Module 12:
Quality Assurance
Global Laboratory Initiative – Xpert MTB/RIF Training Package
Contents of this module


What is quality assurance?
Key components of Xpert MTB/RIF quality assurance
programme
◦ Training and competence assessment
◦ Instrument verification
◦ Method validation
◦ Quality control and lot testing
◦ Quality indicator monitoring
◦ External quality assurance/assessment (EQA)
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Global Laboratory Initiative
Xpert MTB/RIF Training Package
Learning Objectives
At the end of this module, you will be able to:


Describe the function of the two internal quality controls in each Xpert
MTB/RIF cartridge
Understand and apply the requirements for Xpert MTB/RIF instrument
verification

List Xpert MTB/RIF quality indicators to be monitored

Understand and apply the requirements of on-site supervision
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Understand and apply requirements for proficiency testing for Xpert
MTB/RIF
Understand how to develop and apply a comprehensive approach to
quality assurance
Global Laboratory Initiative
Xpert MTB/RIF Training Package
 “Planned and systematic activities to provide confidence that an
organization fulfills requirements for quality.” [CLSI GP26-A4]
 “Encompasses a range of activities that enable laboratories to achieve and
maintain high levels of accuracy and proficiency despite changes in test
methods and the volume of specimens tested.” [www.cdc.gov/labstandards]
 Quality assurance is just one part of a Laboratory Quality Management
System, required to ensure quality of all its processes
 Continuous quality improvement is a critical concept to be adopted by
laboratories
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Global Laboratory Initiative
Xpert MTB/RIF Training Package
Environment
- Safe and
functional
- Temperature
control
Personnel
- Trained and
competent
staff
- Test user is
documented
- Current
SOPs readily
available
Equipment
- Maintained
and serviced
Supplies
- Uninterrupted
supplies
- Appropriate
transport and
storage
conditions
Specimens
- Good quality
Labelled with
unique ID
- Completed
request form
Internal
quality
monitoring
- Test
working
properly
External
Quality
Assessment
(EQA)
- Testing
site‘s work
checked by
another site
Accurate and
timely
reporting
- Turnaround
time
Results
review
Accurate, reliable and timely results
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Xpert MTB/RIF Training Package
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The quality improvement
cycle includes the four steps
Plan (P), Do (D), Check (C)
and Action (A)
Non-conformities identified
during routine testing and
quality assurance activities
should be analysed,
corrective actions
implemented and monitored
Steps should be repeated
over time to ensure
continuous improvements
in lab processes
Global Laboratory Initiative
Xpert MTB/RIF Training Package

Bio-safety requirements similar to direct sputum smear microscopy
◦ Refer to Module 2


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Secure premises for the equipment to prevent theft of the GeneXpert
unit and the computer/laptop
Stable electricity supply or sufficient measures to ensure uninterrupted
supply (generator, solar panels, battery/UPS backup, etc.)
Appropriate measures to prevent ambient temperature exceeding 30°C
in the room where equipment will be installed (e.g. ventilation, air
conditioning)
Appropriate management of biohazardous waste according to local
guidelines
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Global Laboratory Initiative
Xpert MTB/RIF Training Package

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Qualification requirements for testing personnel determined by
country’s Ministry of Health or other governing body
At least 1-2 staff per testing site
◦ Basic computer literacy
◦ Knowledge of laboratory registers
◦ Performs testing and interprets results
◦ Conducts routine equipment maintenance
◦ Troubleshoots common testing problems

Documented initial training and competency assessment

Documented annual competency assessment
◦ Refresher training as needed

Standard Operating Procedures (SOPs) must be up to date and available
onsite
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Xpert MTB/RIF Training Package

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Maintain all laboratory equipment in a good working condition
Perform instrument verification upon installation and after
calibration/module replacement
Daily, weekly, monthly, and annual maintenance tasks performed
◦
Refer to Module 9

All maintenance tasks recorded on appropriate logs

Troubleshooting testing or instrument failures

Documentation of corrective action(s)

Warranty or service contracts in place and terms and conditions adhered to

Maintain dated service records
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Global Laboratory Initiative
Xpert MTB/RIF Training Package

