4 °C for 4-10 days.

Transportation: Specimens should be held at 2–8 °C during transport to the laboratory.

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12

XPERT® MTB/RIF

PROCEDURE FROM FRESH SPUTUM

1- Prepare your sample

• For each of the samples: unscrew the lid of sputum collection container.

• Add directly in the collection container 2 volumes of sample reagent to 1 volume of

sample.

• Replace the lid, and shake vigorously 10-20 times (or vortex) (Note: one back and forth

movement is a single shake.)

• Incubate at room temperature. After 10 min. of incubation, shake (or vortex) the

specimen vigorously 10-20 times.

• After 5 min. of incubation, sample should be perfectly fluid before being processed,

with no visible clumps of sputum. If still viscous, wait 5-10 further minutes before

processing it in the cartridge.

2- Prepare your cartridge

• Label the cartridge with the sample ID by writing on the left or right side of the cartridge

or affix ID label. Open the cartridge. Pipette at least 2 ml with the plastic transfer

pipette from the collection container to the cartridge. Close the cartridge lid.

• Note: do not put the label on the lid of the cartridge or obstruct the existing 2D barcode

on the cartridge.

This summary does not replace the package insert (blue CD-ROM in the

kit) please refer to it for full and complete information

12

13

XPERT® MTB/RIF – PROCEDURE FROM DEPOSIT

1- Prepare your sediment NALC-NaOH-citrate solution (prepared

daily) according to the method of Kent and Kubica

2- Prepare your cartridge with appropriate sediment volume

Collect 0.5 ml of prepared sediment and add 1.5 ml of the sample reagent.

Replace the lid, and shake vigorously 10-20 times. (Note: one back and forth

movement is a single shake.)

Incubate at room temperature. After 10 min. of incubation, shake (or vortex) the

specimen vigorously 10-20 times. 5 minutes later, label the cartridge with the sample

ID by writing on the left or right side of the cartridge or affix ID label.

Open the cartridge. Pipette 2 ml with the plastic transfer pipette from the collection

container to the cartridge. Close the cartridge lid.

Note: do not put the label on the lid of the cartridge or obstruct the existing 2D barcode

on the cartridge

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14

ROUTINE OPERATION – CREATE A TEST

14

Sample ID Fill-in the Sample ID

Start a test

The software displays automatically the module that is less used: do not select a module

1 2

Create Test Scan the cartridge barcode

Load the cartridge on the blinking module

3

5

4

15

VIEW YOUR RESULT

You can visualize one particular result on a full screen

15

Click on VIEW RESULT

1

2 Double-click on the run from the table

16

GENERATE A REPORT

You can generate a report in pdf and print it automatically (if option defined)

1

2

3

16

17

17

18

SOFTWARE KEY MESSAGES

This is crucial to understand the key messages delivered by the software.

Most frequent messages are explained on the coming pages.

• INVALID

• NO RESULT

• ERRORS

– 5007

– 2008

– 2127

– 5011

.

This summary does not replace the Operator Manual (CD-ROM

provided in this quick start kit). For further details, please refer to the

Chapter 11: Troubleshooting section in the CD-ROM

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INVALID

Cause SPC (Internal Control) failed

Origin PCR was inhibited due to inhibitors (pus, food particles)

Solution(s)

Before mixing with Cepheid sample reagent (SR) for decontamination, check that sample does not contain food particles, pus.

Collect a new sample when necessary

Solution

Before mixing with Cepheid sample reagent (SR) fo

19

No amplification of SPC nor targets.

20

NO RESULT

20

Cause

Test could not be terminated and insufficient data were collected

Origin(s) Software stops working before the module due to:

- Windows or Software freeze

- Power failure

- STOP TEST function has been activated (accidentally or deliberately)

Solution(s)

Secure the power supply. This error is independent from the GeneXpert®

Solution(s)

Secure the power supply. This error is in

21

ERRORS

Cause

Many different causes can lead to an ERROR result. Click on Errors to know more about the specific issue

Origin(s) Most frequent issues, linked to sampling, are detailed in the next slides. They should be addressed by operators following the advice contained in this document

Solution(s) To easily reduce an unexpectedly high Error rate, it is essential that all operators identify errors linked to sample preparation, and address them as indicated next slides.

21

All other issues should be reported to Cepheid’s hotline.

22

ERROR 5007

22

Cause

Probe Check control failed and test was stopped before amplification

Origin(s)

Sputum viscosity and/or wrong sample volume, or cartridge reaction tube improperly filled, contains bubbles, or probe integrity issues detected

Solution(s)

After 15 (10+5) minutes of decontamination, if the sample is still too viscous do not load it into the cartridge.