Plan procurement based on actual test consumption data. Rotate stock to
ensure that oldest material is used first
◦
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SOPs for supply and reagent procurement and inventory management
Adequate storage of Xpert MTB/RIF cartridges at recommended temperature
range (2-28°C)
◦
Daily temperature monitoring
◦
Corrective action documentation if temperature out of range
Label all supplies and reagents with date received, and the date first opened
Any material found to be unsatisfactory should be recorded as such and
removed from the laboratory immediately so it is not used
Label prepared disinfectants with name, date prepared, expiry date
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Global Laboratory Initiative
Xpert MTB/RIF Training Package

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Ensure SOPs are available and patients are instructed in providing good
quality specimens
Ensure specimens are labeled correctly and request forms are completed
Reject specimens that are incorrectly labeled, leaking, in broken
containers or of insufficient volume

Record the date specimens arrive in the laboratory

Monitor specimen transport times

Evaluate and record the sputum specimen quality

Specimens should be refrigerated at 2–8°C for a maximum of 10 days
◦
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If necessary, specimens can be stored at a maximum of 35°C for up
to 3 days, and then refrigerated at 2–8°C for a combined maximum
duration of 10 days
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Xpert MTB/RIF Training Package



Slide is optional, for
certain audiences
GeneXpert users may be designated as admin, detailed or basic users
This designation relates to the functions and level of detail visible on the
Xpert MTB/RIF software
Some quality assurance and troubleshooting functions are only available to
staff with admin or detailed user access
◦ e.g. Ct values, graphs and error codes


Ensure the correct staff have appropriate access based on their job function,
e.g. staff responsible for QA and troubleshooting need detailed or admin
access
Functions available to different level users can be customised according to
need
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Global Laboratory Initiative
Xpert MTB/RIF Training Package

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Each cartridge contains internal controls (Sample Processing Control and
Probe Check Control)
Positive and negative controls may be run according to local guidelines
Record the results of control samples, troubleshoot any unexpected
results and monitor trends over time
Control strains should be from well-characterised (phenotypic and
genotypic) clinical isolates
Routinely monitor quality indicators
◦ See quality indicator monitoring slides below
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Global Laboratory Initiative
Xpert MTB/RIF Training Package

Each cartridge includes a Sample Processing Control (SPC), which
contains non-infectious spores in the form of a dry spore cake, to verify
adequate processing of MTB
◦
Verifies that lysis of MTB has occurred
◦
Verifies the specimen processing is adequate
◦
Detects specimen-associated inhibition of the real-time PCR assay

SPC must be positive when the result is MTB Not Detected; and

SPC can be negative or positive when the result is MTB Detected
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The test result is invalid if the SPC is negative when the test result is
negative
Global Laboratory Initiative
Xpert MTB/RIF Training Package
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The Probe Check Control is undertaken by the system before the PCR
reaction starts. The system measures the fluorescence signal from the
probes to monitor:
◦
bead rehydration
◦
reaction-tube filling
◦
probe integrity, and
◦
fluorescent dye stability
Results are automatically compared to the pre-established factory
settings in the software
If Probe Check fails, then the test is stopped, and an Error result is
obtained
Global Laboratory Initiative
Xpert MTB/RIF Training Package
“Inter-laboratory comparisons and other performance evaluations that
may extend throughout all phases of the testing cycle, including
interpretation of results; determination of individual and collective
laboratory performance characteristics of examination procedures by
means of inter-laboratory comparison; NOTE: the primary objectives of
EQA are educational and may be supported by additional elements.” [CLSI
GP27-A2]
EQA:

Is used to improve performance across the laboratory network

Is an important tool for communicating with and motivating staff

Is designed to identify and resolve problems

Is not used to punish staff
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Global Laboratory Initiative
Xpert MTB/RIF Training Package
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Report Xpert MTB/RIF results within 24 hours after the specimen is
received at the testing site to allow rapid treatment initiation
Appropriate sample transportation systems are required to ensure rapid
shipment of samples and the reporting of results to referring sites
Record all work performed in standard format in the Laboratory
Register
Analyze Xpert MTB/RIF results each month to detect changes which may
indicate problems
◦
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See recommended quality indicators
Global Laboratory Initiative
Xpert MTB/RIF Training Package
GLI recommends the following components for a comprehensive approach
to quality assurance of the Xpert MTB/RIF assay:
1.
2.
3.
4.
5.
6.
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Training and user competence assessment
Instrument verification
Quality indicator monitoring
On-site supervision
New lot (incoming) QC testing
Proficiency testing (PT)
Global Laboratory Initiative
Xpert MTB/RIF Training Package


Blinded re-checking (recommended for TB smear microscopy EQA) is
not appropriate for Xpert MTB/RIF testing since the entire specimen is
usually required to perform the test and no specimen can be saved for
later re-checking
If Xpert MTB/RIF is used according to manufacturer’s specifications,
method validation is not required
◦ Use of an alternative protocol or sample that is not included in the
product insert should be validated by the laboratory prior to use
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Global Laboratory Initiative
Xpert MTB/RIF Training Package


Each module should be verified as being “fit for purpose” using known
positive and/or negative material prior to starting testing of clinical
specimens
At least one verification test should be performed per module after:
◦ Instrument installation
◦ Post-calibration or swapping of instrument modules

Verification panels are now distributed routinely by Cepheid with each
new instrument and with recalibrated modules
◦

Verification panels consist of a card containing 5 Dried Culture Spots
(DCS) of a known concentration of whole inactivated Mycobacterium
tuberculosis (rifampicin sensitive) bacilli
DCS samples should be processed according to instructions and one
sample tested per module. All results are expected to be MTB Detected,
RIF resistance Not Detected
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Global Laboratory Initiative
Xpert MTB/RIF Training Package

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If an invalid/error/no result is obtained on any module, repeat the test in
that module using the extra DCS sample provided
In case of not obtaining the expected result in any module, refer to the
Troubleshooting module (Module 9)
Instrument verification results should be reported to the designated
GeneXpert supervisor
Cepheid should be contacted immediately in order to assist with any
problems in the verification process
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Global Laboratory Initiative
Xpert MTB/RIF Training Package

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Site visits should be planned at regular intervals to assess laboratory/testing
site practices
Usually conducted by NRL/NTP and/or partners
◦
◦
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Standardized checklist must be utilized for consistency and completeness of
information
Identifies which practices are ‘good’ and which areas need improving
Collect information for
◦
◦
◦
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Planning & implementation
Monitoring
Continuous quality improvement
Especially critical during early stages of implementation of new technology
Provides motivation and support to staff, especially in peripheral settings
◦
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May be conducted by national level or regional/district level staff
Should be integrated with other on-site supervision where possible (e.g. quarterly
NTP site visits)
Strong relationships with staff encourages rapid reporting of any problems
Enables rapid troubleshooting, re-training and corrective actions
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Xpert MTB/RIF Training Package

A schedule for site visits should be drawn up in advance, preferably
integrated with other supervision activities

Responsibilities for on-site supervision may be decentralised to
regional/district staff
◦
All staff conducting supervision visits need appropriate training and should use
standardised checklists
◦
Reports should be shared with the testing site and NTRL/NTP according to local
practices

On-site supervision should be conducted in conjunction with collection
and review of quality indicators

Proficiency testing and monitoring of quality indicators do not negate the
need for on-site supervision
◦
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Poorly performing testing sites should be prioritised for on-site visits
Global Laboratory Initiative
Xpert MTB/RIF Training Package

Sufficient time should be allocated for supervisory visits, including travel time

All components of Xpert MTB/RIF testing and lab workflow should be evaluated
◦
◦
Comprehensive assessments may be conducted less frequently (e.g. annually) by
expert laboratory staff, with more frequent (e.g. quarterly) visits done by
district/regional supervisors or other appropriately trained staff
The extent of evaluation during each visit will depend on frequency of visit, capacity
of staff and performance of laboratory (more extensive evaluation is needed in poorly
performing sites)
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Assess pre- and post-analytical stages (specimen collection, recording &
reporting results, confirmatory testing)
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Check and analyze trends in Xpert MTB/RIF indicators