Wait up to 10 further minutes until the sample is totally liquefied, and then transfer it into the cartridge using a new disposable pipette. The transferred volume into the cartridge should be between 2 and 4 mL max.

23

ERROR 2008

Solution(s) After 15 (10+5) minutes of decontamination, if the sample is still too viscous do not load it into the cartridge. Wait up to 10 further minutes until the sample is totally liquefied, then transfer it into the cartridge using a new disposable pipette.

Cause

Pressure exceeds the maximum pressure allowed

Origin (s)

Sample is too viscous

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24

ERROR 2127

Note: In case of Laptop, which can run on its own batteries, or modules stops first

Error 2127 will appear

Cause

Module communication loss was detected.

Origin(s)

Power supply issue (main power or UPS fluctuations)

Solution(s)

Unplug and replug Ethernet cable between PC and instrument. Unplug and replug the communication cable between gateway board and GeneXpert®. Restart system. Check temperature (should be below 39°C)

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25

ERROR 5011

Cause

Signal loss detected in the amplification curve

Origin(s)

Loss of tube pressure because the cartridge tube is not airtight, or cartridge valve is not working right

Solution(s)

Do not use that cartridge. Use a new cartridge. If error repeats, this can be module related: modules fluidics are not working well. Contact Cepheid support team.

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26

IN CASE OF TEST UPDATE

In case of test update, before running a test, you need to import the Assay

definition of the test (ADF) from the CD-ROM provided in the kit.

1- Click on DEFINE ASSAYS 2- Click on the import button 3- Locate the CD-ROM from the D drive location 4- Import your file Xpert MTB-RIF G4_5. gxa from the blue CD-ROM

26

27

SAVE YOUR DATA Select: Archive test, Select the run(s), and then select OK

27

Click on Proceed

Click on Save

3

4

To prevent data loss:

Once a month, burn your results on a RW-CD (see p.27)

2

1

Click on OK

Click on Archive Test

28

SAVE YOUR DATA TO A RW-CD/ CD

28

29

29

30

INSTRUMENT TROUBLESHOOTING

30

Communication issue:

• 1- GeneXpert switched on before Computer?

• 2- GX Modules available in software? CHECK STATUS NO

YES Run a test

Ethernet cross-over cable loose, or damaged?

YES NO

C- Computer/or GX LAN Port damaged

Replace the Ethernet cross-over cable

You can run a test

B- IP address lost the GX IP Address needs to be re configured

Contact Technical Support (p.36)

- Test the Computer LAN port with a printer to see if it works or not

- Contact Technical support (p.36)

to define if computer related / GeneXpert® related

A- Right Ethernet port selected (On desktop)?

D- Bad Gateway board

Module or Motherboard needs to be replaced: Contact Technical support (p.36)

31

INSTRUMENT TROUBLESHOOTING

Cartridge integrity testing 2037: at the early beginning of a test, the

GeneXpert® checks the pressure inside the tube. If the pressure is not correct,

the software will not allow you to do the testing. Do not use that cartridge.

Temperature failure 3074/3075:

Cause: heater failure

- Does this error affect only one module? Always the same?

- Does it affect various modules?

Origin(s)

High temperature in the module

Dead fan

Solution(s)

Check the fans at the rear of the instrument

Check the internal temperature of the module in the MAINTENANCE menu

from the software

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32

BARCODE SCANNER TROUBLESHOOTING

Can you hear a BEEP sound when USB cable of the barcode reader: connected to the computer?

YES

Connect the barcode reader to another USB port of the computer. Can you hear a BEEP?

NO

Barcode reader failure

NO YES

Scan your cartridge. Can you scan it?

NO YES

Check if the Assay Definition file is imported

Contact Technical Support (p.36)

Contact Technical Support to learn how to reconfigure your barcode scanner (p.36)

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33

MAINTENANCE

The whole maintenance process needs to be done with a sterile wipe (no cotton) with

a 10% final concentration sodium hypochlorite (bleach) prepared within one day, then

once dry 5 minutes later, wipe with a 70% ethanol or isopropyl alcohol solution

Daily

Maintenance

Discard used cartridges, clean the bench work surround the

instrument

Weekly

Maintenance

Restart the GeneXpert®, computer then software

Disinfect the cartridge bay interior

Monthly

Maintenance

Disinfect the GeneXpert® surfaces

Disinfect the plunger rods

Archive the results and save them on a CD-ROM/RW-CD

Clean the filter at the back of the system with soapy water

Calibration

Calibrate the modules once a year or every 2000 runs/modules,

whichever comes first

Contact the Customer Service Team (see page 36)

This summary does not replace the Operator Manual (CD-ROM provided in this quick

start kit). For further details, please refer to the Chapter 10: Maintenance section in the

CD-ROM

33

34

GENEXPERT SYSTEM LOG-SHEET

This is a sample: have copies of this page and store

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35

DO’S AND DON’TS

DON'TS DO'S

Computer Software

× Never install ANY non-approved software: this computer is dedicated to the GeneXpert®

Install the NORTON INTERNET SECURITY ANTIVIRUS with antispyware provided by Cepheid

× Never alter the computer settings or pre-installed software

Update your antivirus from time to time

× Never turn on or use other non–Windows firewall products

In case the institution requires the use of another antivirus than the one provided, validate data communication between the instrument and the computer before installing

× Never replace the system network connection

× Never change the IP setting for the Ethernet connection to the GeneXpert Dx Software

Disable the “Automatically synchronize with internet time server” from Internet time on the Windows settings by deselecting the adjacent checkbox

× Never install 2 antiviruses at the same time, as the computer will freeze

× Never use USB stick-Flash keys to collect the data Save-Archive your data every week

× Never use a USB hub Log out from the GeneXpert Dx software (NOT WINDOWS) while test in progress: the system will continue to finish the test and save the results

× Never change the Cepheid user profile on Windows Use a hardisk or RW-CD-ROM to collect the data

× Never change Windows update settings Disable the USB ports if you want to avoid Trojan horses/virus problems

× Never accept Windows updates Store the Microsoft CDs provided with the system in a safe place

× Never create different windows profiles

× Never change date/time/time zone when test is in progress

× Never exclude a module from testing without Cepheid’s authorization

× Never change the folders tab where the data are saved

× Never reinstall the GeneXpert DX software without Cepheid’s authorization

× Never run other software while test is in progress

GeneXpert® × Never put the system in a place which is not stable Install the system on a hard sturdy level surface and at

recommended working temperature (15-30 °C)

× Never block the fan exhaust at the rear of the instrument

Power down your complete system at least once a week

× Never move the system when test is in progress Wear disposable gloves for the cleaning procedure

× Never replace system parts without Cepheid’s assistance

Follow the instructions to clean the system for appropriate use

× Never insert the swab inside the ICORE- module slot during cleaning procedure

In case of need to replace parts in the system, wear an ESD wrist protection

× Never install the system in an area with a heat source such as direct sunlight or the exhaust of another instrument

× Never install the instrument on a bench containing an instrument that creates vibrations (such as a centrifuge)

Cartridge

× Never store your cartridges at high or very low temperatures

Store your kits at room temperature (2-28°C)

× Never store your cartridges ready with sample inside in the fridge or the freezer

Store your cartridge out of the pouch up to 30 min at 2-35 °C

× Never pick up the cartridge by the PCR tube with your fingers

Pick-up the cartridge by its body (left and right side)

× Never write the patient ID/sample ID on the barcode sticker at the front of the cartridge

Write the patient ID/ Sample ID on the left or right side of the cartridge

× Never tip the cartridge upside down once sample has been loaded

Discard the cartridge after use

× Never process a cartridge that has been dropped or shaken

× Never process a cartridge with a damaged reaction tube

× Never re-use a spent cartridge

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36

ASSISTANCE FROM CEPHEID

Should you face any problem, please contact your local service provider if

available in your country, or Cepheid directly for a review of your results

and eventually for refresher training.

Service Telephone Email address

Local Service Provider - - - - - -

Training Center (Europe) +33.5.63.82.53.60 training@cepheidhbdc.com

Technical hotline (Europe

based)- Instrument errors

+33.5.63.82.53.19 support@cepheideurope.com

Technical hotline (U.S.A based)-

Instrument errors

+1-888-838-3222,

Option 2

techsupport@cepheid.com

Customer Service +33.5.63.82.53.33 ordershbdc@cepheidhbdc.com

Information of the system

Serial number of your GeneXpert®

(at the back side, near the power button)

Computer Service Express Service Tag Number

Installation date of the system … / … / ….

Windows password (should never be changed) cphd

When contacting Cepheid, please prepare: the serial number of the GeneXpert®,

the recorded error messages, the description of the incident and when possible the

archived runs concerned (p.17).

http://www.cepheidcares.com/tb/resources

HPM40003 – V3.0 – 27th

of August, 2013

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