Run GeneXpert software reports to view frequencies and types of errors

Mentor staff on troubleshooting and error reporting during site visits

Visits are opportunities to:
◦
◦
◦
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learn
discuss concerns
solve problems
Global Laboratory Initiative
Xpert MTB/RIF Training Package
To be customized by
each country
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Routine monitoring of quality indicators (performance indicators) is a critical
element of quality assurance for any diagnostic test and is also an ISO requirement
Every month, each testing site should collect and analyse quality indicators
Any unexplained change in quality indicators (such as increase in error rates,
change in MTB positivity rate or RIF resistance rate or significant change in volume
of tests conducted) should be documented and investigated
Error rates higher than a pre-determined threshold (e.g. 5%) should be investigated
Quality indicators should be reviewed by the laboratory manager and must always
be linked to corrective actions if any unexpected results or trends are observed
A standard set of quality indicators should be used for all sites conducting Xpert
MTB/RIF testing
A system should be in place for centralised reporting of monthly quality indicators
Documentation of corrective actions, and subsequent improvement/normalisation
of lab indicators following corrective action are critical
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Xpert MTB/RIF Training Package
To be customized by
country
Each instrument should be monitored on a monthly basiseach
using
the
following minimum set of indicators to evaluate proper use:
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Number
Number
Number
Number
Number
Number
Number
Number
of tests performed per month
and proportion of MTB detected, RIF resistance not detected
and proportion of MTB detected, RIF resistance detected
and proportion of MTB detected RIF indeterminate
and proportion of MTB not detected
and proportion of errors
and proportion of invalid results
and proportion of no results
Where possible, countries should collect disaggregated data according to
the population group tested (HIV positive, MDR risk, extrapulmonary)
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Xpert MTB/RIF Training Package
Identifying the number and type of various errors can help with
troubleshooting since certain errors may be associated with processing,
instrument or environmental conditions
The following analyses may be performed:
 The number of errors occurring by instrument module
◦ If a particular module produces more errors over time compared with
other modules, it may require repair
 The number of errors occurring by user
◦ If a user has a high number of errors, investigation of the specific
error types is necessary since some errors are due to incorrect
specimen processing
 The number of tests lost due to power outages or surges
 The number, duration and causes of routine interruptions in the Xpert
MTB/RIF testing service
◦ Common causes are cartridge stock-outs or expiration, staff not
available, instrument/computer breakdown
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Xpert MTB/RIF Training Package
To be customized by
each country
Site name
District
Person compiling report
Reporting period (Month/Year)
Combined data for all instruments at one site
Xpert results
# Xpert tests MTB Not detected (N)
Where possible,
countries should
collect disaggregated
data according to the
population group
tested (e.g. HIV
positive, MDR risk,
extrapulmonary)
A
# Xpert tests MTB detected, RIF resistance not
detected (T)
# Xpert tests MTB detected RIFresistance detected
(RR)
# Xpert tests MTB detected RIF indeterminate (TI)
# error results (I)
# invalid results (I)
# no result (I)
Total numbers
# total Xpert tests
# total successful Xpert tests
# total unsuccessful Xpert tests
# total Xpert tests MTB detected
Analysis
Error rate
[E]/[total Xpert tests]
Invalid result rate
[F]/[total Xpert tests]
No result rate
Total unsuccessful test rate
Xpert MTB positivity rate (Xpert MTB detected/all
successful Xpert tests)
Xpert RIF resistant rate (Xpert MTB detected RIF
resistant/all Xpert MTB detected)
Operational issues
Number of days of routine Xpert service interruption
this month
Reason(s) for service interruption (enter no. days
service interrupted due to each cause)
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No. tests
B
C
D
E
F
G
A+B+C+D+E+F+G
A+B+C
D+E+F+G
B+C
[G]/[total Xpert tests]
[E+F+G]/[total Xpert tests]
[B+C]/[total Xpert tests]
C/[B+C]
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Xpert MTB/RIF Training Package
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Several systems are being piloted for remote monitoring of GeneXpert
instruments
Open-source and proprietary options available
Cloud-based servers and in-country servers possible
Connectivity via internet or SMS
Data accessed via web-based dashboards
Remote monitoring can assist with collection of data relating to quality
assurance, procurement and some solutions can be linked to reporting of
patient results
Remote monitoring allows near real-time data to be available
simultaneously to different types and levels of staff
Global Laboratory Initiative
Xpert MTB/RIF Training Package

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Incoming batches of Xpert MTB/RIF cartridges should be tested using a
sample of cartridges and at least one known positive and negative specimen,
to ensure expected performance
QC testing may be centralized at a reference laboratory before distribution of
a new batch of cartridges to sites
In addition to new lot QC testing, continuous monitoring at site level of
performance indicators of tests, including error rates, is important for the
early detection of any problems with cartridge batches due to local storage
conditions or other factors
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Xpert MTB/RIF Training Package
“A program in which multiple specimens are periodically sent to members of a group of
laboratories for analysis and/or identification, in which each laboratory’s results are
compared with those of other laboratories in the group and/or with an assigned value,
and reported to the participating laboratory and others.” [CLSI GP27-A2]
Ideally, a PT program checks key pre-analytical, analytical, and post-analytical
processes occurring in the testing site.
 A number of samples are sent to the laboratory or testing site several times
per year
 Testing site performs Xpert MTB/RIF as they would with routine patient
specimens and report results.
 Results indicate quality of personnel performance and test site operations.
 Results are compared to expected results and across several testing sites.
 Results are monitored for trends over time.
 PT does not measure routine laboratory performance but may identify
laboratories with major deficiencies
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Xpert MTB/RIF Training Package
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PT is recommended at least once per year
Feedback of PT results should be provided in a timely manner to the
testing sites and supervisory staff
◦ Rapid feedback is needed to enable prompt initiation of
correction actions
While on-site supervision and routine monitoring of quality indicators
are the most critical components of QA, PT helps to:
◦ identify major non-conformities
◦ target the most poorly performing laboratories for on-site
supervision
Can be used to evaluate technician performance post-training
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Global
32 Laboratory Initiative
Xpert MTB/RIF Training Package


Several options (different formats) have been evaluated and all were
found to be acceptable formats
◦ For examples, see Scott et al. J. Clin. Microbiol. 2014. 52: 2493-2499.
National reference laboratories may consider preparing their own PT
panels in place of an external PT scheme
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Global Laboratory Initiative
Xpert MTB/RIF Training Package
Summary

Quality assurance includes all the following aspects:
◦ Safe and functional laboratory environment, trained and competent
personnel, maintained equipment, adequate supplies and reagents,
testing of quality specimens, internal quality monitoring, External
Quality Assessment (EQA), and accurate and timely reporting

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A comprehensive quality assurance programme should include the
following, and which are needed to fulfil ISO 15189 requirements:
1. Instrument verification using dried culture spot panels
2. Quality indicator monitoring
3. Regular on-site supervision
4. New lot QC testing
5. Proficiency testing
Global Laboratory Initiative
Xpert MTB/RIF Training Package
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Quality assurance is part of the routine workload and is not a separate
activity
All quality assurance activities must be documented
Feedback to testing sites and implementing corrective and preventive
measures are the most critical aspects of any quality assurance
programme
Quality assurance is needed whether Xpert is placed in a laboratory or
non-laboratory setting
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Xpert MTB/RIF Training Package
Assessment

Which quality assurance activities are recommended for Xpert MTB/RIF?

How does your country address these requirements?

What role does quality indicator monitoring play in quality assurance?

Can proficiency testing be done in place of on-site supervision?
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How would you plan an on-site supervision schedule for sites
performing Xpert MTB/RIF in your country?
What should happen to results of quality assurance activities?
Global Laboratory Initiative
Xpert MTB/RIF Training Package
Acknowledgements
The Xpert MTB/RIF Training Package has been developed by a consortium of
GLI partners, including FIND, KNCV, US CDC, USAID and WHO, with funding
from USAID (TB CARE I).
The modules are based on materials originally developed by FIND, KNCV and
Cepheid.